AnalysisController Object
(
    [name] => Analysis
    [uses] => Array
        (
            [0] => Annotation
            [1] => AnnotSource
            [2] => Configuration
            [3] => Similarities
            [4] => GeneFamily
            [5] => GeneFamilyTypes
            [6] => Msa
            [7] => GfDatum
            [8] => AdExperiments
            [9] => FunctionalClustersExperiments
            [10] => Trees
        )

    [helpers] => Array
        (
            [Session] => 
            [Html] => 
            [Form] => 
            [Cache] => 
        )

    [components] => Array
        (
            [Session] => 
            [DataUtils] => 
            [FunctionalAnnotationUtils] => 
            [GeneFamilies] => 
            [Organism] => 
            [Blast] => 
            [WorkbenchUtils] => 
            [PhylogeneticModuleUtils] => 
            [ExternalPrograms] => 
            [FastaUtils] => 
            [MsaUtils] => 
            [PhylogeneticUtils] => 
            [Sequence] => 
            [RequestHandler] => 
        )

    [request] => CakeRequest Object
        (
            [params] => Array
                (
                    [plugin] => 
                    [controller] => analysis
                    [action] => custom_tree_creation
                    [named] => Array
                        (
                        )

                    [pass] => Array
                        (
                            [0] => gene_id
                            [1] => Cre12.g515850
                        )

                    [isAjax] => 
                )

            [data] => Array
                (
                )

            [query] => Array
                (
                )

            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
            [base] => /plaza.dev/_dev_instances/feedback
            [webroot] => /plaza.dev/_dev_instances/feedback/
            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
            [_detectors:protected] => Array
                (
                    [get] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => GET
                        )

                    [patch] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => PATCH
                        )

                    [post] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => POST
                        )

                    [put] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => PUT
                        )

                    [delete] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => DELETE
                        )

                    [head] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => HEAD
                        )

                    [options] => Array
                        (
                            [env] => REQUEST_METHOD
                            [value] => OPTIONS
                        )

                    [ssl] => Array
                        (
                            [env] => HTTPS
                            [value] => 1
                        )

                    [ajax] => Array
                        (
                            [env] => HTTP_X_REQUESTED_WITH
                            [value] => XMLHttpRequest
                        )

                    [flash] => Array
                        (
                            [env] => HTTP_USER_AGENT
                            [pattern] => /^(Shockwave|Adobe) Flash/
                        )

                    [mobile] => Array
                        (
                            [env] => HTTP_USER_AGENT
                            [options] => Array
                                (
                                    [0] => Android
                                    [1] => AvantGo
                                    [2] => BB10
                                    [3] => BlackBerry
                                    [4] => DoCoMo
                                    [5] => Fennec
                                    [6] => iPod
                                    [7] => iPhone
                                    [8] => iPad
                                    [9] => J2ME
                                    [10] => MIDP
                                    [11] => NetFront
                                    [12] => Nokia
                                    [13] => Opera Mini
                                    [14] => Opera Mobi
                                    [15] => PalmOS
                                    [16] => PalmSource
                                    [17] => portalmmm
                                    [18] => Plucker
                                    [19] => ReqwirelessWeb
                                    [20] => SonyEricsson
                                    [21] => Symbian
                                    [22] => UP\.Browser
                                    [23] => webOS
                                    [24] => Windows CE
                                    [25] => Windows Phone OS
                                    [26] => Xiino
                                )

                        )

                    [requested] => Array
                        (
                            [param] => requested
                            [value] => 1
                        )

                    [json] => Array
                        (
                            [accept] => Array
                                (
                                    [0] => application/json
                                )

                            [param] => ext
                            [value] => json
                        )

                    [xml] => Array
                        (
                            [accept] => Array
                                (
                                    [0] => application/xml
                                    [1] => text/xml
                                )

                            [param] => ext
                            [value] => xml
                        )

                )

            [_input:protected] => 
        )

    [response] => CakeResponse Object
        (
            [_statusCodes:protected] => Array
                (
                    [100] => Continue
                    [101] => Switching Protocols
                    [200] => OK
                    [201] => Created
                    [202] => Accepted
                    [203] => Non-Authoritative Information
                    [204] => No Content
                    [205] => Reset Content
                    [206] => Partial Content
                    [300] => Multiple Choices
                    [301] => Moved Permanently
                    [302] => Found
                    [303] => See Other
                    [304] => Not Modified
                    [305] => Use Proxy
                    [307] => Temporary Redirect
                    [400] => Bad Request
                    [401] => Unauthorized
                    [402] => Payment Required
                    [403] => Forbidden
                    [404] => Not Found
                    [405] => Method Not Allowed
                    [406] => Not Acceptable
                    [407] => Proxy Authentication Required
                    [408] => Request Time-out
                    [409] => Conflict
                    [410] => Gone
                    [411] => Length Required
                    [412] => Precondition Failed
                    [413] => Request Entity Too Large
                    [414] => Request-URI Too Large
                    [415] => Unsupported Media Type
                    [416] => Requested range not satisfiable
                    [417] => Expectation Failed
                    [429] => Too Many Requests
                    [500] => Internal Server Error
                    [501] => Not Implemented
                    [502] => Bad Gateway
                    [503] => Service Unavailable
                    [504] => Gateway Time-out
                    [505] => Unsupported Version
                )

            [_mimeTypes:protected] => Array
                (
                    [html] => Array
                        (
                            [0] => text/html
                            [1] => */*
                        )

                    [json] => application/json
                    [xml] => Array
                        (
                            [0] => application/xml
                            [1] => text/xml
                        )

                    [rss] => application/rss+xml
                    [ai] => application/postscript
                    [bcpio] => application/x-bcpio
                    [bin] => application/octet-stream
                    [ccad] => application/clariscad
                    [cdf] => application/x-netcdf
                    [class] => application/octet-stream
                    [cpio] => application/x-cpio
                    [cpt] => application/mac-compactpro
                    [csh] => application/x-csh
                    [csv] => Array
                        (
                            [0] => text/csv
                            [1] => application/vnd.ms-excel
                        )

                    [dcr] => application/x-director
                    [dir] => application/x-director
                    [dms] => application/octet-stream
                    [doc] => application/msword
                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                    [drw] => application/drafting
                    [dvi] => application/x-dvi
                    [dwg] => application/acad
                    [dxf] => application/dxf
                    [dxr] => application/x-director
                    [eot] => application/vnd.ms-fontobject
                    [eps] => application/postscript
                    [exe] => application/octet-stream
                    [ez] => application/andrew-inset
                    [flv] => video/x-flv
                    [gtar] => application/x-gtar
                    [gz] => application/x-gzip
                    [bz2] => application/x-bzip
                    [7z] => application/x-7z-compressed
                    [hdf] => application/x-hdf
                    [hqx] => application/mac-binhex40
                    [ico] => image/x-icon
                    [ips] => application/x-ipscript
                    [ipx] => application/x-ipix
                    [js] => application/javascript
                    [jsonapi] => application/vnd.api+json
                    [latex] => application/x-latex
                    [lha] => application/octet-stream
                    [lsp] => application/x-lisp
                    [lzh] => application/octet-stream
                    [man] => application/x-troff-man
                    [me] => application/x-troff-me
                    [mif] => application/vnd.mif
                    [ms] => application/x-troff-ms
                    [nc] => application/x-netcdf
                    [oda] => application/oda
                    [otf] => font/otf
                    [pdf] => application/pdf
                    [pgn] => application/x-chess-pgn
                    [pot] => application/vnd.ms-powerpoint
                    [pps] => application/vnd.ms-powerpoint
                    [ppt] => application/vnd.ms-powerpoint
                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                    [ppz] => application/vnd.ms-powerpoint
                    [pre] => application/x-freelance
                    [prt] => application/pro_eng
                    [ps] => application/postscript
                    [roff] => application/x-troff
                    [scm] => application/x-lotusscreencam
                    [set] => application/set
                    [sh] => application/x-sh
                    [shar] => application/x-shar
                    [sit] => application/x-stuffit
                    [skd] => application/x-koan
                    [skm] => application/x-koan
                    [skp] => application/x-koan
                    [skt] => application/x-koan
                    [smi] => application/smil
                    [smil] => application/smil
                    [sol] => application/solids
                    [spl] => application/x-futuresplash
                    [src] => application/x-wais-source
                    [step] => application/STEP
                    [stl] => application/SLA
                    [stp] => application/STEP
                    [sv4cpio] => application/x-sv4cpio
                    [sv4crc] => application/x-sv4crc
                    [svg] => image/svg+xml
                    [svgz] => image/svg+xml
                    [swf] => application/x-shockwave-flash
                    [t] => application/x-troff
                    [tar] => application/x-tar
                    [tcl] => application/x-tcl
                    [tex] => application/x-tex
                    [texi] => application/x-texinfo
                    [texinfo] => application/x-texinfo
                    [tr] => application/x-troff
                    [tsp] => application/dsptype
                    [ttc] => font/ttf
                    [ttf] => font/ttf
                    [unv] => application/i-deas
                    [ustar] => application/x-ustar
                    [vcd] => application/x-cdlink
                    [vda] => application/vda
                    [xlc] => application/vnd.ms-excel
                    [xll] => application/vnd.ms-excel
                    [xlm] => application/vnd.ms-excel
                    [xls] => application/vnd.ms-excel
                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                    [xlw] => application/vnd.ms-excel
                    [zip] => application/zip
                    [aif] => audio/x-aiff
                    [aifc] => audio/x-aiff
                    [aiff] => audio/x-aiff
                    [au] => audio/basic
                    [kar] => audio/midi
                    [mid] => audio/midi
                    [midi] => audio/midi
                    [mp2] => audio/mpeg
                    [mp3] => audio/mpeg
                    [mpga] => audio/mpeg
                    [ogg] => audio/ogg
                    [oga] => audio/ogg
                    [spx] => audio/ogg
                    [ra] => audio/x-realaudio
                    [ram] => audio/x-pn-realaudio
                    [rm] => audio/x-pn-realaudio
                    [rpm] => audio/x-pn-realaudio-plugin
                    [snd] => audio/basic
                    [tsi] => audio/TSP-audio
                    [wav] => audio/x-wav
                    [aac] => audio/aac
                    [asc] => text/plain
                    [c] => text/plain
                    [cc] => text/plain
                    [css] => text/css
                    [etx] => text/x-setext
                    [f] => text/plain
                    [f90] => text/plain
                    [h] => text/plain
                    [hh] => text/plain
                    [htm] => Array
                        (
                            [0] => text/html
                            [1] => */*
                        )

                    [ics] => text/calendar
                    [m] => text/plain
                    [rtf] => text/rtf
                    [rtx] => text/richtext
                    [sgm] => text/sgml
                    [sgml] => text/sgml
                    [tsv] => text/tab-separated-values
                    [tpl] => text/template
                    [txt] => text/plain
                    [text] => text/plain
                    [avi] => video/x-msvideo
                    [fli] => video/x-fli
                    [mov] => video/quicktime
                    [movie] => video/x-sgi-movie
                    [mpe] => video/mpeg
                    [mpeg] => video/mpeg
                    [mpg] => video/mpeg
                    [qt] => video/quicktime
                    [viv] => video/vnd.vivo
                    [vivo] => video/vnd.vivo
                    [ogv] => video/ogg
                    [webm] => video/webm
                    [mp4] => video/mp4
                    [m4v] => video/mp4
                    [f4v] => video/mp4
                    [f4p] => video/mp4
                    [m4a] => audio/mp4
                    [f4a] => audio/mp4
                    [f4b] => audio/mp4
                    [gif] => image/gif
                    [ief] => image/ief
                    [jpg] => image/jpeg
                    [jpeg] => image/jpeg
                    [jpe] => image/jpeg
                    [pbm] => image/x-portable-bitmap
                    [pgm] => image/x-portable-graymap
                    [png] => image/png
                    [pnm] => image/x-portable-anymap
                    [ppm] => image/x-portable-pixmap
                    [ras] => image/cmu-raster
                    [rgb] => image/x-rgb
                    [tif] => image/tiff
                    [tiff] => image/tiff
                    [xbm] => image/x-xbitmap
                    [xpm] => image/x-xpixmap
                    [xwd] => image/x-xwindowdump
                    [psd] => Array
                        (
                            [0] => application/photoshop
                            [1] => application/psd
                            [2] => image/psd
                            [3] => image/x-photoshop
                            [4] => image/photoshop
                            [5] => zz-application/zz-winassoc-psd
                        )

                    [ice] => x-conference/x-cooltalk
                    [iges] => model/iges
                    [igs] => model/iges
                    [mesh] => model/mesh
                    [msh] => model/mesh
                    [silo] => model/mesh
                    [vrml] => model/vrml
                    [wrl] => model/vrml
                    [mime] => www/mime
                    [pdb] => chemical/x-pdb
                    [xyz] => chemical/x-pdb
                    [javascript] => application/javascript
                    [form] => application/x-www-form-urlencoded
                    [file] => multipart/form-data
                    [xhtml] => Array
                        (
                            [0] => application/xhtml+xml
                            [1] => application/xhtml
                            [2] => text/xhtml
                        )

                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                    [atom] => application/atom+xml
                    [amf] => application/x-amf
                    [wap] => Array
                        (
                            [0] => text/vnd.wap.wml
                            [1] => text/vnd.wap.wmlscript
                            [2] => image/vnd.wap.wbmp
                        )

                    [wml] => text/vnd.wap.wml
                    [wmlscript] => text/vnd.wap.wmlscript
                    [wbmp] => image/vnd.wap.wbmp
                    [woff] => application/x-font-woff
                    [webp] => image/webp
                    [appcache] => text/cache-manifest
                    [manifest] => text/cache-manifest
                    [htc] => text/x-component
                    [rdf] => application/xml
                    [crx] => application/x-chrome-extension
                    [oex] => application/x-opera-extension
                    [xpi] => application/x-xpinstall
                    [safariextz] => application/octet-stream
                    [webapp] => application/x-web-app-manifest+json
                    [vcf] => text/x-vcard
                    [vtt] => text/vtt
                    [mkv] => video/x-matroska
                    [pkpass] => application/vnd.apple.pkpass
                    [ajax] => text/html
                )

            [_protocol:protected] => HTTP/1.1
            [_status:protected] => 200
            [_contentType:protected] => text/html
            [_headers:protected] => Array
                (
                )

            [_body:protected] => 
            [_file:protected] => 
            [_fileRange:protected] => 
            [_charset:protected] => UTF-8
            [_cacheDirectives:protected] => Array
                (
                )

            [_cookies:protected] => Array
                (
                )

        )

    [_responseClass:protected] => CakeResponse
    [viewPath] => Analysis
    [layoutPath] => 
    [viewVars] => Array
        (
            [sidebar] => gene_sidebar
            [navigation_bar_info] => Array
                (
                    [num_colinearity_runs] => 1
                    [num_colinearity_with_dating_runs] => 0
                    [num_functional_clusters_runs] => 6
                    [has_pan_genomes] => 
                    [has_blast_db] => 1
                )

            [allowed_extra_sequences_types] => Array
                (
                    [aa] => Protein
                    [dna] => DNA
                )

            [allowed_editing_methods] => Array
                (
                    [column] => Positions only
                    [row] => Genes only
                    [column_row] => Positions and Genes
                    [none] => No editing
                )

            [allowed_tree_programs] => Array
                (
                    [fasttree] => FastTree
                    [iqtree] => IQ-TREE (includes model testing)
                    [raxml] => RAxML
                    [phyml] => PhyML
                )

            [allowed_msa_programs] => Array
                (
                    [muscle] => MUSCLE
                    [mafft] => MAFFT
                )

            [allowed_number_blasthits] => Array
                (
                    [0] => all
                    [1] => 20
                    [2] => 10
                    [3] => 5
                    [4] => 1
                )

            [similarity_hits_genes] => Array
                (
                    [Cre12.g515850] => Array
                        (
                            [gene_id] => Cre12.g515850
                            [e_value] => 1.1e-145
                            [bit_score] => 520.0
                            [alignment_length] => 269
                            [identity_percentage] => 100.0
                            [species] => cre
                            [common_name] => Chlamydomonas reinhardtii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MCO09G325] => Array
                        (
                            [gene_id] => MCO09G325
                            [e_value] => 1.9e-97
                            [bit_score] => 359.8
                            [alignment_length] => 259
                            [identity_percentage] => 66.0
                            [species] => mco
                            [common_name] => Micromonas commoda
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Nn2g11338] => Array
                        (
                            [gene_id] => Nn2g11338
                            [e_value] => 4.2e-97
                            [bit_score] => 358.6
                            [alignment_length] => 260
                            [identity_percentage] => 63.8
                            [species] => nnu
                            [common_name] => Nelumbo nucifera
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HPP92_018042] => Array
                        (
                            [gene_id] => HPP92_018042
                            [e_value] => 4.2e-97
                            [bit_score] => 358.6
                            [alignment_length] => 260
                            [identity_percentage] => 64.6
                            [species] => vpl
                            [common_name] => Vanilla planifolia
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [VMungo0540G1433] => Array
                        (
                            [gene_id] => VMungo0540G1433
                            [e_value] => 9.3e-97
                            [bit_score] => 357.5
                            [alignment_length] => 260
                            [identity_percentage] => 63.8
                            [species] => vmu
                            [common_name] => Vigna mungo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Actinidia29670] => Array
                        (
                            [gene_id] => Actinidia29670
                            [e_value] => 2.1e-96
                            [bit_score] => 356.3
                            [alignment_length] => 268
                            [identity_percentage] => 62.7
                            [species] => ach
                            [common_name] => Actinidia chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HanXRQChr05g0135561] => Array
                        (
                            [gene_id] => HanXRQChr05g0135561
                            [e_value] => 2.7e-96
                            [bit_score] => 355.9
                            [alignment_length] => 260
                            [identity_percentage] => 63.5
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cpa.g.sc112.81] => Array
                        (
                            [gene_id] => Cpa.g.sc112.81
                            [e_value] => 3.5e-96
                            [bit_score] => 355.5
                            [alignment_length] => 259
                            [identity_percentage] => 63.3
                            [species] => cpa
                            [common_name] => Carica papaya
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CDE09G0989] => Array
                        (
                            [gene_id] => CDE09G0989
                            [e_value] => 3.5e-96
                            [bit_score] => 355.5
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => cde
                            [common_name] => Ceratophyllum demersum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lsat_1_v5_gn_5_171040] => Array
                        (
                            [gene_id] => Lsat_1_v5_gn_5_171040
                            [e_value] => 4.6e-96
                            [bit_score] => 355.1
                            [alignment_length] => 260
                            [identity_percentage] => 63.5
                            [species] => lsa
                            [common_name] => Lactuca sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Aqoxy1G00741] => Array
                        (
                            [gene_id] => Aqoxy1G00741
                            [e_value] => 6.0e-96
                            [bit_score] => 354.8
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => aox
                            [common_name] => Aquilegia oxysepala
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ECA248G2035] => Array
                        (
                            [gene_id] => ECA248G2035
                            [e_value] => 6.0e-96
                            [bit_score] => 354.8
                            [alignment_length] => 260
                            [identity_percentage] => 63.5
                            [species] => eca
                            [common_name] => Erigeron canadensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Os02g0805200] => Array
                        (
                            [gene_id] => Os02g0805200
                            [e_value] => 6.0e-96
                            [bit_score] => 354.8
                            [alignment_length] => 261
                            [identity_percentage] => 61.7
                            [species] => osa
                            [common_name] => Oryza sativa ssp. japonica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SEGI_27416] => Array
                        (
                            [gene_id] => SEGI_27416
                            [e_value] => 6.0e-96
                            [bit_score] => 354.8
                            [alignment_length] => 261
                            [identity_percentage] => 62.5
                            [species] => sgi
                            [common_name] => Sequoiadendron giganteum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Thecc.09G307900] => Array
                        (
                            [gene_id] => Thecc.09G307900
                            [e_value] => 6.0e-96
                            [bit_score] => 354.8
                            [alignment_length] => 261
                            [identity_percentage] => 64.0
                            [species] => tca
                            [common_name] => Theobroma cacao
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CANSAT78G2483] => Array
                        (
                            [gene_id] => CANSAT78G2483
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => cansat
                            [common_name] => Cannabis sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Haze_24235] => Array
                        (
                            [gene_id] => Haze_24235
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 261
                            [identity_percentage] => 64.4
                            [species] => cav
                            [common_name] => Corylus avellana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Oeu035018.1] => Array
                        (
                            [gene_id] => Oeu035018.1
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 260
                            [identity_percentage] => 63.5
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SalBow3G1232] => Array
                        (
                            [gene_id] => SalBow3G1232
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SalBow3G1958] => Array
                        (
                            [gene_id] => SalBow3G1958
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SHI38242] => Array
                        (
                            [gene_id] => SHI38242
                            [e_value] => 7.9e-96
                            [bit_score] => 354.4
                            [alignment_length] => 262
                            [identity_percentage] => 63.7
                            [species] => shi
                            [common_name] => Sapria himalayana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CiPaw.14G062600] => Array
                        (
                            [gene_id] => CiPaw.14G062600
                            [e_value] => 1.0e-95
                            [bit_score] => 354.0
                            [alignment_length] => 266
                            [identity_percentage] => 62.0
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [COL.COLO4_19083] => Array
                        (
                            [gene_id] => COL.COLO4_19083
                            [e_value] => 1.0e-95
                            [bit_score] => 354.0
                            [alignment_length] => 261
                            [identity_percentage] => 63.6
                            [species] => col
                            [common_name] => Corchorus olitorius
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Phvul.006G137800] => Array
                        (
                            [gene_id] => Phvul.006G137800
                            [e_value] => 1.0e-95
                            [bit_score] => 354.0
                            [alignment_length] => 260
                            [identity_percentage] => 63.5
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [unitig_747.g22020] => Array
                        (
                            [gene_id] => unitig_747.g22020
                            [e_value] => 1.0e-95
                            [bit_score] => 354.0
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => ugi
                            [common_name] => Utricularia gibba
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PGR102G0182] => Array
                        (
                            [gene_id] => PGR102G0182
                            [e_value] => 1.3e-95
                            [bit_score] => 353.6
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => pgr
                            [common_name] => Punica granatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [THA.LOC104826301] => Array
                        (
                            [gene_id] => THA.LOC104826301
                            [e_value] => 1.3e-95
                            [bit_score] => 353.6
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => tha
                            [common_name] => Tarenaya hassleriana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Actinidia34442] => Array
                        (
                            [gene_id] => Actinidia34442
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => ach
                            [common_name] => Actinidia chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CANSAT54G2750] => Array
                        (
                            [gene_id] => CANSAT54G2750
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => cansat
                            [common_name] => Cannabis sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gohir.A03G048100] => Array
                        (
                            [gene_id] => Gohir.A03G048100
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 261
                            [identity_percentage] => 63.6
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HanXRQChr01g0011001] => Array
                        (
                            [gene_id] => HanXRQChr01g0011001
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Oeu049279.1] => Array
                        (
                            [gene_id] => Oeu049279.1
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Hund04899] => Array
                        (
                            [gene_id] => Hund04899
                            [e_value] => 1.8e-95
                            [bit_score] => 353.2
                            [alignment_length] => 259
                            [identity_percentage] => 62.9
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CARHR122910] => Array
                        (
                            [gene_id] => CARHR122910
                            [e_value] => 2.3e-95
                            [bit_score] => 352.8
                            [alignment_length] => 261
                            [identity_percentage] => 61.3
                            [species] => chi
                            [common_name] => Cardamine hirsuta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cfa011630] => Array
                        (
                            [gene_id] => Cfa011630
                            [e_value] => 2.3e-95
                            [bit_score] => 352.8
                            [alignment_length] => 261
                            [identity_percentage] => 64.0
                            [species] => cfa
                            [common_name] => Carpinus fangiana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PRCOL_00005339] => Array
                        (
                            [gene_id] => PRCOL_00005339
                            [e_value] => 2.3e-95
                            [bit_score] => 352.8
                            [alignment_length] => 261
                            [identity_percentage] => 64.4
                            [species] => pco
                            [common_name] => Prasinoderma coloniale
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Hund18869] => Array
                        (
                            [gene_id] => Hund18869
                            [e_value] => 2.3e-95
                            [bit_score] => 352.8
                            [alignment_length] => 259
                            [identity_percentage] => 62.9
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TAR636G2785] => Array
                        (
                            [gene_id] => TAR636G2785
                            [e_value] => 2.3e-95
                            [bit_score] => 352.8
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Atru.chr3.4053] => Array
                        (
                            [gene_id] => Atru.chr3.4053
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 267
                            [identity_percentage] => 61.4
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Actinidia33951] => Array
                        (
                            [gene_id] => Actinidia33951
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 259
                            [identity_percentage] => 62.9
                            [species] => ach
                            [common_name] => Actinidia chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Migut.D02143] => Array
                        (
                            [gene_id] => Migut.D02143
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 260
                            [identity_percentage] => 63.1
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Eucgr.J01951] => Array
                        (
                            [gene_id] => Eucgr.J01951
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 261
                            [identity_percentage] => 63.6
                            [species] => egr
                            [common_name] => Eucalyptus grandis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Glyma.08G334900] => Array
                        (
                            [gene_id] => Glyma.08G334900
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gohir.D03G118900] => Array
                        (
                            [gene_id] => Gohir.D03G118900
                            [e_value] => 3.0e-95
                            [bit_score] => 352.4
                            [alignment_length] => 261
                            [identity_percentage] => 64.0
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MSTRG.18604] => Array
                        (
                            [gene_id] => MSTRG.18604
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => ama
                            [common_name] => Avicennia marina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Ca_14888_v3] => Array
                        (
                            [gene_id] => Ca_14888_v3
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 260
                            [identity_percentage] => 62.3
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gohir.A13G225400] => Array
                        (
                            [gene_id] => Gohir.A13G225400
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.8
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gohir.D13G230500] => Array
                        (
                            [gene_id] => Gohir.D13G230500
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.8
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gorai.013G261100] => Array
                        (
                            [gene_id] => Gorai.013G261100
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.8
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lj6g0014589] => Array
                        (
                            [gene_id] => Lj6g0014589
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 260
                            [identity_percentage] => 62.3
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Potri.001G247700] => Array
                        (
                            [gene_id] => Potri.001G247700
                            [e_value] => 3.9e-95
                            [bit_score] => 352.1
                            [alignment_length] => 267
                            [identity_percentage] => 61.0
                            [species] => ptr
                            [common_name] => Populus trichocarpa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MSTRG.21172] => Array
                        (
                            [gene_id] => MSTRG.21172
                            [e_value] => 5.1e-95
                            [bit_score] => 351.7
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => ama
                            [common_name] => Avicennia marina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Ciclev10029070m.g] => Array
                        (
                            [gene_id] => Ciclev10029070m.g
                            [e_value] => 5.1e-95
                            [bit_score] => 351.7
                            [alignment_length] => 261
                            [identity_percentage] => 63.6
                            [species] => ccl
                            [common_name] => Citrus clementina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Glyma.18G067800] => Array
                        (
                            [gene_id] => Glyma.18G067800
                            [e_value] => 5.1e-95
                            [bit_score] => 351.7
                            [alignment_length] => 260
                            [identity_percentage] => 62.7
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CSS0029507] => Array
                        (
                            [gene_id] => CSS0029507
                            [e_value] => 6.7e-95
                            [bit_score] => 351.3
                            [alignment_length] => 265
                            [identity_percentage] => 61.5
                            [species] => camsi
                            [common_name] => Camellia sinensis var. sinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HanXRQChr08g0222181] => Array
                        (
                            [gene_id] => HanXRQChr08g0222181
                            [e_value] => 6.7e-95
                            [bit_score] => 351.3
                            [alignment_length] => 267
                            [identity_percentage] => 60.7
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lsat_1_v5_gn_8_12580] => Array
                        (
                            [gene_id] => Lsat_1_v5_gn_8_12580
                            [e_value] => 6.7e-95
                            [bit_score] => 351.3
                            [alignment_length] => 262
                            [identity_percentage] => 61.5
                            [species] => lsa
                            [common_name] => Lactuca sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sc12g0001020] => Array
                        (
                            [gene_id] => Sc12g0001020
                            [e_value] => 6.7e-95
                            [bit_score] => 351.3
                            [alignment_length] => 261
                            [identity_percentage] => 64.0
                            [species] => sci
                            [common_name] => Simmondsia chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CiPaw.13G083600] => Array
                        (
                            [gene_id] => CiPaw.13G083600
                            [e_value] => 8.7e-95
                            [bit_score] => 350.9
                            [alignment_length] => 260
                            [identity_percentage] => 61.9
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SEGI_13348] => Array
                        (
                            [gene_id] => SEGI_13348
                            [e_value] => 8.7e-95
                            [bit_score] => 350.9
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => sgi
                            [common_name] => Sequoiadendron giganteum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TWI31G0565] => Array
                        (
                            [gene_id] => TWI31G0565
                            [e_value] => 8.7e-95
                            [bit_score] => 350.9
                            [alignment_length] => 261
                            [identity_percentage] => 63.2
                            [species] => twi
                            [common_name] => Tripterygium wilfordii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AL1G17520] => Array
                        (
                            [gene_id] => AL1G17520
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AT1G07370] => Array
                        (
                            [gene_id] => AT1G07370
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => ath
                            [common_name] => Arabidopsis thaliana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CSS0001422] => Array
                        (
                            [gene_id] => CSS0001422
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 269
                            [identity_percentage] => 61.7
                            [species] => camsi
                            [common_name] => Camellia sinensis var. sinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CSS0025335] => Array
                        (
                            [gene_id] => CSS0025335
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 269
                            [identity_percentage] => 61.7
                            [species] => camsi
                            [common_name] => Camellia sinensis var. sinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gorai.003G125300] => Array
                        (
                            [gene_id] => Gorai.003G125300
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 261
                            [identity_percentage] => 63.6
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lj2A1074T37] => Array
                        (
                            [gene_id] => Lj2A1074T37
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 260
                            [identity_percentage] => 62.3
                            [species] => lonja
                            [common_name] => Lonicera japonica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Manes.01G165500] => Array
                        (
                            [gene_id] => Manes.01G165500
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 261
                            [identity_percentage] => 62.5
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PSO384G1519] => Array
                        (
                            [gene_id] => PSO384G1519
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 260
                            [identity_percentage] => 61.5
                            [species] => pso
                            [common_name] => Papaver somniferum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PSO585G0022] => Array
                        (
                            [gene_id] => PSO585G0022
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 260
                            [identity_percentage] => 61.5
                            [species] => pso
                            [common_name] => Papaver somniferum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Rhsim01G0234200] => Array
                        (
                            [gene_id] => Rhsim01G0234200
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 267
                            [identity_percentage] => 61.8
                            [species] => rsi
                            [common_name] => Rhododendron simsii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sed0001054] => Array
                        (
                            [gene_id] => Sed0001054
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 259
                            [identity_percentage] => 62.5
                            [species] => sed
                            [common_name] => Sechium edule
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [vmacro14574] => Array
                        (
                            [gene_id] => vmacro14574
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 267
                            [identity_percentage] => 61.8
                            [species] => vma
                            [common_name] => Vaccinium macrocarpon
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Zm00001eb192050] => Array
                        (
                            [gene_id] => Zm00001eb192050
                            [e_value] => 1.1e-94
                            [bit_score] => 350.5
                            [alignment_length] => 261
                            [identity_percentage] => 61.7
                            [species] => zma
                            [common_name] => Zea mays
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Carub.0004s1063] => Array
                        (
                            [gene_id] => Carub.0004s1063
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => cru
                            [common_name] => Capsella rubella
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MELO3C025879.2] => Array
                        (
                            [gene_id] => MELO3C025879.2
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 266
                            [identity_percentage] => 61.3
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Duzib150G0009] => Array
                        (
                            [gene_id] => Duzib150G0009
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 267
                            [identity_percentage] => 61.8
                            [species] => dzi
                            [common_name] => Durio zibethinus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Manes.02G123000] => Array
                        (
                            [gene_id] => Manes.02G123000
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.5
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Medtr3g462130] => Array
                        (
                            [gene_id] => Medtr3g462130
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 265
                            [identity_percentage] => 60.8
                            [species] => mtr
                            [common_name] => Medicago truncatula
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PGR119G1764] => Array
                        (
                            [gene_id] => PGR119G1764
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 269
                            [identity_percentage] => 61.3
                            [species] => pgr
                            [common_name] => Punica granatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sed0018009] => Array
                        (
                            [gene_id] => Sed0018009
                            [e_value] => 1.5e-94
                            [bit_score] => 350.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.8
                            [species] => sed
                            [common_name] => Sechium edule
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Ah.14g082670] => Array
                        (
                            [gene_id] => Ah.14g082670
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 259
                            [identity_percentage] => 61.8
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ATR0680G321] => Array
                        (
                            [gene_id] => ATR0680G321
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 260
                            [identity_percentage] => 61.9
                            [species] => atr
                            [common_name] => Amborella trichopoda
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CsaV3_6G016510] => Array
                        (
                            [gene_id] => CsaV3_6G016510
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 266
                            [identity_percentage] => 61.3
                            [species] => csa
                            [common_name] => Cucumis sativus L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Duzib170G0557] => Array
                        (
                            [gene_id] => Duzib170G0557
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 261
                            [identity_percentage] => 63.2
                            [species] => dzi
                            [common_name] => Durio zibethinus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lsat_1_v5_gn_8_72200] => Array
                        (
                            [gene_id] => Lsat_1_v5_gn_8_72200
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 260
                            [identity_percentage] => 62.3
                            [species] => lsa
                            [common_name] => Lactuca sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PGR044G0110] => Array
                        (
                            [gene_id] => PGR044G0110
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 269
                            [identity_percentage] => 61.3
                            [species] => pgr
                            [common_name] => Punica granatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TAR633G0461] => Array
                        (
                            [gene_id] => TAR633G0461
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 260
                            [identity_percentage] => 61.5
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [vmacro07002] => Array
                        (
                            [gene_id] => vmacro07002
                            [e_value] => 1.9e-94
                            [bit_score] => 349.7
                            [alignment_length] => 259
                            [identity_percentage] => 62.5
                            [species] => vma
                            [common_name] => Vaccinium macrocarpon
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AL4G24290] => Array
                        (
                            [gene_id] => AL4G24290
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CARHR007080] => Array
                        (
                            [gene_id] => CARHR007080
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => chi
                            [common_name] => Cardamine hirsuta
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AUR62001707] => Array
                        (
                            [gene_id] => AUR62001707
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 259
                            [identity_percentage] => 61.8
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AUR62020074] => Array
                        (
                            [gene_id] => AUR62020074
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 259
                            [identity_percentage] => 61.8
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MBI14_g32930_MAGBIO] => Array
                        (
                            [gene_id] => MBI14_g32930_MAGBIO
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 266
                            [identity_percentage] => 59.8
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Nitab4.5_0000744g0120] => Array
                        (
                            [gene_id] => Nitab4.5_0000744g0120
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 260
                            [identity_percentage] => 61.5
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Peaxi162Scf01058g00150] => Array
                        (
                            [gene_id] => Peaxi162Scf01058g00150
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 260
                            [identity_percentage] => 61.9
                            [species] => pax
                            [common_name] => Petunia axillaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SMO172G0020] => Array
                        (
                            [gene_id] => SMO172G0020
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 259
                            [identity_percentage] => 62.9
                            [species] => smo
                            [common_name] => Selaginella moellendorffii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TPR.G30115] => Array
                        (
                            [gene_id] => TPR.G30115
                            [e_value] => 2.5e-94
                            [bit_score] => 349.4
                            [alignment_length] => 265
                            [identity_percentage] => 60.8
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [C04p21270] => Array
                        (
                            [gene_id] => C04p21270
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BolC4t23656H] => Array
                        (
                            [gene_id] => BolC4t23656H
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => bol
                            [common_name] => Brassica oleracea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ECA233G2070] => Array
                        (
                            [gene_id] => ECA233G2070
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 267
                            [identity_percentage] => 59.6
                            [species] => eca
                            [common_name] => Erigeron canadensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lalb_Chr15g0082601] => Array
                        (
                            [gene_id] => Lalb_Chr15g0082601
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 260
                            [identity_percentage] => 61.2
                            [species] => lal
                            [common_name] => Lupinus albus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Nitab4.5_0011134g0030] => Array
                        (
                            [gene_id] => Nitab4.5_0011134g0030
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 260
                            [identity_percentage] => 61.9
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Pp3c12_18160] => Array
                        (
                            [gene_id] => Pp3c12_18160
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 261
                            [identity_percentage] => 60.5
                            [species] => ppa
                            [common_name] => Physcomitrium patens
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [THA.LOC104815801] => Array
                        (
                            [gene_id] => THA.LOC104815801
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 260
                            [identity_percentage] => 62.3
                            [species] => tha
                            [common_name] => Tarenaya hassleriana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TWI75G1109] => Array
                        (
                            [gene_id] => TWI75G1109
                            [e_value] => 3.3e-94
                            [bit_score] => 349.0
                            [alignment_length] => 261
                            [identity_percentage] => 62.5
                            [species] => twi
                            [common_name] => Tripterygium wilfordii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [QL01p029015] => Array
                        (
                            [gene_id] => QL01p029015
                            [e_value] => 4.3e-94
                            [bit_score] => 348.6
                            [alignment_length] => 266
                            [identity_percentage] => 60.2
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AT2G29570] => Array
                        (
                            [gene_id] => AT2G29570
                            [e_value] => 5.6e-94
                            [bit_score] => 348.2
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => ath
                            [common_name] => Arabidopsis thaliana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BcaB02g10263] => Array
                        (
                            [gene_id] => BcaB02g10263
                            [e_value] => 5.6e-94
                            [bit_score] => 348.2
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => bca
                            [common_name] => Brassica carinata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lalb_Chr18g0050611] => Array
                        (
                            [gene_id] => Lalb_Chr18g0050611
                            [e_value] => 5.6e-94
                            [bit_score] => 348.2
                            [alignment_length] => 260
                            [identity_percentage] => 61.2
                            [species] => lal
                            [common_name] => Lupinus albus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sp4g12300] => Array
                        (
                            [gene_id] => Sp4g12300
                            [e_value] => 5.6e-94
                            [bit_score] => 348.2
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => spa
                            [common_name] => Schrenkiella parvula
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SGA_v2.0_scaffold77G25326] => Array
                        (
                            [gene_id] => SGA_v2.0_scaffold77G25326
                            [e_value] => 5.6e-94
                            [bit_score] => 348.2
                            [alignment_length] => 260
                            [identity_percentage] => 61.5
                            [species] => sas
                            [common_name] => Striga asiatica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Ah.08g220430] => Array
                        (
                            [gene_id] => Ah.08g220430
                            [e_value] => 7.4e-94
                            [bit_score] => 347.8
                            [alignment_length] => 259
                            [identity_percentage] => 60.2
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [A05p15830] => Array
                        (
                            [gene_id] => A05p15830
                            [e_value] => 7.4e-94
                            [bit_score] => 347.8
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BraA05t20496Z] => Array
                        (
                            [gene_id] => BraA05t20496Z
                            [e_value] => 7.4e-94
                            [bit_score] => 347.8
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => bra
                            [common_name] => Brassica rapa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ClCG02G019790] => Array
                        (
                            [gene_id] => ClCG02G019790
                            [e_value] => 7.4e-94
                            [bit_score] => 347.8
                            [alignment_length] => 266
                            [identity_percentage] => 60.9
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Prupe.6G063300] => Array
                        (
                            [gene_id] => Prupe.6G063300
                            [e_value] => 9.6e-94
                            [bit_score] => 347.4
                            [alignment_length] => 261
                            [identity_percentage] => 62.5
                            [species] => ppe
                            [common_name] => Prunus persica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Thhalv10017099m.g] => Array
                        (
                            [gene_id] => Thhalv10017099m.g
                            [e_value] => 1.3e-93
                            [bit_score] => 347.1
                            [alignment_length] => 259
                            [identity_percentage] => 60.6
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Psat5g162720] => Array
                        (
                            [gene_id] => Psat5g162720
                            [e_value] => 1.3e-93
                            [bit_score] => 347.1
                            [alignment_length] => 266
                            [identity_percentage] => 60.2
                            [species] => psa
                            [common_name] => Pisum sativum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Zm00001eb258230] => Array
                        (
                            [gene_id] => Zm00001eb258230
                            [e_value] => 1.3e-93
                            [bit_score] => 347.1
                            [alignment_length] => 261
                            [identity_percentage] => 60.9
                            [species] => zma
                            [common_name] => Zea mays
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FvH4_3g37710] => Array
                        (
                            [gene_id] => FvH4_3g37710
                            [e_value] => 1.6e-93
                            [bit_score] => 346.7
                            [alignment_length] => 260
                            [identity_percentage] => 61.2
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN16G1397] => Array
                        (
                            [gene_id] => FAN16G1397
                            [e_value] => 1.6e-93
                            [bit_score] => 346.7
                            [alignment_length] => 260
                            [identity_percentage] => 61.2
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN21G0265] => Array
                        (
                            [gene_id] => FAN21G0265
                            [e_value] => 1.6e-93
                            [bit_score] => 346.7
                            [alignment_length] => 260
                            [identity_percentage] => 61.2
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sp1g06120] => Array
                        (
                            [gene_id] => Sp1g06120
                            [e_value] => 1.6e-93
                            [bit_score] => 346.7
                            [alignment_length] => 259
                            [identity_percentage] => 60.6
                            [species] => spa
                            [common_name] => Schrenkiella parvula
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BcaC07g42462] => Array
                        (
                            [gene_id] => BcaC07g42462
                            [e_value] => 2.1e-93
                            [bit_score] => 346.3
                            [alignment_length] => 260
                            [identity_percentage] => 60.0
                            [species] => bca
                            [common_name] => Brassica carinata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN11G3986] => Array
                        (
                            [gene_id] => FAN11G3986
                            [e_value] => 2.1e-93
                            [bit_score] => 346.3
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ATR0618G446] => Array
                        (
                            [gene_id] => ATR0618G446
                            [e_value] => 2.8e-93
                            [bit_score] => 345.9
                            [alignment_length] => 258
                            [identity_percentage] => 62.0
                            [species] => atr
                            [common_name] => Amborella trichopoda
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Thhalv10008509m.g] => Array
                        (
                            [gene_id] => Thhalv10008509m.g
                            [e_value] => 2.8e-93
                            [bit_score] => 345.9
                            [alignment_length] => 259
                            [identity_percentage] => 60.2
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Hma1.2p1_0710F.1_g207410] => Array
                        (
                            [gene_id] => Hma1.2p1_0710F.1_g207410
                            [e_value] => 2.8e-93
                            [bit_score] => 345.9
                            [alignment_length] => 267
                            [identity_percentage] => 60.7
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [RcHm_v2.0_Chr5g0067981] => Array
                        (
                            [gene_id] => RcHm_v2.0_Chr5g0067981
                            [e_value] => 2.8e-93
                            [bit_score] => 345.9
                            [alignment_length] => 261
                            [identity_percentage] => 61.7
                            [species] => rch
                            [common_name] => Rosa chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BcaC07g42007] => Array
                        (
                            [gene_id] => BcaC07g42007
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 59.6
                            [species] => bca
                            [common_name] => Brassica carinata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [C08p50640] => Array
                        (
                            [gene_id] => C08p50640
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 59.6
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BolC8t52592H] => Array
                        (
                            [gene_id] => BolC8t52592H
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 59.6
                            [species] => bol
                            [common_name] => Brassica oleracea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [BraA09t41985Z] => Array
                        (
                            [gene_id] => BraA09t41985Z
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 59.6
                            [species] => bra
                            [common_name] => Brassica rapa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Solyc06g076660.3] => Array
                        (
                            [gene_id] => Solyc06g076660.3
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => sly
                            [common_name] => Solanum lycopersicum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sopen06g033050] => Array
                        (
                            [gene_id] => Sopen06g033050
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [PGSC0003DMG400030432] => Array
                        (
                            [gene_id] => PGSC0003DMG400030432
                            [e_value] => 3.6e-93
                            [bit_score] => 345.5
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => stu
                            [common_name] => Solanum tuberosum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CAN.G394.99] => Array
                        (
                            [gene_id] => CAN.G394.99
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => can
                            [common_name] => Capsicum annuum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cc02_g07010] => Array
                        (
                            [gene_id] => Cc02_g07010
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 268
                            [identity_percentage] => 59.7
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [DCAR_007406] => Array
                        (
                            [gene_id] => DCAR_007406
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 267
                            [identity_percentage] => 59.9
                            [species] => dca
                            [common_name] => Daucus carota
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Dinv34434] => Array
                        (
                            [gene_id] => Dinv34434
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 262
                            [identity_percentage] => 60.3
                            [species] => din
                            [common_name] => Davidia involucrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FvH4_6g24870] => Array
                        (
                            [gene_id] => FvH4_6g24870
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.1
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN05G4258] => Array
                        (
                            [gene_id] => FAN05G4258
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 261
                            [identity_percentage] => 62.1
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sabra16G0150400] => Array
                        (
                            [gene_id] => Sabra16G0150400
                            [e_value] => 4.8e-93
                            [bit_score] => 345.1
                            [alignment_length] => 265
                            [identity_percentage] => 61.5
                            [species] => sbr
                            [common_name] => Salix brachista
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cc01_g13700] => Array
                        (
                            [gene_id] => Cc01_g13700
                            [e_value] => 6.2e-93
                            [bit_score] => 344.7
                            [alignment_length] => 260
                            [identity_percentage] => 60.0
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MD03G1078300] => Array
                        (
                            [gene_id] => MD03G1078300
                            [e_value] => 6.2e-93
                            [bit_score] => 344.7
                            [alignment_length] => 261
                            [identity_percentage] => 62.1
                            [species] => mdo
                            [common_name] => Malus domestica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Rhsim03G0139300] => Array
                        (
                            [gene_id] => Rhsim03G0139300
                            [e_value] => 6.2e-93
                            [bit_score] => 344.7
                            [alignment_length] => 259
                            [identity_percentage] => 61.4
                            [species] => rsi
                            [common_name] => Rhododendron simsii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Aa31LG5G6890] => Array
                        (
                            [gene_id] => Aa31LG5G6890
                            [e_value] => 8.1e-93
                            [bit_score] => 344.4
                            [alignment_length] => 259
                            [identity_percentage] => 61.0
                            [species] => aar
                            [common_name] => Aethionema arabicum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN25G0398] => Array
                        (
                            [gene_id] => FAN25G0398
                            [e_value] => 8.1e-93
                            [bit_score] => 344.4
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MBI18_g09770_MAGBIO] => Array
                        (
                            [gene_id] => MBI18_g09770_MAGBIO
                            [e_value] => 1.1e-92
                            [bit_score] => 344.0
                            [alignment_length] => 259
                            [identity_percentage] => 62.2
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MD11G1083000] => Array
                        (
                            [gene_id] => MD11G1083000
                            [e_value] => 1.1e-92
                            [bit_score] => 344.0
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => mdo
                            [common_name] => Malus domestica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MD13G1227300] => Array
                        (
                            [gene_id] => MD13G1227300
                            [e_value] => 1.1e-92
                            [bit_score] => 344.0
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => mdo
                            [common_name] => Malus domestica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN14G3520] => Array
                        (
                            [gene_id] => FAN14G3520
                            [e_value] => 1.4e-92
                            [bit_score] => 343.6
                            [alignment_length] => 267
                            [identity_percentage] => 60.7
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SGA_v2.0_scaffold95G28680] => Array
                        (
                            [gene_id] => SGA_v2.0_scaffold95G28680
                            [e_value] => 1.4e-92
                            [bit_score] => 343.6
                            [alignment_length] => 266
                            [identity_percentage] => 60.5
                            [species] => sas
                            [common_name] => Striga asiatica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.6QL4ST] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.6QL4ST
                            [e_value] => 1.8e-92
                            [bit_score] => 343.2
                            [alignment_length] => 265
                            [identity_percentage] => 60.0
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.L4PA5N] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.L4PA5N
                            [e_value] => 1.8e-92
                            [bit_score] => 343.2
                            [alignment_length] => 265
                            [identity_percentage] => 59.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.U7GG8I] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.U7GG8I
                            [e_value] => 1.8e-92
                            [bit_score] => 343.2
                            [alignment_length] => 265
                            [identity_percentage] => 59.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Mapoly0075s0032] => Array
                        (
                            [gene_id] => Mapoly0075s0032
                            [e_value] => 2.4e-92
                            [bit_score] => 342.8
                            [alignment_length] => 260
                            [identity_percentage] => 60.4
                            [species] => mpo
                            [common_name] => Marchantia polymorpha
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [ClCG07G003870] => Array
                        (
                            [gene_id] => ClCG07G003870
                            [e_value] => 3.1e-92
                            [bit_score] => 342.4
                            [alignment_length] => 260
                            [identity_percentage] => 60.4
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CsaV3_5G008820] => Array
                        (
                            [gene_id] => CsaV3_5G008820
                            [e_value] => 5.3e-92
                            [bit_score] => 341.7
                            [alignment_length] => 260
                            [identity_percentage] => 60.8
                            [species] => csa
                            [common_name] => Cucumis sativus L.
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [DCAR_011777] => Array
                        (
                            [gene_id] => DCAR_011777
                            [e_value] => 6.9e-92
                            [bit_score] => 341.3
                            [alignment_length] => 260
                            [identity_percentage] => 59.6
                            [species] => dca
                            [common_name] => Daucus carota
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Potri.009G040900] => Array
                        (
                            [gene_id] => Potri.009G040900
                            [e_value] => 9.0e-92
                            [bit_score] => 340.9
                            [alignment_length] => 259
                            [identity_percentage] => 59.8
                            [species] => ptr
                            [common_name] => Populus trichocarpa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Oeu032673.1] => Array
                        (
                            [gene_id] => Oeu032673.1
                            [e_value] => 1.7e-90
                            [bit_score] => 336.7
                            [alignment_length] => 269
                            [identity_percentage] => 58.4
                            [species] => oeu
                            [common_name] => Olea europaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sc10g0002110] => Array
                        (
                            [gene_id] => Sc10g0002110
                            [e_value] => 1.6e-88
                            [bit_score] => 330.1
                            [alignment_length] => 260
                            [identity_percentage] => 58.8
                            [species] => sci
                            [common_name] => Simmondsia chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [SGA_v2.0_scaffold2G01058] => Array
                        (
                            [gene_id] => SGA_v2.0_scaffold2G01058
                            [e_value] => 2.1e-88
                            [bit_score] => 329.7
                            [alignment_length] => 260
                            [identity_percentage] => 58.5
                            [species] => sas
                            [common_name] => Striga asiatica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.PUR3G8] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.PUR3G8
                            [e_value] => 6.0e-88
                            [bit_score] => 328.2
                            [alignment_length] => 265
                            [identity_percentage] => 56.6
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Mapoly0086s0078] => Array
                        (
                            [gene_id] => Mapoly0086s0078
                            [e_value] => 6.0e-88
                            [bit_score] => 328.2
                            [alignment_length] => 259
                            [identity_percentage] => 59.5
                            [species] => mpo
                            [common_name] => Marchantia polymorpha
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sed0017261] => Array
                        (
                            [gene_id] => Sed0017261
                            [e_value] => 1.0e-87
                            [bit_score] => 327.4
                            [alignment_length] => 265
                            [identity_percentage] => 57.0
                            [species] => sed
                            [common_name] => Sechium edule
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lj1A143T40] => Array
                        (
                            [gene_id] => Lj1A143T40
                            [e_value] => 1.3e-87
                            [bit_score] => 327.0
                            [alignment_length] => 260
                            [identity_percentage] => 59.2
                            [species] => lonja
                            [common_name] => Lonicera japonica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [EL10Ac7g16103] => Array
                        (
                            [gene_id] => EL10Ac7g16103
                            [e_value] => 2.3e-87
                            [bit_score] => 326.2
                            [alignment_length] => 295
                            [identity_percentage] => 53.2
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AUR62022826] => Array
                        (
                            [gene_id] => AUR62022826
                            [e_value] => 2.3e-87
                            [bit_score] => 326.2
                            [alignment_length] => 259
                            [identity_percentage] => 58.3
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AUR62012192] => Array
                        (
                            [gene_id] => AUR62012192
                            [e_value] => 3.9e-87
                            [bit_score] => 325.5
                            [alignment_length] => 258
                            [identity_percentage] => 58.1
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Rhsim01G0234300] => Array
                        (
                            [gene_id] => Rhsim01G0234300
                            [e_value] => 8.7e-87
                            [bit_score] => 324.3
                            [alignment_length] => 259
                            [identity_percentage] => 59.1
                            [species] => rsi
                            [common_name] => Rhododendron simsii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Ah.10g036710] => Array
                        (
                            [gene_id] => Ah.10g036710
                            [e_value] => 1.9e-86
                            [bit_score] => 323.2
                            [alignment_length] => 268
                            [identity_percentage] => 57.1
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MELO3C025142.2] => Array
                        (
                            [gene_id] => MELO3C025142.2
                            [e_value] => 4.8e-85
                            [bit_score] => 318.5
                            [alignment_length] => 260
                            [identity_percentage] => 58.1
                            [species] => cme
                            [common_name] => Cucumis melo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [QL08p062470] => Array
                        (
                            [gene_id] => QL08p062470
                            [e_value] => 1.1e-84
                            [bit_score] => 317.4
                            [alignment_length] => 322
                            [identity_percentage] => 48.1
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TPR.G15751] => Array
                        (
                            [gene_id] => TPR.G15751
                            [e_value] => 1.1e-84
                            [bit_score] => 317.4
                            [alignment_length] => 259
                            [identity_percentage] => 57.9
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Dinv14480] => Array
                        (
                            [gene_id] => Dinv14480
                            [e_value] => 6.5e-82
                            [bit_score] => 308.1
                            [alignment_length] => 222
                            [identity_percentage] => 64.4
                            [species] => din
                            [common_name] => Davidia involucrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [GSVIVG01024815001] => Array
                        (
                            [gene_id] => GSVIVG01024815001
                            [e_value] => 8.4e-82
                            [bit_score] => 307.8
                            [alignment_length] => 227
                            [identity_percentage] => 62.1
                            [species] => vvi
                            [common_name] => Vitis vinifera
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [EL10Ac2g04771] => Array
                        (
                            [gene_id] => EL10Ac2g04771
                            [e_value] => 4.2e-81
                            [bit_score] => 305.4
                            [alignment_length] => 259
                            [identity_percentage] => 55.2
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [MBI05_g36637_MAGBIO] => Array
                        (
                            [gene_id] => MBI05_g36637_MAGBIO
                            [e_value] => 1.6e-80
                            [bit_score] => 303.5
                            [alignment_length] => 221
                            [identity_percentage] => 63.8
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [unitig_0.g1546] => Array
                        (
                            [gene_id] => unitig_0.g1546
                            [e_value] => 2.7e-80
                            [bit_score] => 302.8
                            [alignment_length] => 219
                            [identity_percentage] => 64.4
                            [species] => ugi
                            [common_name] => Utricularia gibba
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Pp3c4_11630] => Array
                        (
                            [gene_id] => Pp3c4_11630
                            [e_value] => 1.3e-79
                            [bit_score] => 300.4
                            [alignment_length] => 222
                            [identity_percentage] => 60.4
                            [species] => ppa
                            [common_name] => Physcomitrium patens
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Lj1A949T60] => Array
                        (
                            [gene_id] => Lj1A949T60
                            [e_value] => 3.0e-79
                            [bit_score] => 299.3
                            [alignment_length] => 289
                            [identity_percentage] => 51.9
                            [species] => lonja
                            [common_name] => Lonicera japonica
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FvH4_4g13930] => Array
                        (
                            [gene_id] => FvH4_4g13930
                            [e_value] => 3.3e-78
                            [bit_score] => 295.8
                            [alignment_length] => 260
                            [identity_percentage] => 52.7
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Sabra09G0028700] => Array
                        (
                            [gene_id] => Sabra09G0028700
                            [e_value] => 3.1e-76
                            [bit_score] => 289.3
                            [alignment_length] => 264
                            [identity_percentage] => 52.3
                            [species] => sbr
                            [common_name] => Salix brachista
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CANSAT78G2202] => Array
                        (
                            [gene_id] => CANSAT78G2202
                            [e_value] => 6.9e-76
                            [bit_score] => 288.1
                            [alignment_length] => 209
                            [identity_percentage] => 64.1
                            [species] => cansat
                            [common_name] => Cannabis sativa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [EL10Ac5g10804] => Array
                        (
                            [gene_id] => EL10Ac5g10804
                            [e_value] => 4.3e-70
                            [bit_score] => 268.9
                            [alignment_length] => 260
                            [identity_percentage] => 49.6
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Haze_27443] => Array
                        (
                            [gene_id] => Haze_27443
                            [e_value] => 1.3e-69
                            [bit_score] => 267.3
                            [alignment_length] => 271
                            [identity_percentage] => 45.4
                            [species] => cav
                            [common_name] => Corylus avellana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [AagrBONN_evm.TU.Sc2ySwM_368.185] => Array
                        (
                            [gene_id] => AagrBONN_evm.TU.Sc2ySwM_368.185
                            [e_value] => 9.1e-68
                            [bit_score] => 261.2
                            [alignment_length] => 190
                            [identity_percentage] => 63.2
                            [species] => aag
                            [common_name] => Anthoceros agrestis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CiPaw.01G294900] => Array
                        (
                            [gene_id] => CiPaw.01G294900
                            [e_value] => 1.5e-67
                            [bit_score] => 260.4
                            [alignment_length] => 259
                            [identity_percentage] => 49.8
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cc01_g09170] => Array
                        (
                            [gene_id] => Cc01_g09170
                            [e_value] => 2.6e-67
                            [bit_score] => 259.6
                            [alignment_length] => 260
                            [identity_percentage] => 50.0
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Gorai.012G075000] => Array
                        (
                            [gene_id] => Gorai.012G075000
                            [e_value] => 4.5e-67
                            [bit_score] => 258.8
                            [alignment_length] => 258
                            [identity_percentage] => 49.2
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HanXRQChr12g0369341] => Array
                        (
                            [gene_id] => HanXRQChr12g0369341
                            [e_value] => 1.4e-65
                            [bit_score] => 253.8
                            [alignment_length] => 261
                            [identity_percentage] => 46.7
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN12G0397] => Array
                        (
                            [gene_id] => FAN12G0397
                            [e_value] => 1.9e-65
                            [bit_score] => 253.4
                            [alignment_length] => 221
                            [identity_percentage] => 52.5
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CBR_g8027] => Array
                        (
                            [gene_id] => CBR_g8027
                            [e_value] => 1.6e-64
                            [bit_score] => 250.4
                            [alignment_length] => 204
                            [identity_percentage] => 59.3
                            [species] => cbr
                            [common_name] => Chara braunii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [CDE02G0969] => Array
                        (
                            [gene_id] => CDE02G0969
                            [e_value] => 5.7e-62
                            [bit_score] => 241.9
                            [alignment_length] => 245
                            [identity_percentage] => 48.6
                            [species] => cde
                            [common_name] => Ceratophyllum demersum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN17G2398] => Array
                        (
                            [gene_id] => FAN17G2398
                            [e_value] => 5.3e-60
                            [bit_score] => 235.3
                            [alignment_length] => 257
                            [identity_percentage] => 44.4
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Migut.F01240] => Array
                        (
                            [gene_id] => Migut.F01240
                            [e_value] => 4.5e-59
                            [bit_score] => 232.3
                            [alignment_length] => 256
                            [identity_percentage] => 44.5
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Phvul.005G019800] => Array
                        (
                            [gene_id] => Phvul.005G019800
                            [e_value] => 6.5e-58
                            [bit_score] => 228.4
                            [alignment_length] => 256
                            [identity_percentage] => 43.8
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Cc01_g19170] => Array
                        (
                            [gene_id] => Cc01_g19170
                            [e_value] => 2.5e-57
                            [bit_score] => 226.5
                            [alignment_length] => 260
                            [identity_percentage] => 45.0
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Migut.F01239] => Array
                        (
                            [gene_id] => Migut.F01239
                            [e_value] => 4.7e-56
                            [bit_score] => 222.2
                            [alignment_length] => 249
                            [identity_percentage] => 43.8
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D190287
                                )

                        )

                    [AL4G24280] => Array
                        (
                            [gene_id] => AL4G24280
                            [e_value] => 2.8e-53
                            [bit_score] => 213.0
                            [alignment_length] => 193
                            [identity_percentage] => 52.8
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.7KT8N3] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.7KT8N3
                            [e_value] => 9.1e-52
                            [bit_score] => 208.0
                            [alignment_length] => 177
                            [identity_percentage] => 56.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [FAN22G0348] => Array
                        (
                            [gene_id] => FAN22G0348
                            [e_value] => 1.6e-51
                            [bit_score] => 207.2
                            [alignment_length] => 191
                            [identity_percentage] => 50.3
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Hund13825] => Array
                        (
                            [gene_id] => Hund13825
                            [e_value] => 6.7e-47
                            [bit_score] => 191.8
                            [alignment_length] => 259
                            [identity_percentage] => 39.0
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D383501
                                )

                        )

                    [Phvul.008G283900] => Array
                        (
                            [gene_id] => Phvul.008G283900
                            [e_value] => 3.3e-46
                            [bit_score] => 189.5
                            [alignment_length] => 265
                            [identity_percentage] => 37.4
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D307174
                                )

                        )

                    [C05p05420] => Array
                        (
                            [gene_id] => C05p05420
                            [e_value] => 7.5e-46
                            [bit_score] => 188.3
                            [alignment_length] => 152
                            [identity_percentage] => 58.6
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Phvul.L010543] => Array
                        (
                            [gene_id] => Phvul.L010543
                            [e_value] => 9.7e-46
                            [bit_score] => 188.0
                            [alignment_length] => 257
                            [identity_percentage] => 37.7
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D307408
                                )

                        )

                    [TWI81G0926] => Array
                        (
                            [gene_id] => TWI81G0926
                            [e_value] => 9.7e-46
                            [bit_score] => 188.0
                            [alignment_length] => 235
                            [identity_percentage] => 41.7
                            [species] => twi
                            [common_name] => Tripterygium wilfordii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D413704
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.2VD0DE] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.2VD0DE
                            [e_value] => 1.2e-40
                            [bit_score] => 171.0
                            [alignment_length] => 171
                            [identity_percentage] => 49.1
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [Duzib114G1052] => Array
                        (
                            [gene_id] => Duzib114G1052
                            [e_value] => 1.6e-40
                            [bit_score] => 170.6
                            [alignment_length] => 192
                            [identity_percentage] => 46.9
                            [species] => dzi
                            [common_name] => Durio zibethinus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D186062
                                )

                        )

                    [Dinv28595] => Array
                        (
                            [gene_id] => Dinv28595
                            [e_value] => 2.7e-40
                            [bit_score] => 169.9
                            [alignment_length] => 154
                            [identity_percentage] => 54.5
                            [species] => din
                            [common_name] => Davidia involucrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [GSVIVG01024814001] => Array
                        (
                            [gene_id] => GSVIVG01024814001
                            [e_value] => 4.7e-40
                            [bit_score] => 169.1
                            [alignment_length] => 146
                            [identity_percentage] => 54.1
                            [species] => vvi
                            [common_name] => Vitis vinifera
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D438409
                                )

                        )

                    [Carub.0004s1062] => Array
                        (
                            [gene_id] => Carub.0004s1062
                            [e_value] => 4.0e-39
                            [bit_score] => 166.0
                            [alignment_length] => 227
                            [identity_percentage] => 39.6
                            [species] => cru
                            [common_name] => Capsella rubella
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D114336
                                )

                        )

                    [MBI05_g34805_MAGBIO] => Array
                        (
                            [gene_id] => MBI05_g34805_MAGBIO
                            [e_value] => 2.0e-38
                            [bit_score] => 163.7
                            [alignment_length] => 221
                            [identity_percentage] => 40.3
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [TAR375G0102] => Array
                        (
                            [gene_id] => TAR375G0102
                            [e_value] => 5.7e-38
                            [bit_score] => 162.2
                            [alignment_length] => 255
                            [identity_percentage] => 36.5
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D415948
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.03KRNB] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.03KRNB
                            [e_value] => 2.7e-35
                            [bit_score] => 153.3
                            [alignment_length] => 126
                            [identity_percentage] => 59.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [arahy.Tifrunner.gnm1.ann1.C93DVI] => Array
                        (
                            [gene_id] => arahy.Tifrunner.gnm1.ann1.C93DVI
                            [e_value] => 2.7e-35
                            [bit_score] => 153.3
                            [alignment_length] => 126
                            [identity_percentage] => 59.5
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [HanXRQChr12g0369351] => Array
                        (
                            [gene_id] => HanXRQChr12g0369351
                            [e_value] => 2.5e-33
                            [bit_score] => 146.7
                            [alignment_length] => 163
                            [identity_percentage] => 46.6
                            [species] => han
                            [common_name] => Helianthus annuus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D223853
                                )

                        )

                    [Nn2g13583] => Array
                        (
                            [gene_id] => Nn2g13583
                            [e_value] => 3.2e-33
                            [bit_score] => 146.4
                            [alignment_length] => 108
                            [identity_percentage] => 60.2
                            [species] => nnu
                            [common_name] => Nelumbo nucifera
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D029955
                                )

                        )

                    [Glyma.14G009500] => Array
                        (
                            [gene_id] => Glyma.14G009500
                            [e_value] => 7.2e-33
                            [bit_score] => 145.2
                            [alignment_length] => 184
                            [identity_percentage] => 44.6
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D214078
                                )

                        )

                    [SEGI_20540] => Array
                        (
                            [gene_id] => SEGI_20540
                            [e_value] => 2.1e-32
                            [bit_score] => 143.7
                            [alignment_length] => 126
                            [identity_percentage] => 52.4
                            [species] => sgi
                            [common_name] => Sequoiadendron giganteum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D384695
                                )

                        )

                    [PGR091G0001] => Array
                        (
                            [gene_id] => PGR091G0001
                            [e_value] => 2.8e-32
                            [bit_score] => 143.3
                            [alignment_length] => 105
                            [identity_percentage] => 60.0
                            [species] => pgr
                            [common_name] => Punica granatum
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D029955
                                )

                        )

                    [Cc02_g02530] => Array
                        (
                            [gene_id] => Cc02_g02530
                            [e_value] => 1.5e-30
                            [bit_score] => 137.5
                            [alignment_length] => 162
                            [identity_percentage] => 45.7
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D153768
                                )

                        )

                    [Migut.F01526] => Array
                        (
                            [gene_id] => Migut.F01526
                            [e_value] => 1.5e-30
                            [bit_score] => 137.5
                            [alignment_length] => 255
                            [identity_percentage] => 35.7
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D190339
                                )

                        )

                    [Migut.F01528] => Array
                        (
                            [gene_id] => Migut.F01528
                            [e_value] => 3.4e-30
                            [bit_score] => 136.3
                            [alignment_length] => 255
                            [identity_percentage] => 35.7
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D189732
                                )

                        )

                    [Carub.0001s0667] => Array
                        (
                            [gene_id] => Carub.0001s0667
                            [e_value] => 6.3e-29
                            [bit_score] => 132.1
                            [alignment_length] => 116
                            [identity_percentage] => 56.0
                            [species] => cru
                            [common_name] => Capsella rubella
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [TAR636G0236] => Array
                        (
                            [gene_id] => TAR636G0236
                            [e_value] => 1.6e-27
                            [bit_score] => 127.5
                            [alignment_length] => 254
                            [identity_percentage] => 31.5
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D416028
                                )

                        )

                    [Hma1.2p1_0342F.1_g130700] => Array
                        (
                            [gene_id] => Hma1.2p1_0342F.1_g130700
                            [e_value] => 2.0e-27
                            [bit_score] => 127.1
                            [alignment_length] => 105
                            [identity_percentage] => 55.2
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D029955
                                )

                        )

                    [SalBow5G5047] => Array
                        (
                            [gene_id] => SalBow5G5047
                            [e_value] => 1.7e-26
                            [bit_score] => 124.0
                            [alignment_length] => 106
                            [identity_percentage] => 61.3
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D363293
                                )

                        )

                    [TAR374G0519] => Array
                        (
                            [gene_id] => TAR374G0519
                            [e_value] => 5.0e-26
                            [bit_score] => 122.5
                            [alignment_length] => 257
                            [identity_percentage] => 32.3
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414107
                                )

                        )

                    [TAR374G1473] => Array
                        (
                            [gene_id] => TAR374G1473
                            [e_value] => 1.5e-25
                            [bit_score] => 120.9
                            [alignment_length] => 254
                            [identity_percentage] => 29.5
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414303
                                )

                        )

                    [TAR374G1596] => Array
                        (
                            [gene_id] => TAR374G1596
                            [e_value] => 8.9e-23
                            [bit_score] => 111.7
                            [alignment_length] => 256
                            [identity_percentage] => 29.3
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414903
                                )

                        )

                    [TAR375G0427] => Array
                        (
                            [gene_id] => TAR375G0427
                            [e_value] => 1.5e-22
                            [bit_score] => 110.9
                            [alignment_length] => 254
                            [identity_percentage] => 31.1
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D415801
                                )

                        )

                    [TAR374G0089] => Array
                        (
                            [gene_id] => TAR374G0089
                            [e_value] => 5.7e-22
                            [bit_score] => 109.0
                            [alignment_length] => 250
                            [identity_percentage] => 29.2
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414833
                                )

                        )

                    [CiPaw.15G124600] => Array
                        (
                            [gene_id] => CiPaw.15G124600
                            [e_value] => 7.5e-22
                            [bit_score] => 108.6
                            [alignment_length] => 162
                            [identity_percentage] => 40.7
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D003647
                                )

                        )

                    [QL93p0331_0124] => Array
                        (
                            [gene_id] => QL93p0331_0124
                            [e_value] => 7.8e-19
                            [bit_score] => 98.6
                            [alignment_length] => 68
                            [identity_percentage] => 60.3
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D029955
                                )

                        )

                    [TAR374G0750] => Array
                        (
                            [gene_id] => TAR374G0750
                            [e_value] => 1.2e-16
                            [bit_score] => 91.3
                            [alignment_length] => 152
                            [identity_percentage] => 32.9
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414369
                                )

                        )

                    [Migut.F01525] => Array
                        (
                            [gene_id] => Migut.F01525
                            [e_value] => 6.2e-16
                            [bit_score] => 89.0
                            [alignment_length] => 265
                            [identity_percentage] => 25.3
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D190644
                                )

                        )

                    [Migut.F01527] => Array
                        (
                            [gene_id] => Migut.F01527
                            [e_value] => 8.0e-16
                            [bit_score] => 88.6
                            [alignment_length] => 266
                            [identity_percentage] => 25.2
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D189253
                                )

                        )

                    [Dinv29454] => Array
                        (
                            [gene_id] => Dinv29454
                            [e_value] => 5.2e-15
                            [bit_score] => 85.9
                            [alignment_length] => 68
                            [identity_percentage] => 55.9
                            [species] => din
                            [common_name] => Davidia involucrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [Ciclev10030011m.g] => Array
                        (
                            [gene_id] => Ciclev10030011m.g
                            [e_value] => 6.8e-15
                            [bit_score] => 85.5
                            [alignment_length] => 65
                            [identity_percentage] => 55.4
                            [species] => ccl
                            [common_name] => Citrus clementina
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [RcHm_v2.0_Chr1g0365091] => Array
                        (
                            [gene_id] => RcHm_v2.0_Chr1g0365091
                            [e_value] => 9.8e-14
                            [bit_score] => 81.6
                            [alignment_length] => 225
                            [identity_percentage] => 26.2
                            [species] => rch
                            [common_name] => Rosa chinensis
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D025387
                                )

                        )

                    [Phvul.003G297300] => Array
                        (
                            [gene_id] => Phvul.003G297300
                            [e_value] => 1.1e-12
                            [bit_score] => 78.2
                            [alignment_length] => 173
                            [identity_percentage] => 31.2
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D307945
                                )

                        )

                    [FAN06G0269] => Array
                        (
                            [gene_id] => FAN06G0269
                            [e_value] => 2.4e-12
                            [bit_score] => 77.0
                            [alignment_length] => 247
                            [identity_percentage] => 26.3
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D025387
                                )

                        )

                    [FvH4_7g20850] => Array
                        (
                            [gene_id] => FvH4_7g20850
                            [e_value] => 4.1e-12
                            [bit_score] => 76.3
                            [alignment_length] => 248
                            [identity_percentage] => 26.2
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D025387
                                )

                        )

                    [Cfa003957] => Array
                        (
                            [gene_id] => Cfa003957
                            [e_value] => 1.7e-10
                            [bit_score] => 70.9
                            [alignment_length] => 264
                            [identity_percentage] => 25.4
                            [species] => cfa
                            [common_name] => Carpinus fangiana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D029117
                                    [ORTHOFAM] => ORTHO05D011417
                                )

                        )

                    [Glyma.02G304300] => Array
                        (
                            [gene_id] => Glyma.02G304300
                            [e_value] => 1.7e-10
                            [bit_score] => 70.9
                            [alignment_length] => 161
                            [identity_percentage] => 29.8
                            [species] => gma
                            [common_name] => Glycine max
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D212978
                                )

                        )

                    [MBI14_g13658_MAGBIO] => Array
                        (
                            [gene_id] => MBI14_g13658_MAGBIO
                            [e_value] => 3.9e-10
                            [bit_score] => 69.7
                            [alignment_length] => 65
                            [identity_percentage] => 49.2
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D030039
                                )

                        )

                    [MBI17_g28777_MAGBIO] => Array
                        (
                            [gene_id] => MBI17_g28777_MAGBIO
                            [e_value] => 8.6e-10
                            [bit_score] => 68.6
                            [alignment_length] => 52
                            [identity_percentage] => 59.6
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D028395
                                )

                        )

                    [MBI18_g30544_MAGBIO] => Array
                        (
                            [gene_id] => MBI18_g30544_MAGBIO
                            [e_value] => 8.6e-10
                            [bit_score] => 68.6
                            [alignment_length] => 52
                            [identity_percentage] => 59.6
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D028395
                                )

                        )

                    [TAR374G0509] => Array
                        (
                            [gene_id] => TAR374G0509
                            [e_value] => 1.9e-09
                            [bit_score] => 67.4
                            [alignment_length] => 105
                            [identity_percentage] => 34.3
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D414285
                                )

                        )

                    [Dinv32451] => Array
                        (
                            [gene_id] => Dinv32451
                            [e_value] => 4.3e-09
                            [bit_score] => 66.2
                            [alignment_length] => 229
                            [identity_percentage] => 24.5
                            [species] => din
                            [common_name] => Davidia involucrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D011417
                                )

                        )

                    [SalBow5G5737] => Array
                        (
                            [gene_id] => SalBow5G5737
                            [e_value] => 5.6e-09
                            [bit_score] => 65.9
                            [alignment_length] => 52
                            [identity_percentage] => 57.7
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D352944
                                )

                        )

                    [VMungo0647G0649] => Array
                        (
                            [gene_id] => VMungo0647G0649
                            [e_value] => 9.5e-09
                            [bit_score] => 65.1
                            [alignment_length] => 107
                            [identity_percentage] => 34.6
                            [species] => vmu
                            [common_name] => Vigna mungo
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D433490
                                )

                        )

                    [TAR374G1334] => Array
                        (
                            [gene_id] => TAR374G1334
                            [e_value] => 2.1e-08
                            [bit_score] => 63.9
                            [alignment_length] => 101
                            [identity_percentage] => 32.7
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D415265
                                )

                        )

                    [FAN03G0088] => Array
                        (
                            [gene_id] => FAN03G0088
                            [e_value] => 2.8e-08
                            [bit_score] => 63.5
                            [alignment_length] => 143
                            [identity_percentage] => 30.8
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D025387
                                )

                        )

                    [BcaB05g22504] => Array
                        (
                            [gene_id] => BcaB05g22504
                            [e_value] => 3.6e-08
                            [bit_score] => 63.2
                            [alignment_length] => 48
                            [identity_percentage] => 52.1
                            [species] => bca
                            [common_name] => Brassica carinata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [C08p02990] => Array
                        (
                            [gene_id] => C08p02990
                            [e_value] => 4.7e-08
                            [bit_score] => 62.8
                            [alignment_length] => 55
                            [identity_percentage] => 50.9
                            [species] => bna
                            [common_name] => Brassica napus
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [BolC8t47099H] => Array
                        (
                            [gene_id] => BolC8t47099H
                            [e_value] => 4.7e-08
                            [bit_score] => 62.8
                            [alignment_length] => 55
                            [identity_percentage] => 50.9
                            [species] => bol
                            [common_name] => Brassica oleracea
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D021775
                                )

                        )

                    [FAN03G3437] => Array
                        (
                            [gene_id] => FAN03G3437
                            [e_value] => 3.1e-07
                            [bit_score] => 60.1
                            [alignment_length] => 73
                            [identity_percentage] => 43.8
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D025387
                                )

                        )

                    [TAR374G0620] => Array
                        (
                            [gene_id] => TAR374G0620
                            [e_value] => 4.0e-07
                            [bit_score] => 59.7
                            [alignment_length] => 77
                            [identity_percentage] => 39.0
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D415313
                                )

                        )

                    [TAR375G0508] => Array
                        (
                            [gene_id] => TAR375G0508
                            [e_value] => 5.2e-07
                            [bit_score] => 59.3
                            [alignment_length] => 184
                            [identity_percentage] => 28.8
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D416239
                                )

                        )

                    [AL4G32460] => Array
                        (
                            [gene_id] => AL4G32460
                            [e_value] => 6.8e-07
                            [bit_score] => 58.9
                            [alignment_length] => 47
                            [identity_percentage] => 59.6
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D079774
                                )

                        )

                    [EL10Ac5g10992] => Array
                        (
                            [gene_id] => EL10Ac5g10992
                            [e_value] => 2.0e-06
                            [bit_score] => 57.4
                            [alignment_length] => 42
                            [identity_percentage] => 54.8
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [gf] => Array
                                (
                                    [HOMFAM] => HOM05D002404
                                    [ORTHOFAM] => ORTHO05D007748
                                )

                        )

                )

            [similarity_hits_species] => Array
                (
                    [cre] => Array
                        (
                            [0] => Cre12.g515850
                        )

                    [mco] => Array
                        (
                            [0] => MCO09G325
                        )

                    [nnu] => Array
                        (
                            [0] => Nn2g11338
                            [1] => Nn2g13583
                        )

                    [vpl] => Array
                        (
                            [0] => HPP92_018042
                        )

                    [vmu] => Array
                        (
                            [0] => VMungo0540G1433
                            [1] => VMungo0647G0649
                        )

                    [ach] => Array
                        (
                            [0] => Actinidia29670
                            [1] => Actinidia34442
                            [2] => Actinidia33951
                        )

                    [han] => Array
                        (
                            [0] => HanXRQChr05g0135561
                            [1] => HanXRQChr01g0011001
                            [2] => HanXRQChr08g0222181
                            [3] => HanXRQChr12g0369341
                            [4] => HanXRQChr12g0369351
                        )

                    [cpa] => Array
                        (
                            [0] => Cpa.g.sc112.81
                        )

                    [cde] => Array
                        (
                            [0] => CDE09G0989
                            [1] => CDE02G0969
                        )

                    [lsa] => Array
                        (
                            [0] => Lsat_1_v5_gn_5_171040
                            [1] => Lsat_1_v5_gn_8_12580
                            [2] => Lsat_1_v5_gn_8_72200
                        )

                    [aox] => Array
                        (
                            [0] => Aqoxy1G00741
                        )

                    [eca] => Array
                        (
                            [0] => ECA248G2035
                            [1] => ECA233G2070
                        )

                    [osa] => Array
                        (
                            [0] => Os02g0805200
                        )

                    [sgi] => Array
                        (
                            [0] => SEGI_27416
                            [1] => SEGI_13348
                            [2] => SEGI_20540
                        )

                    [tca] => Array
                        (
                            [0] => Thecc.09G307900
                        )

                    [cansat] => Array
                        (
                            [0] => CANSAT78G2483
                            [1] => CANSAT54G2750
                            [2] => CANSAT78G2202
                        )

                    [cav] => Array
                        (
                            [0] => Haze_24235
                            [1] => Haze_27443
                        )

                    [oeu] => Array
                        (
                            [0] => Oeu035018.1
                            [1] => Oeu049279.1
                            [2] => Oeu032673.1
                        )

                    [sbo] => Array
                        (
                            [0] => SalBow3G1232
                            [1] => SalBow3G1958
                            [2] => SalBow5G5047
                            [3] => SalBow5G5737
                        )

                    [shi] => Array
                        (
                            [0] => SHI38242
                        )

                    [cil] => Array
                        (
                            [0] => CiPaw.14G062600
                            [1] => CiPaw.13G083600
                            [2] => CiPaw.01G294900
                            [3] => CiPaw.15G124600
                        )

                    [col] => Array
                        (
                            [0] => COL.COLO4_19083
                        )

                    [pvu] => Array
                        (
                            [0] => Phvul.006G137800
                            [1] => Phvul.005G019800
                            [2] => Phvul.008G283900
                            [3] => Phvul.L010543
                            [4] => Phvul.003G297300
                        )

                    [ugi] => Array
                        (
                            [0] => unitig_747.g22020
                            [1] => unitig_0.g1546
                        )

                    [pgr] => Array
                        (
                            [0] => PGR102G0182
                            [1] => PGR119G1764
                            [2] => PGR044G0110
                            [3] => PGR091G0001
                        )

                    [tha] => Array
                        (
                            [0] => THA.LOC104826301
                            [1] => THA.LOC104815801
                        )

                    [ghi] => Array
                        (
                            [0] => Gohir.A03G048100
                            [1] => Gohir.D03G118900
                            [2] => Gohir.A13G225400
                            [3] => Gohir.D13G230500
                        )

                    [sun] => Array
                        (
                            [0] => Hund04899
                            [1] => Hund18869
                            [2] => Hund13825
                        )

                    [chi] => Array
                        (
                            [0] => CARHR122910
                            [1] => CARHR007080
                        )

                    [cfa] => Array
                        (
                            [0] => Cfa011630
                            [1] => Cfa003957
                        )

                    [pco] => Array
                        (
                            [0] => PRCOL_00005339
                        )

                    [tar] => Array
                        (
                            [0] => TAR636G2785
                            [1] => TAR633G0461
                            [2] => TAR375G0102
                            [3] => TAR636G0236
                            [4] => TAR374G0519
                            [5] => TAR374G1473
                            [6] => TAR374G1596
                            [7] => TAR375G0427
                            [8] => TAR374G0089
                            [9] => TAR374G0750
                            [10] => TAR374G0509
                            [11] => TAR374G1334
                            [12] => TAR374G0620
                            [13] => TAR375G0508
                        )

                    [acertr] => Array
                        (
                            [0] => Atru.chr3.4053
                        )

                    [egut] => Array
                        (
                            [0] => Migut.D02143
                            [1] => Migut.F01240
                            [2] => Migut.F01239
                            [3] => Migut.F01526
                            [4] => Migut.F01528
                            [5] => Migut.F01525
                            [6] => Migut.F01527
                        )

                    [egr] => Array
                        (
                            [0] => Eucgr.J01951
                        )

                    [gma] => Array
                        (
                            [0] => Glyma.08G334900
                            [1] => Glyma.18G067800
                            [2] => Glyma.14G009500
                            [3] => Glyma.02G304300
                        )

                    [ama] => Array
                        (
                            [0] => MSTRG.18604
                            [1] => MSTRG.21172
                        )

                    [car] => Array
                        (
                            [0] => Ca_14888_v3
                        )

                    [gra] => Array
                        (
                            [0] => Gorai.013G261100
                            [1] => Gorai.003G125300
                            [2] => Gorai.012G075000
                        )

                    [lja] => Array
                        (
                            [0] => Lj6g0014589
                        )

                    [ptr] => Array
                        (
                            [0] => Potri.001G247700
                            [1] => Potri.009G040900
                        )

                    [ccl] => Array
                        (
                            [0] => Ciclev10029070m.g
                            [1] => Ciclev10030011m.g
                        )

                    [camsi] => Array
                        (
                            [0] => CSS0029507
                            [1] => CSS0001422
                            [2] => CSS0025335
                        )

                    [sci] => Array
                        (
                            [0] => Sc12g0001020
                            [1] => Sc10g0002110
                        )

                    [twi] => Array
                        (
                            [0] => TWI31G0565
                            [1] => TWI75G1109
                            [2] => TWI81G0926
                        )

                    [aly] => Array
                        (
                            [0] => AL1G17520
                            [1] => AL4G24290
                            [2] => AL4G24280
                            [3] => AL4G32460
                        )

                    [ath] => Array
                        (
                            [0] => AT1G07370
                            [1] => AT2G29570
                        )

                    [lonja] => Array
                        (
                            [0] => Lj2A1074T37
                            [1] => Lj1A143T40
                            [2] => Lj1A949T60
                        )

                    [mes] => Array
                        (
                            [0] => Manes.01G165500
                            [1] => Manes.02G123000
                        )

                    [pso] => Array
                        (
                            [0] => PSO384G1519
                            [1] => PSO585G0022
                        )

                    [rsi] => Array
                        (
                            [0] => Rhsim01G0234200
                            [1] => Rhsim03G0139300
                            [2] => Rhsim01G0234300
                        )

                    [sed] => Array
                        (
                            [0] => Sed0001054
                            [1] => Sed0018009
                            [2] => Sed0017261
                        )

                    [vma] => Array
                        (
                            [0] => vmacro14574
                            [1] => vmacro07002
                        )

                    [zma] => Array
                        (
                            [0] => Zm00001eb192050
                            [1] => Zm00001eb258230
                        )

                    [cru] => Array
                        (
                            [0] => Carub.0004s1063
                            [1] => Carub.0004s1062
                            [2] => Carub.0001s0667
                        )

                    [cme] => Array
                        (
                            [0] => MELO3C025879.2
                            [1] => MELO3C025142.2
                        )

                    [dzi] => Array
                        (
                            [0] => Duzib150G0009
                            [1] => Duzib170G0557
                            [2] => Duzib114G1052
                        )

                    [mtr] => Array
                        (
                            [0] => Medtr3g462130
                        )

                    [amhyb] => Array
                        (
                            [0] => Ah.14g082670
                            [1] => Ah.08g220430
                            [2] => Ah.10g036710
                        )

                    [atr] => Array
                        (
                            [0] => ATR0680G321
                            [1] => ATR0618G446
                        )

                    [csa] => Array
                        (
                            [0] => CsaV3_6G016510
                            [1] => CsaV3_5G008820
                        )

                    [cqu] => Array
                        (
                            [0] => AUR62001707
                            [1] => AUR62020074
                            [2] => AUR62022826
                            [3] => AUR62012192
                        )

                    [mbi] => Array
                        (
                            [0] => MBI14_g32930_MAGBIO
                            [1] => MBI18_g09770_MAGBIO
                            [2] => MBI05_g36637_MAGBIO
                            [3] => MBI05_g34805_MAGBIO
                            [4] => MBI14_g13658_MAGBIO
                            [5] => MBI17_g28777_MAGBIO
                            [6] => MBI18_g30544_MAGBIO
                        )

                    [nta] => Array
                        (
                            [0] => Nitab4.5_0000744g0120
                            [1] => Nitab4.5_0011134g0030
                        )

                    [pax] => Array
                        (
                            [0] => Peaxi162Scf01058g00150
                        )

                    [smo] => Array
                        (
                            [0] => SMO172G0020
                        )

                    [tpr] => Array
                        (
                            [0] => TPR.G30115
                            [1] => TPR.G15751
                        )

                    [bna] => Array
                        (
                            [0] => C04p21270
                            [1] => A05p15830
                            [2] => C08p50640
                            [3] => C05p05420
                            [4] => C08p02990
                        )

                    [bol] => Array
                        (
                            [0] => BolC4t23656H
                            [1] => BolC8t52592H
                            [2] => BolC8t47099H
                        )

                    [lal] => Array
                        (
                            [0] => Lalb_Chr15g0082601
                            [1] => Lalb_Chr18g0050611
                        )

                    [ppa] => Array
                        (
                            [0] => Pp3c12_18160
                            [1] => Pp3c4_11630
                        )

                    [qlo] => Array
                        (
                            [0] => QL01p029015
                            [1] => QL08p062470
                            [2] => QL93p0331_0124
                        )

                    [bca] => Array
                        (
                            [0] => BcaB02g10263
                            [1] => BcaC07g42462
                            [2] => BcaC07g42007
                            [3] => BcaB05g22504
                        )

                    [spa] => Array
                        (
                            [0] => Sp4g12300
                            [1] => Sp1g06120
                        )

                    [sas] => Array
                        (
                            [0] => SGA_v2.0_scaffold77G25326
                            [1] => SGA_v2.0_scaffold95G28680
                            [2] => SGA_v2.0_scaffold2G01058
                        )

                    [bra] => Array
                        (
                            [0] => BraA05t20496Z
                            [1] => BraA09t41985Z
                        )

                    [cla] => Array
                        (
                            [0] => ClCG02G019790
                            [1] => ClCG07G003870
                        )

                    [ppe] => Array
                        (
                            [0] => Prupe.6G063300
                        )

                    [esa] => Array
                        (
                            [0] => Thhalv10017099m.g
                            [1] => Thhalv10008509m.g
                        )

                    [psa] => Array
                        (
                            [0] => Psat5g162720
                        )

                    [fve] => Array
                        (
                            [0] => FvH4_3g37710
                            [1] => FvH4_6g24870
                            [2] => FvH4_4g13930
                            [3] => FvH4_7g20850
                        )

                    [fan] => Array
                        (
                            [0] => FAN16G1397
                            [1] => FAN21G0265
                            [2] => FAN11G3986
                            [3] => FAN05G4258
                            [4] => FAN25G0398
                            [5] => FAN14G3520
                            [6] => FAN12G0397
                            [7] => FAN17G2398
                            [8] => FAN22G0348
                            [9] => FAN06G0269
                            [10] => FAN03G0088
                            [11] => FAN03G3437
                        )

                    [hma] => Array
                        (
                            [0] => Hma1.2p1_0710F.1_g207410
                            [1] => Hma1.2p1_0342F.1_g130700
                        )

                    [rch] => Array
                        (
                            [0] => RcHm_v2.0_Chr5g0067981
                            [1] => RcHm_v2.0_Chr1g0365091
                        )

                    [sly] => Array
                        (
                            [0] => Solyc06g076660.3
                        )

                    [spe] => Array
                        (
                            [0] => Sopen06g033050
                        )

                    [stu] => Array
                        (
                            [0] => PGSC0003DMG400030432
                        )

                    [can] => Array
                        (
                            [0] => CAN.G394.99
                        )

                    [ccan] => Array
                        (
                            [0] => Cc02_g07010
                            [1] => Cc01_g13700
                            [2] => Cc01_g09170
                            [3] => Cc01_g19170
                            [4] => Cc02_g02530
                        )

                    [dca] => Array
                        (
                            [0] => DCAR_007406
                            [1] => DCAR_011777
                        )

                    [din] => Array
                        (
                            [0] => Dinv34434
                            [1] => Dinv14480
                            [2] => Dinv28595
                            [3] => Dinv29454
                            [4] => Dinv32451
                        )

                    [sbr] => Array
                        (
                            [0] => Sabra16G0150400
                            [1] => Sabra09G0028700
                        )

                    [mdo] => Array
                        (
                            [0] => MD03G1078300
                            [1] => MD11G1083000
                            [2] => MD13G1227300
                        )

                    [aar] => Array
                        (
                            [0] => Aa31LG5G6890
                        )

                    [arhy] => Array
                        (
                            [0] => arahy.Tifrunner.gnm1.ann1.6QL4ST
                            [1] => arahy.Tifrunner.gnm1.ann1.L4PA5N
                            [2] => arahy.Tifrunner.gnm1.ann1.U7GG8I
                            [3] => arahy.Tifrunner.gnm1.ann1.PUR3G8
                            [4] => arahy.Tifrunner.gnm1.ann1.7KT8N3
                            [5] => arahy.Tifrunner.gnm1.ann1.2VD0DE
                            [6] => arahy.Tifrunner.gnm1.ann1.03KRNB
                            [7] => arahy.Tifrunner.gnm1.ann1.C93DVI
                        )

                    [mpo] => Array
                        (
                            [0] => Mapoly0075s0032
                            [1] => Mapoly0086s0078
                        )

                    [bvu] => Array
                        (
                            [0] => EL10Ac7g16103
                            [1] => EL10Ac2g04771
                            [2] => EL10Ac5g10804
                            [3] => EL10Ac5g10992
                        )

                    [vvi] => Array
                        (
                            [0] => GSVIVG01024815001
                            [1] => GSVIVG01024814001
                        )

                    [aag] => Array
                        (
                            [0] => AagrBONN_evm.TU.Sc2ySwM_368.185
                        )

                    [cbr] => Array
                        (
                            [0] => CBR_g8027
                        )

                )

            [gene_id] => CBR_g8027
            [gf_types_information] => Array
                (
                    [HOMFAM] => Array
                        (
                            [id] => HOMFAM
                            [name] => Homologous gene family
                            [gene_type] => coding
                            [parent_id] => 
                            [ancestry] => homology
                        )

                    [ORTHOFAM] => Array
                        (
                            [id] => ORTHOFAM
                            [name] => Orthologous gene family
                            [gene_type] => coding
                            [parent_id] => HOMFAM
                            [ancestry] => orthology
                        )

                )

            [gf_types_configuration] => Array
                (
                    [HOMFAM] => Array
                        (
                            [order] => 1
                            [show_parentless_subfamilies] => false
                            [show_table] => true
                            [show_orphan] => 
                        )

                    [ORTHOFAM] => Array
                        (
                            [order] => 2
                            [show_parentless_subfamilies] => false
                            [show_table] => true
                            [show_orphan] => 
                        )

                )

            [all_species] => Array
                (
                    [acertr] => Array
                        (
                            [species] => acertr
                            [common_name] => Acer truncatum
                            [tax_id] => 47965
                            [version] => v2.0
                        )

                    [ach] => Array
                        (
                            [species] => ach
                            [common_name] => Actinidia chinensis
                            [tax_id] => 3625
                            [version] => V3.0
                        )

                    [aar] => Array
                        (
                            [species] => aar
                            [common_name] => Aethionema arabicum
                            [tax_id] => 228871
                            [version] => v3.1
                        )

                    [amhyb] => Array
                        (
                            [species] => amhyb
                            [common_name] => Amaranthus hybridus
                            [tax_id] => 3565
                            [version] => v1.0
                        )

                    [atr] => Array
                        (
                            [species] => atr
                            [common_name] => Amborella trichopoda
                            [tax_id] => 13333
                            [version] => JGI v1.0
                        )

                    [aag] => Array
                        (
                            [species] => aag
                            [common_name] => Anthoceros agrestis
                            [tax_id] => 41834
                            [version] => v1.1
                        )

                    [aox] => Array
                        (
                            [species] => aox
                            [common_name] => Aquilegia oxysepala
                            [tax_id] => 432649
                            [version] => v1.0
                        )

                    [aly] => Array
                        (
                            [species] => aly
                            [common_name] => Arabidopsis lyrata
                            [tax_id] => 59689
                            [version] => JGI v2.1
                        )

                    [ath] => Array
                        (
                            [species] => ath
                            [common_name] => Arabidopsis thaliana
                            [tax_id] => 3702
                            [version] => Araport11
                        )

                    [arhy] => Array
                        (
                            [species] => arhy
                            [common_name] => Arachis hypogaea
                            [tax_id] => 3818
                            [version] => v1.0
                        )

                    [ama] => Array
                        (
                            [species] => ama
                            [common_name] => Avicennia marina
                            [tax_id] => 82927
                            [version] => v1.1 20200527
                        )

                    [bvu] => Array
                        (
                            [species] => bvu
                            [common_name] => Beta vulgaris
                            [tax_id] => 161934
                            [version] => EL10_1.0
                        )

                    [bca] => Array
                        (
                            [species] => bca
                            [common_name] => Brassica carinata
                            [tax_id] => 52824
                            [version] => V1.0
                        )

                    [bna] => Array
                        (
                            [species] => bna
                            [common_name] => Brassica napus
                            [tax_id] => 3708
                            [version] => v2.0
                        )

                    [bol] => Array
                        (
                            [species] => bol
                            [common_name] => Brassica oleracea
                            [tax_id] => 109376
                            [version] => v1.0
                        )

                    [bra] => Array
                        (
                            [species] => bra
                            [common_name] => Brassica rapa
                            [tax_id] => 3711
                            [version] => v1.0
                        )

                    [camsi] => Array
                        (
                            [species] => camsi
                            [common_name] => Camellia sinensis var. sinensis
                            [tax_id] => 542762
                            [version] => CSS_ChrLev_20200506
                        )

                    [cansat] => Array
                        (
                            [species] => cansat
                            [common_name] => Cannabis sativa
                            [tax_id] => 3483
                            [version] => cs10
                        )

                    [cru] => Array
                        (
                            [species] => cru
                            [common_name] => Capsella rubella
                            [tax_id] => 81985
                            [version] => JGI v1.1
                        )

                    [can] => Array
                        (
                            [species] => can
                            [common_name] => Capsicum annuum
                            [tax_id] => 4072
                            [version] => Pepper Genome v2.0
                        )

                    [chi] => Array
                        (
                            [species] => chi
                            [common_name] => Cardamine hirsuta
                            [tax_id] => 50463
                            [version] => v1.0
                        )

                    [cpa] => Array
                        (
                            [species] => cpa
                            [common_name] => Carica papaya
                            [tax_id] => 3649
                            [version] => JGI ASGPB0.4
                        )

                    [cfa] => Array
                        (
                            [species] => cfa
                            [common_name] => Carpinus fangiana
                            [tax_id] => 176857
                            [version] => v1.0
                        )

                    [cil] => Array
                        (
                            [species] => cil
                            [common_name] => Carya illinoinensis
                            [tax_id] => 32201
                            [version] => v1.1
                        )

                    [cde] => Array
                        (
                            [species] => cde
                            [common_name] => Ceratophyllum demersum
                            [tax_id] => 4428
                            [version] => v1.0
                        )

                    [cbr] => Array
                        (
                            [species] => cbr
                            [common_name] => Chara braunii
                            [tax_id] => 69332
                            [version] => Cbr1.0
                        )

                    [cqu] => Array
                        (
                            [species] => cqu
                            [common_name] => Chenopodium quinoa
                            [tax_id] => 63459
                            [version] => KAUST v1.0
                        )

                    [cre] => Array
                        (
                            [species] => cre
                            [common_name] => Chlamydomonas reinhardtii
                            [tax_id] => 3055
                            [version] => JGI v5.5
                        )

                    [car] => Array
                        (
                            [species] => car
                            [common_name] => Cicer arietinum L.
                            [tax_id] => 3827
                            [version] => v3.0
                        )

                    [cla] => Array
                        (
                            [species] => cla
                            [common_name] => Citrullus lanatus
                            [tax_id] => 3654
                            [version] => WCG v2.0
                        )

                    [ccl] => Array
                        (
                            [species] => ccl
                            [common_name] => Citrus clementina
                            [tax_id] => 85681
                            [version] => JGI v1.0
                        )

                    [ccan] => Array
                        (
                            [species] => ccan
                            [common_name] => Coffea canephora
                            [tax_id] => 49390
                            [version] => Coffee Genome Hub v1
                        )

                    [col] => Array
                        (
                            [species] => col
                            [common_name] => Corchorus olitorius
                            [tax_id] => 93759
                            [version] => GenBank v1.0
                        )

                    [cav] => Array
                        (
                            [species] => cav
                            [common_name] => Corylus avellana
                            [tax_id] => 13451
                            [version] => v1.0
                        )

                    [cme] => Array
                        (
                            [species] => cme
                            [common_name] => Cucumis melo
                            [tax_id] => 3656
                            [version] => Melonomics v3.6.1
                        )

                    [csa] => Array
                        (
                            [species] => csa
                            [common_name] => Cucumis sativus L.
                            [tax_id] => 3659
                            [version] => v3.0
                        )

                    [dca] => Array
                        (
                            [species] => dca
                            [common_name] => Daucus carota
                            [tax_id] => 4039
                            [version] => JGI v2.0
                        )

                    [din] => Array
                        (
                            [species] => din
                            [common_name] => Davidia involucrata
                            [tax_id] => 16924
                            [version] => v1.0
                        )

                    [dzi] => Array
                        (
                            [species] => dzi
                            [common_name] => Durio zibethinus
                            [tax_id] => 66656
                            [version] => Duzib1.0
                        )

                    [eca] => Array
                        (
                            [species] => eca
                            [common_name] => Erigeron canadensis
                            [tax_id] => 72917
                            [version] => V1.0
                        )

                    [egut] => Array
                        (
                            [species] => egut
                            [common_name] => Erythranthe guttata
                            [tax_id] => 4155
                            [version] => v2.0
                        )

                    [egr] => Array
                        (
                            [species] => egr
                            [common_name] => Eucalyptus grandis
                            [tax_id] => 71139
                            [version] => v2.0
                        )

                    [esa] => Array
                        (
                            [species] => esa
                            [common_name] => Eutrema salsugineum
                            [tax_id] => 72664
                            [version] => v1.0
                        )

                    [fve] => Array
                        (
                            [species] => fve
                            [common_name] => Fragaria vesca
                            [tax_id] => 57918
                            [version] => V4.0.a2
                        )

                    [fan] => Array
                        (
                            [species] => fan
                            [common_name] => Fragaria x ananassa
                            [tax_id] => 3747
                            [version] => V1.0.a1
                        )

                    [gma] => Array
                        (
                            [species] => gma
                            [common_name] => Glycine max
                            [tax_id] => 3847
                            [version] => JGI Wm82.a4.v1
                        )

                    [ghi] => Array
                        (
                            [species] => ghi
                            [common_name] => Gossypium hirsutum
                            [tax_id] => 3635
                            [version] => v2.1
                        )

                    [gra] => Array
                        (
                            [species] => gra
                            [common_name] => Gossypium raimondii
                            [tax_id] => 29730
                            [version] => v2.1
                        )

                    [han] => Array
                        (
                            [species] => han
                            [common_name] => Helianthus annuus
                            [tax_id] => 4232
                            [version] => r1.2
                        )

                    [hma] => Array
                        (
                            [species] => hma
                            [common_name] => Hydrangea macrophylla
                            [tax_id] => 23110
                            [version] => v2.1
                        )

                    [lsa] => Array
                        (
                            [species] => lsa
                            [common_name] => Lactuca sativa
                            [tax_id] => 4236
                            [version] => v8.0
                        )

                    [lonja] => Array
                        (
                            [species] => lonja
                            [common_name] => Lonicera japonica
                            [tax_id] => 105884
                            [version] => v1.0
                        )

                    [lja] => Array
                        (
                            [species] => lja
                            [common_name] => Lotus japonicus
                            [tax_id] => 34305
                            [version] => Lj1.0v1
                        )

                    [lal] => Array
                        (
                            [species] => lal
                            [common_name] => Lupinus albus
                            [tax_id] => 3870
                            [version] => v1.0
                        )

                    [mbi] => Array
                        (
                            [species] => mbi
                            [common_name] => Magnolia biondii
                            [tax_id] => 86725
                            [version] => v1.0
                        )

                    [mdo] => Array
                        (
                            [species] => mdo
                            [common_name] => Malus domestica
                            [tax_id] => 3750
                            [version] => GDDH13 v1.1
                        )

                    [mes] => Array
                        (
                            [species] => mes
                            [common_name] => Manihot esculenta
                            [tax_id] => 3983
                            [version] => v8.1
                        )

                    [mpo] => Array
                        (
                            [species] => mpo
                            [common_name] => Marchantia polymorpha
                            [tax_id] => 3197
                            [version] => JGI v3.1
                        )

                    [mtr] => Array
                        (
                            [species] => mtr
                            [common_name] => Medicago truncatula
                            [tax_id] => 3880
                            [version] => JGI Mt4.0v1
                        )

                    [mco] => Array
                        (
                            [species] => mco
                            [common_name] => Micromonas commoda
                            [tax_id] => 296587
                            [version] => JGI v3.0
                        )

                    [nnu] => Array
                        (
                            [species] => nnu
                            [common_name] => Nelumbo nucifera
                            [tax_id] => 4432
                            [version] => v2.0
                        )

                    [nta] => Array
                        (
                            [species] => nta
                            [common_name] => Nicotiana tabacum
                            [tax_id] => 4097
                            [version] => Edwards2017
                        )

                    [oeu] => Array
                        (
                            [species] => oeu
                            [common_name] => Olea europaea
                            [tax_id] => 4146
                            [version] => v1.0
                        )

                    [osa] => Array
                        (
                            [species] => osa
                            [common_name] => Oryza sativa ssp. japonica
                            [tax_id] => 39947
                            [version] => IRGSP-1.0-2021-05-10
                        )

                    [pso] => Array
                        (
                            [species] => pso
                            [common_name] => Papaver somniferum
                            [tax_id] => 3469
                            [version] => ASM357369v1
                        )

                    [pax] => Array
                        (
                            [species] => pax
                            [common_name] => Petunia axillaris
                            [tax_id] => 33119
                            [version] => Sol Genomics v1.6.2
                        )

                    [pvu] => Array
                        (
                            [species] => pvu
                            [common_name] => Phaseolus vulgaris
                            [tax_id] => 3885
                            [version] => v2.1
                        )

                    [ppa] => Array
                        (
                            [species] => ppa
                            [common_name] => Physcomitrium patens
                            [tax_id] => 3218
                            [version] => JGI v3.3
                        )

                    [psa] => Array
                        (
                            [species] => psa
                            [common_name] => Pisum sativum
                            [tax_id] => 3888
                            [version] => V1.0a
                        )

                    [ptr] => Array
                        (
                            [species] => ptr
                            [common_name] => Populus trichocarpa
                            [tax_id] => 3694
                            [version] => JGI v4.1
                        )

                    [pco] => Array
                        (
                            [species] => pco
                            [common_name] => Prasinoderma coloniale
                            [tax_id] => 156133
                            [version] => v1.0
                        )

                    [ppe] => Array
                        (
                            [species] => ppe
                            [common_name] => Prunus persica
                            [tax_id] => 3760
                            [version] => v2.1
                        )

                    [pgr] => Array
                        (
                            [species] => pgr
                            [common_name] => Punica granatum
                            [tax_id] => 22663
                            [version] => ASM765513v2
                        )

                    [qlo] => Array
                        (
                            [species] => qlo
                            [common_name] => Quercus lobata
                            [tax_id] => 97700
                            [version] => v3.0
                        )

                    [rsi] => Array
                        (
                            [species] => rsi
                            [common_name] => Rhododendron simsii
                            [tax_id] => 118357
                            [version] => v1.0
                        )

                    [rch] => Array
                        (
                            [species] => rch
                            [common_name] => Rosa chinensis
                            [tax_id] => 74649
                            [version] => v2.0
                        )

                    [sbr] => Array
                        (
                            [species] => sbr
                            [common_name] => Salix brachista
                            [tax_id] => 2182728
                            [version] => v1.0
                        )

                    [sbo] => Array
                        (
                            [species] => sbo
                            [common_name] => Salvia bowleyana
                            [tax_id] => 424416
                            [version] => v1.0
                        )

                    [shi] => Array
                        (
                            [species] => shi
                            [common_name] => Sapria himalayana
                            [tax_id] => 289637
                            [version] => v1.0
                        )

                    [spa] => Array
                        (
                            [species] => spa
                            [common_name] => Schrenkiella parvula
                            [tax_id] => 98039
                            [version] => v2.2
                        )

                    [sed] => Array
                        (
                            [species] => sed
                            [common_name] => Sechium edule
                            [tax_id] => 184140
                            [version] => v1.0
                        )

                    [smo] => Array
                        (
                            [species] => smo
                            [common_name] => Selaginella moellendorffii
                            [tax_id] => 88036
                            [version] => v1.0
                        )

                    [sun] => Array
                        (
                            [species] => sun
                            [common_name] => Selenicereus undatus
                            [tax_id] => 176265
                            [version] => v1.0
                        )

                    [sgi] => Array
                        (
                            [species] => sgi
                            [common_name] => Sequoiadendron giganteum
                            [tax_id] => 99814
                            [version] => V2.0
                        )

                    [sci] => Array
                        (
                            [species] => sci
                            [common_name] => Simmondsia chinensis
                            [tax_id] => 3999
                            [version] => sc1
                        )

                    [sly] => Array
                        (
                            [species] => sly
                            [common_name] => Solanum lycopersicum
                            [tax_id] => 4081
                            [version] => ITAG4.0
                        )

                    [spe] => Array
                        (
                            [species] => spe
                            [common_name] => Solanum pennellii
                            [tax_id] => 28526
                            [version] => V2.0
                        )

                    [stu] => Array
                        (
                            [species] => stu
                            [common_name] => Solanum tuberosum
                            [tax_id] => 4113
                            [version] => JGI v4.03
                        )

                    [sas] => Array
                        (
                            [species] => sas
                            [common_name] => Striga asiatica
                            [tax_id] => 4170
                            [version] => v2.02
                        )

                    [tha] => Array
                        (
                            [species] => tha
                            [common_name] => Tarenaya hassleriana
                            [tax_id] => 28532
                            [version] => RefSeq v1
                        )

                    [tca] => Array
                        (
                            [species] => tca
                            [common_name] => Theobroma cacao
                            [tax_id] => 3641
                            [version] => V2.1
                        )

                    [tpr] => Array
                        (
                            [species] => tpr
                            [common_name] => Trifolium pratense
                            [tax_id] => 57577
                            [version] => V2.0
                        )

                    [twi] => Array
                        (
                            [species] => twi
                            [common_name] => Tripterygium wilfordii
                            [tax_id] => 458696
                            [version] => ASM1340144v1
                        )

                    [tar] => Array
                        (
                            [species] => tar
                            [common_name] => Trochodendron aralioides
                            [tax_id] => 4407
                            [version] => v1.0
                        )

                    [ugi] => Array
                        (
                            [species] => ugi
                            [common_name] => Utricularia gibba
                            [tax_id] => 13748
                            [version] => v1.1F
                        )

                    [vma] => Array
                        (
                            [species] => vma
                            [common_name] => Vaccinium macrocarpon
                            [tax_id] => 13750
                            [version] => V1.0
                        )

                    [vpl] => Array
                        (
                            [species] => vpl
                            [common_name] => Vanilla planifolia
                            [tax_id] => 51239
                            [version] => Elo Vpla-A Principal v1.0
                        )

                    [vmu] => Array
                        (
                            [species] => vmu
                            [common_name] => Vigna mungo
                            [tax_id] => 3915
                            [version] => ASM1342719v1
                        )

                    [vvi] => Array
                        (
                            [species] => vvi
                            [common_name] => Vitis vinifera
                            [tax_id] => 29760
                            [version] => Genoscope.12x
                        )

                    [zma] => Array
                        (
                            [species] => zma
                            [common_name] => Zea mays
                            [tax_id] => 4577
                            [version] => NAM v5.0
                        )

                )

            [allow_async_use] => 1
            [sidebar_information] => Array
                (
                    [type] => gene_id
                    [id] => Cre12.g515850
                )

            [data_identifier] => Cre12.g515850
            [data_type] => gene_id
        )

    [view] => custom_tree_creation
    [layout] => toolbox_layout
    [autoRender] => 1
    [autoLayout] => 1
    [Components] => ComponentCollection Object
        (
            [_Controller:protected] => AnalysisController Object
 *RECURSION*
            [_enabled:protected] => Array
                (
                    [Session] => Array
                        (
                            [0] => 10
                            [1] => 1
                        )

                    [DataUtils] => Array
                        (
                            [0] => 10
                            [1] => 2
                        )

                    [FunctionalAnnotationUtils] => Array
                        (
                            [0] => 10
                            [1] => 3
                        )

                    [GeneFamilies] => Array
                        (
                            [0] => 10
                            [1] => 4
                        )

                    [Organism] => Array
                        (
                            [0] => 10
                            [1] => 5
                        )

                    [Blast] => Array
                        (
                            [0] => 10
                            [1] => 6
                        )

                    [WorkbenchUtils] => Array
                        (
                            [0] => 10
                            [1] => 7
                        )

                    [PhylogeneticModuleUtils] => Array
                        (
                            [0] => 10
                            [1] => 8
                        )

                    [ExternalPrograms] => Array
                        (
                            [0] => 10
                            [1] => 9
                        )

                    [FastaUtils] => Array
                        (
                            [0] => 10
                            [1] => 10
                        )

                    [MsaUtils] => Array
                        (
                            [0] => 10
                            [1] => 11
                        )

                    [PhylogeneticUtils] => Array
                        (
                            [0] => 10
                            [1] => 12
                        )

                    [Sequence] => Array
                        (
                            [0] => 10
                            [1] => 13
                        )

                    [RequestHandler] => Array
                        (
                            [0] => 10
                            [1] => 14
                        )

                )

            [_loaded:protected] => Array
                (
                    [Session] => SessionComponent Object
                        (
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [DataUtils] => DataUtilsComponent Object
                        (
                            [name] => DataUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FunctionalUtils
                                    [2] => GeneFamilies
                                    [3] => GenomeBrowser
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [class] => GeneFamilies
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GenomeBrowser] => Array
                                        (
                                            [class] => GenomeBrowser
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                        )

                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                        (
                            [name] => FunctionalAnnotationUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => FunctionalUtils
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [GeneFamilies] => GeneFamiliesComponent Object
                        (
                            [name] => GeneFamilies
                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [Organism] => OrganismComponent Object
                        (
                            [name] => Organism
                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => GenomeBrowser
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [GenomeBrowser] => Array
                                        (
                                            [class] => GenomeBrowser
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [Blast] => BlastComponent Object
                        (
                            [name] => Blast
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                        (
                            [name] => WorkbenchUtils
                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FormUtils
                                    [2] => FunctionalUtils
                                    [3] => GeneFamilies
                                    [4] => WorkbenchSharedAccessRights
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FormUtils] => Array
                                        (
                                            [class] => FormUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FunctionalUtils] => Array
                                        (
                                            [class] => FunctionalUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [class] => GeneFamilies
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [WorkbenchSharedAccessRights] => Array
                                        (
                                            [class] => WorkbenchSharedAccessRights
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                        (
                            [name] => PhylogeneticModuleUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                    [1] => FastaUtils
                                    [2] => MsaUtils
                                    [3] => PhylogeneticUtils
                                    [4] => Sequence
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [FastaUtils] => Array
                                        (
                                            [class] => FastaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [MsaUtils] => Array
                                        (
                                            [class] => MsaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [PhylogeneticUtils] => Array
                                        (
                                            [class] => PhylogeneticUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [Sequence] => Array
                                        (
                                            [class] => Sequence
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [ExternalPrograms] => ExternalProgramsComponent Object
                        (
                            [name] => ExternalPrograms
                            [components] => Array
                                (
                                    [0] => FastaUtils
                                )

                            [program_paths:ExternalProgramsComponent:private] => Array
                                (
                                    [java] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => java/x86_64/21.0.2
                                                        )

                                                    [command] => java -Djava.awt.headless=true
                                                )

                                            [local_settings] => java -Djava.awt.headless=true
                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                        )

                                    [perl] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => perl
                                                        )

                                                    [command] => perl -w
                                                )

                                            [local_settings] => /usr/bin/perl
                                        )

                                    [bash] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => 
                                        )

                                    [bedops] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => bedops/x86_64/2.4.37
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => 
                                        )

                                    [blastdbcmd] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => blast
                                                        )

                                                    [command] => blastdbcmd
                                                )

                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                        )

                                    [blast] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => blast
                                                        )

                                                    [command] => 
                                                )

                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                        )

                                    [muscle] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => muscle/x86_64/3.8.31
                                                        )

                                                )

                                        )

                                    [mafft] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => mafft/x86_64/7.187
                                                        )

                                                )

                                        )

                                    [phyml] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => phyml/x86_64/20150219
                                                        )

                                                )

                                        )

                                    [fasttree] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => fasttree/x86_64/2.1.7
                                                        )

                                                )

                                        )

                                    [raxml] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => raxml/x86_64/8.2.8
                                                        )

                                                )

                                        )

                                    [iqtree] => Array
                                        (
                                            [cluster_settings] => Array
                                                (
                                                    [modules] => Array
                                                        (
                                                            [0] => iqtree/x86_64/1.5.5
                                                        )

                                                )

                                        )

                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [FastaUtils] => Array
                                        (
                                            [class] => FastaUtils
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [FastaUtils] => FastaUtilsComponent Object
                        (
                            [name] => FastaUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [MsaUtils] => MsaUtilsComponent Object
                        (
                            [name] => MsaUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                        )

                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                        (
                            [name] => PhylogeneticUtils
                            [controller] => AnalysisController Object
 *RECURSION*
                            [components] => Array
                                (
                                    [0] => ExternalPrograms
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                        )

                    [Sequence] => SequenceComponent Object
                        (
                            [name] => Sequence
                            [components] => Array
                                (
                                    [0] => Blast
                                    [1] => Coordinates
                                    [2] => ExternalPrograms
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                    [Blast] => Array
                                        (
                                            [class] => Blast
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [Coordinates] => Array
                                        (
                                            [class] => Coordinates
                                            [settings] => Array
                                                (
                                                )

                                        )

                                    [ExternalPrograms] => Array
                                        (
                                            [class] => ExternalPrograms
                                            [settings] => Array
                                                (
                                                )

                                        )

                                )

                            [controller] => AnalysisController Object
 *RECURSION*
                        )

                    [RequestHandler] => RequestHandlerComponent Object
                        (
                            [ajaxLayout] => ajax
                            [enabled] => 1
                            [request] => CakeRequest Object
                                (
                                    [params] => Array
                                        (
                                            [plugin] => 
                                            [controller] => analysis
                                            [action] => custom_tree_creation
                                            [named] => Array
                                                (
                                                )

                                            [pass] => Array
                                                (
                                                    [0] => gene_id
                                                    [1] => Cre12.g515850
                                                )

                                            [isAjax] => 
                                        )

                                    [data] => Array
                                        (
                                        )

                                    [query] => Array
                                        (
                                        )

                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                    [base] => /plaza.dev/_dev_instances/feedback
                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                    [_detectors:protected] => Array
                                        (
                                            [get] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => GET
                                                )

                                            [patch] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PATCH
                                                )

                                            [post] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => POST
                                                )

                                            [put] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PUT
                                                )

                                            [delete] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => DELETE
                                                )

                                            [head] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => HEAD
                                                )

                                            [options] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => OPTIONS
                                                )

                                            [ssl] => Array
                                                (
                                                    [env] => HTTPS
                                                    [value] => 1
                                                )

                                            [ajax] => Array
                                                (
                                                    [env] => HTTP_X_REQUESTED_WITH
                                                    [value] => XMLHttpRequest
                                                )

                                            [flash] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                )

                                            [mobile] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [options] => Array
                                                        (
                                                            [0] => Android
                                                            [1] => AvantGo
                                                            [2] => BB10
                                                            [3] => BlackBerry
                                                            [4] => DoCoMo
                                                            [5] => Fennec
                                                            [6] => iPod
                                                            [7] => iPhone
                                                            [8] => iPad
                                                            [9] => J2ME
                                                            [10] => MIDP
                                                            [11] => NetFront
                                                            [12] => Nokia
                                                            [13] => Opera Mini
                                                            [14] => Opera Mobi
                                                            [15] => PalmOS
                                                            [16] => PalmSource
                                                            [17] => portalmmm
                                                            [18] => Plucker
                                                            [19] => ReqwirelessWeb
                                                            [20] => SonyEricsson
                                                            [21] => Symbian
                                                            [22] => UP\.Browser
                                                            [23] => webOS
                                                            [24] => Windows CE
                                                            [25] => Windows Phone OS
                                                            [26] => Xiino
                                                        )

                                                )

                                            [requested] => Array
                                                (
                                                    [param] => requested
                                                    [value] => 1
                                                )

                                            [json] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/json
                                                        )

                                                    [param] => ext
                                                    [value] => json
                                                )

                                            [xml] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [param] => ext
                                                    [value] => xml
                                                )

                                        )

                                    [_input:protected] => 
                                )

                            [response] => CakeResponse Object
                                (
                                    [_statusCodes:protected] => Array
                                        (
                                            [100] => Continue
                                            [101] => Switching Protocols
                                            [200] => OK
                                            [201] => Created
                                            [202] => Accepted
                                            [203] => Non-Authoritative Information
                                            [204] => No Content
                                            [205] => Reset Content
                                            [206] => Partial Content
                                            [300] => Multiple Choices
                                            [301] => Moved Permanently
                                            [302] => Found
                                            [303] => See Other
                                            [304] => Not Modified
                                            [305] => Use Proxy
                                            [307] => Temporary Redirect
                                            [400] => Bad Request
                                            [401] => Unauthorized
                                            [402] => Payment Required
                                            [403] => Forbidden
                                            [404] => Not Found
                                            [405] => Method Not Allowed
                                            [406] => Not Acceptable
                                            [407] => Proxy Authentication Required
                                            [408] => Request Time-out
                                            [409] => Conflict
                                            [410] => Gone
                                            [411] => Length Required
                                            [412] => Precondition Failed
                                            [413] => Request Entity Too Large
                                            [414] => Request-URI Too Large
                                            [415] => Unsupported Media Type
                                            [416] => Requested range not satisfiable
                                            [417] => Expectation Failed
                                            [429] => Too Many Requests
                                            [500] => Internal Server Error
                                            [501] => Not Implemented
                                            [502] => Bad Gateway
                                            [503] => Service Unavailable
                                            [504] => Gateway Time-out
                                            [505] => Unsupported Version
                                        )

                                    [_mimeTypes:protected] => Array
                                        (
                                            [html] => Array
                                                (
                                                    [0] => text/html
                                                    [1] => */*
                                                )

                                            [json] => application/json
                                            [xml] => Array
                                                (
                                                    [0] => application/xml
                                                    [1] => text/xml
                                                )

                                            [rss] => application/rss+xml
                                            [ai] => application/postscript
                                            [bcpio] => application/x-bcpio
                                            [bin] => application/octet-stream
                                            [ccad] => application/clariscad
                                            [cdf] => application/x-netcdf
                                            [class] => application/octet-stream
                                            [cpio] => application/x-cpio
                                            [cpt] => application/mac-compactpro
                                            [csh] => application/x-csh
                                            [csv] => Array
                                                (
                                                    [0] => text/csv
                                                    [1] => application/vnd.ms-excel
                                                )

                                            [dcr] => application/x-director
                                            [dir] => application/x-director
                                            [dms] => application/octet-stream
                                            [doc] => application/msword
                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                            [drw] => application/drafting
                                            [dvi] => application/x-dvi
                                            [dwg] => application/acad
                                            [dxf] => application/dxf
                                            [dxr] => application/x-director
                                            [eot] => application/vnd.ms-fontobject
                                            [eps] => application/postscript
                                            [exe] => application/octet-stream
                                            [ez] => application/andrew-inset
                                            [flv] => video/x-flv
                                            [gtar] => application/x-gtar
                                            [gz] => application/x-gzip
                                            [bz2] => application/x-bzip
                                            [7z] => application/x-7z-compressed
                                            [hdf] => application/x-hdf
                                            [hqx] => application/mac-binhex40
                                            [ico] => image/x-icon
                                            [ips] => application/x-ipscript
                                            [ipx] => application/x-ipix
                                            [js] => application/javascript
                                            [jsonapi] => application/vnd.api+json
                                            [latex] => application/x-latex
                                            [lha] => application/octet-stream
                                            [lsp] => application/x-lisp
                                            [lzh] => application/octet-stream
                                            [man] => application/x-troff-man
                                            [me] => application/x-troff-me
                                            [mif] => application/vnd.mif
                                            [ms] => application/x-troff-ms
                                            [nc] => application/x-netcdf
                                            [oda] => application/oda
                                            [otf] => font/otf
                                            [pdf] => application/pdf
                                            [pgn] => application/x-chess-pgn
                                            [pot] => application/vnd.ms-powerpoint
                                            [pps] => application/vnd.ms-powerpoint
                                            [ppt] => application/vnd.ms-powerpoint
                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                            [ppz] => application/vnd.ms-powerpoint
                                            [pre] => application/x-freelance
                                            [prt] => application/pro_eng
                                            [ps] => application/postscript
                                            [roff] => application/x-troff
                                            [scm] => application/x-lotusscreencam
                                            [set] => application/set
                                            [sh] => application/x-sh
                                            [shar] => application/x-shar
                                            [sit] => application/x-stuffit
                                            [skd] => application/x-koan
                                            [skm] => application/x-koan
                                            [skp] => application/x-koan
                                            [skt] => application/x-koan
                                            [smi] => application/smil
                                            [smil] => application/smil
                                            [sol] => application/solids
                                            [spl] => application/x-futuresplash
                                            [src] => application/x-wais-source
                                            [step] => application/STEP
                                            [stl] => application/SLA
                                            [stp] => application/STEP
                                            [sv4cpio] => application/x-sv4cpio
                                            [sv4crc] => application/x-sv4crc
                                            [svg] => image/svg+xml
                                            [svgz] => image/svg+xml
                                            [swf] => application/x-shockwave-flash
                                            [t] => application/x-troff
                                            [tar] => application/x-tar
                                            [tcl] => application/x-tcl
                                            [tex] => application/x-tex
                                            [texi] => application/x-texinfo
                                            [texinfo] => application/x-texinfo
                                            [tr] => application/x-troff
                                            [tsp] => application/dsptype
                                            [ttc] => font/ttf
                                            [ttf] => font/ttf
                                            [unv] => application/i-deas
                                            [ustar] => application/x-ustar
                                            [vcd] => application/x-cdlink
                                            [vda] => application/vda
                                            [xlc] => application/vnd.ms-excel
                                            [xll] => application/vnd.ms-excel
                                            [xlm] => application/vnd.ms-excel
                                            [xls] => application/vnd.ms-excel
                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                            [xlw] => application/vnd.ms-excel
                                            [zip] => application/zip
                                            [aif] => audio/x-aiff
                                            [aifc] => audio/x-aiff
                                            [aiff] => audio/x-aiff
                                            [au] => audio/basic
                                            [kar] => audio/midi
                                            [mid] => audio/midi
                                            [midi] => audio/midi
                                            [mp2] => audio/mpeg
                                            [mp3] => audio/mpeg
                                            [mpga] => audio/mpeg
                                            [ogg] => audio/ogg
                                            [oga] => audio/ogg
                                            [spx] => audio/ogg
                                            [ra] => audio/x-realaudio
                                            [ram] => audio/x-pn-realaudio
                                            [rm] => audio/x-pn-realaudio
                                            [rpm] => audio/x-pn-realaudio-plugin
                                            [snd] => audio/basic
                                            [tsi] => audio/TSP-audio
                                            [wav] => audio/x-wav
                                            [aac] => audio/aac
                                            [asc] => text/plain
                                            [c] => text/plain
                                            [cc] => text/plain
                                            [css] => text/css
                                            [etx] => text/x-setext
                                            [f] => text/plain
                                            [f90] => text/plain
                                            [h] => text/plain
                                            [hh] => text/plain
                                            [htm] => Array
                                                (
                                                    [0] => text/html
                                                    [1] => */*
                                                )

                                            [ics] => text/calendar
                                            [m] => text/plain
                                            [rtf] => text/rtf
                                            [rtx] => text/richtext
                                            [sgm] => text/sgml
                                            [sgml] => text/sgml
                                            [tsv] => text/tab-separated-values
                                            [tpl] => text/template
                                            [txt] => text/plain
                                            [text] => text/plain
                                            [avi] => video/x-msvideo
                                            [fli] => video/x-fli
                                            [mov] => video/quicktime
                                            [movie] => video/x-sgi-movie
                                            [mpe] => video/mpeg
                                            [mpeg] => video/mpeg
                                            [mpg] => video/mpeg
                                            [qt] => video/quicktime
                                            [viv] => video/vnd.vivo
                                            [vivo] => video/vnd.vivo
                                            [ogv] => video/ogg
                                            [webm] => video/webm
                                            [mp4] => video/mp4
                                            [m4v] => video/mp4
                                            [f4v] => video/mp4
                                            [f4p] => video/mp4
                                            [m4a] => audio/mp4
                                            [f4a] => audio/mp4
                                            [f4b] => audio/mp4
                                            [gif] => image/gif
                                            [ief] => image/ief
                                            [jpg] => image/jpeg
                                            [jpeg] => image/jpeg
                                            [jpe] => image/jpeg
                                            [pbm] => image/x-portable-bitmap
                                            [pgm] => image/x-portable-graymap
                                            [png] => image/png
                                            [pnm] => image/x-portable-anymap
                                            [ppm] => image/x-portable-pixmap
                                            [ras] => image/cmu-raster
                                            [rgb] => image/x-rgb
                                            [tif] => image/tiff
                                            [tiff] => image/tiff
                                            [xbm] => image/x-xbitmap
                                            [xpm] => image/x-xpixmap
                                            [xwd] => image/x-xwindowdump
                                            [psd] => Array
                                                (
                                                    [0] => application/photoshop
                                                    [1] => application/psd
                                                    [2] => image/psd
                                                    [3] => image/x-photoshop
                                                    [4] => image/photoshop
                                                    [5] => zz-application/zz-winassoc-psd
                                                )

                                            [ice] => x-conference/x-cooltalk
                                            [iges] => model/iges
                                            [igs] => model/iges
                                            [mesh] => model/mesh
                                            [msh] => model/mesh
                                            [silo] => model/mesh
                                            [vrml] => model/vrml
                                            [wrl] => model/vrml
                                            [mime] => www/mime
                                            [pdb] => chemical/x-pdb
                                            [xyz] => chemical/x-pdb
                                            [javascript] => application/javascript
                                            [form] => application/x-www-form-urlencoded
                                            [file] => multipart/form-data
                                            [xhtml] => Array
                                                (
                                                    [0] => application/xhtml+xml
                                                    [1] => application/xhtml
                                                    [2] => text/xhtml
                                                )

                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                            [atom] => application/atom+xml
                                            [amf] => application/x-amf
                                            [wap] => Array
                                                (
                                                    [0] => text/vnd.wap.wml
                                                    [1] => text/vnd.wap.wmlscript
                                                    [2] => image/vnd.wap.wbmp
                                                )

                                            [wml] => text/vnd.wap.wml
                                            [wmlscript] => text/vnd.wap.wmlscript
                                            [wbmp] => image/vnd.wap.wbmp
                                            [woff] => application/x-font-woff
                                            [webp] => image/webp
                                            [appcache] => text/cache-manifest
                                            [manifest] => text/cache-manifest
                                            [htc] => text/x-component
                                            [rdf] => application/xml
                                            [crx] => application/x-chrome-extension
                                            [oex] => application/x-opera-extension
                                            [xpi] => application/x-xpinstall
                                            [safariextz] => application/octet-stream
                                            [webapp] => application/x-web-app-manifest+json
                                            [vcf] => text/x-vcard
                                            [vtt] => text/vtt
                                            [mkv] => video/x-matroska
                                            [pkpass] => application/vnd.apple.pkpass
                                            [ajax] => text/html
                                        )

                                    [_protocol:protected] => HTTP/1.1
                                    [_status:protected] => 200
                                    [_contentType:protected] => text/html
                                    [_headers:protected] => Array
                                        (
                                        )

                                    [_body:protected] => 
                                    [_file:protected] => 
                                    [_fileRange:protected] => 
                                    [_charset:protected] => UTF-8
                                    [_cacheDirectives:protected] => Array
                                        (
                                        )

                                    [_cookies:protected] => Array
                                        (
                                        )

                                )

                            [ext] => 
                            [_renderType:protected] => 
                            [_inputTypeMap:protected] => Array
                                (
                                    [json] => Array
                                        (
                                            [0] => json_decode
                                            [1] => 1
                                        )

                                    [xml] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                    [1] => convertXml
                                                )

                                        )

                                )

                            [_viewClassMap:protected] => Array
                                (
                                    [json] => Json
                                    [xml] => Xml
                                )

                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                            [settings] => Array
                                (
                                    [checkHttpCache] => 1
                                )

                            [components] => Array
                                (
                                )

                            [_componentMap:protected] => Array
                                (
                                )

                            [params] => CakeRequest Object
                                (
                                    [params] => Array
                                        (
                                            [plugin] => 
                                            [controller] => analysis
                                            [action] => custom_tree_creation
                                            [named] => Array
                                                (
                                                )

                                            [pass] => Array
                                                (
                                                    [0] => gene_id
                                                    [1] => Cre12.g515850
                                                )

                                            [isAjax] => 
                                        )

                                    [data] => Array
                                        (
                                        )

                                    [query] => Array
                                        (
                                        )

                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                    [base] => /plaza.dev/_dev_instances/feedback
                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                    [_detectors:protected] => Array
                                        (
                                            [get] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => GET
                                                )

                                            [patch] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PATCH
                                                )

                                            [post] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => POST
                                                )

                                            [put] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => PUT
                                                )

                                            [delete] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => DELETE
                                                )

                                            [head] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => HEAD
                                                )

                                            [options] => Array
                                                (
                                                    [env] => REQUEST_METHOD
                                                    [value] => OPTIONS
                                                )

                                            [ssl] => Array
                                                (
                                                    [env] => HTTPS
                                                    [value] => 1
                                                )

                                            [ajax] => Array
                                                (
                                                    [env] => HTTP_X_REQUESTED_WITH
                                                    [value] => XMLHttpRequest
                                                )

                                            [flash] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                )

                                            [mobile] => Array
                                                (
                                                    [env] => HTTP_USER_AGENT
                                                    [options] => Array
                                                        (
                                                            [0] => Android
                                                            [1] => AvantGo
                                                            [2] => BB10
                                                            [3] => BlackBerry
                                                            [4] => DoCoMo
                                                            [5] => Fennec
                                                            [6] => iPod
                                                            [7] => iPhone
                                                            [8] => iPad
                                                            [9] => J2ME
                                                            [10] => MIDP
                                                            [11] => NetFront
                                                            [12] => Nokia
                                                            [13] => Opera Mini
                                                            [14] => Opera Mobi
                                                            [15] => PalmOS
                                                            [16] => PalmSource
                                                            [17] => portalmmm
                                                            [18] => Plucker
                                                            [19] => ReqwirelessWeb
                                                            [20] => SonyEricsson
                                                            [21] => Symbian
                                                            [22] => UP\.Browser
                                                            [23] => webOS
                                                            [24] => Windows CE
                                                            [25] => Windows Phone OS
                                                            [26] => Xiino
                                                        )

                                                )

                                            [requested] => Array
                                                (
                                                    [param] => requested
                                                    [value] => 1
                                                )

                                            [json] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/json
                                                        )

                                                    [param] => ext
                                                    [value] => json
                                                )

                                            [xml] => Array
                                                (
                                                    [accept] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [param] => ext
                                                    [value] => xml
                                                )

                                        )

                                    [_input:protected] => 
                                )

                        )

                )

            [defaultPriority] => 10
        )

    [viewClass] => View
    [View] => 
    [ext] => .ctp
    [plugin] => 
    [cacheAction] => 
    [passedArgs] => Array
        (
            [0] => gene_id
            [1] => Cre12.g515850
        )

    [scaffold] => 
    [methods] => Array
        (
            [0] => view_result
            [1] => custom_tree_creation
        )

    [modelClass] => Annotation
    [modelKey] => analysi
    [validationErrors] => 
    [_mergeParent:protected] => AppController
    [_eventManager:protected] => CakeEventManager Object
        (
            [_listeners:protected] => Array
                (
                    [Controller.initialize] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeFilter
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.startup] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.beforeRender] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeRender
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                    [Controller.beforeRedirect] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => beforeRedirect
                                                )

                                            [passParams] => 1
                                        )

                                )

                        )

                    [Controller.shutdown] => Array
                        (
                            [10] => Array
                                (
                                    [0] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => ComponentCollection Object
                                                        (
                                                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                                                            [_enabled:protected] => Array
                                                                (
                                                                    [Session] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 1
                                                                        )

                                                                    [DataUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 2
                                                                        )

                                                                    [FunctionalAnnotationUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 3
                                                                        )

                                                                    [GeneFamilies] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 4
                                                                        )

                                                                    [Organism] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 5
                                                                        )

                                                                    [Blast] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 6
                                                                        )

                                                                    [WorkbenchUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 7
                                                                        )

                                                                    [PhylogeneticModuleUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 8
                                                                        )

                                                                    [ExternalPrograms] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 9
                                                                        )

                                                                    [FastaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 10
                                                                        )

                                                                    [MsaUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 11
                                                                        )

                                                                    [PhylogeneticUtils] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 12
                                                                        )

                                                                    [Sequence] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 13
                                                                        )

                                                                    [RequestHandler] => Array
                                                                        (
                                                                            [0] => 10
                                                                            [1] => 14
                                                                        )

                                                                )

                                                            [_loaded:protected] => Array
                                                                (
                                                                    [Session] => SessionComponent Object
                                                                        (
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [DataUtils] => DataUtilsComponent Object
                                                                        (
                                                                            [name] => DataUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FunctionalUtils
                                                                                    [2] => GeneFamilies
                                                                                    [3] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [GeneFamilies] => GeneFamiliesComponent Object
                                                                                (
                                                                                    [name] => GeneFamilies
                                                                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                                    [settings] => Array
                                                                                        (
                                                                                        )

                                                                                    [components] => Array
                                                                                        (
                                                                                        )

                                                                                    [_componentMap:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                        )

                                                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                                                        (
                                                                            [name] => FunctionalAnnotationUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FunctionalUtils
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [GeneFamilies] => GeneFamiliesComponent Object
                                                                        (
                                                                            [name] => GeneFamilies
                                                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [Organism] => OrganismComponent Object
                                                                        (
                                                                            [name] => Organism
                                                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => GenomeBrowser
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [GenomeBrowser] => Array
                                                                                        (
                                                                                            [class] => GenomeBrowser
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Blast] => BlastComponent Object
                                                                        (
                                                                            [name] => Blast
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                                                        (
                                                                            [name] => WorkbenchUtils
                                                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FormUtils
                                                                                    [2] => FunctionalUtils
                                                                                    [3] => GeneFamilies
                                                                                    [4] => WorkbenchSharedAccessRights
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FormUtils] => Array
                                                                                        (
                                                                                            [class] => FormUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FunctionalUtils] => Array
                                                                                        (
                                                                                            [class] => FunctionalUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [GeneFamilies] => Array
                                                                                        (
                                                                                            [class] => GeneFamilies
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [WorkbenchSharedAccessRights] => Array
                                                                                        (
                                                                                            [class] => WorkbenchSharedAccessRights
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticModuleUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                    [1] => FastaUtils
                                                                                    [2] => MsaUtils
                                                                                    [3] => PhylogeneticUtils
                                                                                    [4] => Sequence
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [MsaUtils] => Array
                                                                                        (
                                                                                            [class] => MsaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [PhylogeneticUtils] => Array
                                                                                        (
                                                                                            [class] => PhylogeneticUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Sequence] => Array
                                                                                        (
                                                                                            [class] => Sequence
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                                                        (
                                                                            [name] => ExternalPrograms
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => FastaUtils
                                                                                )

                                                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                                                (
                                                                                    [java] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => java/x86_64/21.0.2
                                                                                                        )

                                                                                                    [command] => java -Djava.awt.headless=true
                                                                                                )

                                                                                            [local_settings] => java -Djava.awt.headless=true
                                                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                                                        )

                                                                                    [perl] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => perl
                                                                                                        )

                                                                                                    [command] => perl -w
                                                                                                )

                                                                                            [local_settings] => /usr/bin/perl
                                                                                        )

                                                                                    [bash] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [bedops] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => bedops/x86_64/2.4.37
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => 
                                                                                        )

                                                                                    [blastdbcmd] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => blastdbcmd
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                                                        )

                                                                                    [blast] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => blast
                                                                                                        )

                                                                                                    [command] => 
                                                                                                )

                                                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                                                        )

                                                                                    [muscle] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => muscle/x86_64/3.8.31
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [mafft] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => mafft/x86_64/7.187
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [phyml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => phyml/x86_64/20150219
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [fasttree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => fasttree/x86_64/2.1.7
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [raxml] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => raxml/x86_64/8.2.8
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                    [iqtree] => Array
                                                                                        (
                                                                                            [cluster_settings] => Array
                                                                                                (
                                                                                                    [modules] => Array
                                                                                                        (
                                                                                                            [0] => iqtree/x86_64/1.5.5
                                                                                                        )

                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [FastaUtils] => Array
                                                                                        (
                                                                                            [class] => FastaUtils
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [FastaUtils] => FastaUtilsComponent Object
                                                                        (
                                                                            [name] => FastaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [MsaUtils] => MsaUtilsComponent Object
                                                                        (
                                                                            [name] => MsaUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                        )

                                                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                                                        (
                                                                            [name] => PhylogeneticUtils
                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                        )

                                                                    [Sequence] => SequenceComponent Object
                                                                        (
                                                                            [name] => Sequence
                                                                            [components] => Array
                                                                                (
                                                                                    [0] => Blast
                                                                                    [1] => Coordinates
                                                                                    [2] => ExternalPrograms
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                    [Blast] => Array
                                                                                        (
                                                                                            [class] => Blast
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [Coordinates] => Array
                                                                                        (
                                                                                            [class] => Coordinates
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                    [ExternalPrograms] => Array
                                                                                        (
                                                                                            [class] => ExternalPrograms
                                                                                            [settings] => Array
                                                                                                (
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [controller] => AnalysisController Object
 *RECURSION*
                                                                        )

                                                                    [RequestHandler] => RequestHandlerComponent Object
                                                                        (
                                                                            [ajaxLayout] => ajax
                                                                            [enabled] => 1
                                                                            [request] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                            [response] => CakeResponse Object
                                                                                (
                                                                                    [_statusCodes:protected] => Array
                                                                                        (
                                                                                            [100] => Continue
                                                                                            [101] => Switching Protocols
                                                                                            [200] => OK
                                                                                            [201] => Created
                                                                                            [202] => Accepted
                                                                                            [203] => Non-Authoritative Information
                                                                                            [204] => No Content
                                                                                            [205] => Reset Content
                                                                                            [206] => Partial Content
                                                                                            [300] => Multiple Choices
                                                                                            [301] => Moved Permanently
                                                                                            [302] => Found
                                                                                            [303] => See Other
                                                                                            [304] => Not Modified
                                                                                            [305] => Use Proxy
                                                                                            [307] => Temporary Redirect
                                                                                            [400] => Bad Request
                                                                                            [401] => Unauthorized
                                                                                            [402] => Payment Required
                                                                                            [403] => Forbidden
                                                                                            [404] => Not Found
                                                                                            [405] => Method Not Allowed
                                                                                            [406] => Not Acceptable
                                                                                            [407] => Proxy Authentication Required
                                                                                            [408] => Request Time-out
                                                                                            [409] => Conflict
                                                                                            [410] => Gone
                                                                                            [411] => Length Required
                                                                                            [412] => Precondition Failed
                                                                                            [413] => Request Entity Too Large
                                                                                            [414] => Request-URI Too Large
                                                                                            [415] => Unsupported Media Type
                                                                                            [416] => Requested range not satisfiable
                                                                                            [417] => Expectation Failed
                                                                                            [429] => Too Many Requests
                                                                                            [500] => Internal Server Error
                                                                                            [501] => Not Implemented
                                                                                            [502] => Bad Gateway
                                                                                            [503] => Service Unavailable
                                                                                            [504] => Gateway Time-out
                                                                                            [505] => Unsupported Version
                                                                                        )

                                                                                    [_mimeTypes:protected] => Array
                                                                                        (
                                                                                            [html] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [json] => application/json
                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [0] => application/xml
                                                                                                    [1] => text/xml
                                                                                                )

                                                                                            [rss] => application/rss+xml
                                                                                            [ai] => application/postscript
                                                                                            [bcpio] => application/x-bcpio
                                                                                            [bin] => application/octet-stream
                                                                                            [ccad] => application/clariscad
                                                                                            [cdf] => application/x-netcdf
                                                                                            [class] => application/octet-stream
                                                                                            [cpio] => application/x-cpio
                                                                                            [cpt] => application/mac-compactpro
                                                                                            [csh] => application/x-csh
                                                                                            [csv] => Array
                                                                                                (
                                                                                                    [0] => text/csv
                                                                                                    [1] => application/vnd.ms-excel
                                                                                                )

                                                                                            [dcr] => application/x-director
                                                                                            [dir] => application/x-director
                                                                                            [dms] => application/octet-stream
                                                                                            [doc] => application/msword
                                                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                                                            [drw] => application/drafting
                                                                                            [dvi] => application/x-dvi
                                                                                            [dwg] => application/acad
                                                                                            [dxf] => application/dxf
                                                                                            [dxr] => application/x-director
                                                                                            [eot] => application/vnd.ms-fontobject
                                                                                            [eps] => application/postscript
                                                                                            [exe] => application/octet-stream
                                                                                            [ez] => application/andrew-inset
                                                                                            [flv] => video/x-flv
                                                                                            [gtar] => application/x-gtar
                                                                                            [gz] => application/x-gzip
                                                                                            [bz2] => application/x-bzip
                                                                                            [7z] => application/x-7z-compressed
                                                                                            [hdf] => application/x-hdf
                                                                                            [hqx] => application/mac-binhex40
                                                                                            [ico] => image/x-icon
                                                                                            [ips] => application/x-ipscript
                                                                                            [ipx] => application/x-ipix
                                                                                            [js] => application/javascript
                                                                                            [jsonapi] => application/vnd.api+json
                                                                                            [latex] => application/x-latex
                                                                                            [lha] => application/octet-stream
                                                                                            [lsp] => application/x-lisp
                                                                                            [lzh] => application/octet-stream
                                                                                            [man] => application/x-troff-man
                                                                                            [me] => application/x-troff-me
                                                                                            [mif] => application/vnd.mif
                                                                                            [ms] => application/x-troff-ms
                                                                                            [nc] => application/x-netcdf
                                                                                            [oda] => application/oda
                                                                                            [otf] => font/otf
                                                                                            [pdf] => application/pdf
                                                                                            [pgn] => application/x-chess-pgn
                                                                                            [pot] => application/vnd.ms-powerpoint
                                                                                            [pps] => application/vnd.ms-powerpoint
                                                                                            [ppt] => application/vnd.ms-powerpoint
                                                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                                                            [ppz] => application/vnd.ms-powerpoint
                                                                                            [pre] => application/x-freelance
                                                                                            [prt] => application/pro_eng
                                                                                            [ps] => application/postscript
                                                                                            [roff] => application/x-troff
                                                                                            [scm] => application/x-lotusscreencam
                                                                                            [set] => application/set
                                                                                            [sh] => application/x-sh
                                                                                            [shar] => application/x-shar
                                                                                            [sit] => application/x-stuffit
                                                                                            [skd] => application/x-koan
                                                                                            [skm] => application/x-koan
                                                                                            [skp] => application/x-koan
                                                                                            [skt] => application/x-koan
                                                                                            [smi] => application/smil
                                                                                            [smil] => application/smil
                                                                                            [sol] => application/solids
                                                                                            [spl] => application/x-futuresplash
                                                                                            [src] => application/x-wais-source
                                                                                            [step] => application/STEP
                                                                                            [stl] => application/SLA
                                                                                            [stp] => application/STEP
                                                                                            [sv4cpio] => application/x-sv4cpio
                                                                                            [sv4crc] => application/x-sv4crc
                                                                                            [svg] => image/svg+xml
                                                                                            [svgz] => image/svg+xml
                                                                                            [swf] => application/x-shockwave-flash
                                                                                            [t] => application/x-troff
                                                                                            [tar] => application/x-tar
                                                                                            [tcl] => application/x-tcl
                                                                                            [tex] => application/x-tex
                                                                                            [texi] => application/x-texinfo
                                                                                            [texinfo] => application/x-texinfo
                                                                                            [tr] => application/x-troff
                                                                                            [tsp] => application/dsptype
                                                                                            [ttc] => font/ttf
                                                                                            [ttf] => font/ttf
                                                                                            [unv] => application/i-deas
                                                                                            [ustar] => application/x-ustar
                                                                                            [vcd] => application/x-cdlink
                                                                                            [vda] => application/vda
                                                                                            [xlc] => application/vnd.ms-excel
                                                                                            [xll] => application/vnd.ms-excel
                                                                                            [xlm] => application/vnd.ms-excel
                                                                                            [xls] => application/vnd.ms-excel
                                                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                                                            [xlw] => application/vnd.ms-excel
                                                                                            [zip] => application/zip
                                                                                            [aif] => audio/x-aiff
                                                                                            [aifc] => audio/x-aiff
                                                                                            [aiff] => audio/x-aiff
                                                                                            [au] => audio/basic
                                                                                            [kar] => audio/midi
                                                                                            [mid] => audio/midi
                                                                                            [midi] => audio/midi
                                                                                            [mp2] => audio/mpeg
                                                                                            [mp3] => audio/mpeg
                                                                                            [mpga] => audio/mpeg
                                                                                            [ogg] => audio/ogg
                                                                                            [oga] => audio/ogg
                                                                                            [spx] => audio/ogg
                                                                                            [ra] => audio/x-realaudio
                                                                                            [ram] => audio/x-pn-realaudio
                                                                                            [rm] => audio/x-pn-realaudio
                                                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                                                            [snd] => audio/basic
                                                                                            [tsi] => audio/TSP-audio
                                                                                            [wav] => audio/x-wav
                                                                                            [aac] => audio/aac
                                                                                            [asc] => text/plain
                                                                                            [c] => text/plain
                                                                                            [cc] => text/plain
                                                                                            [css] => text/css
                                                                                            [etx] => text/x-setext
                                                                                            [f] => text/plain
                                                                                            [f90] => text/plain
                                                                                            [h] => text/plain
                                                                                            [hh] => text/plain
                                                                                            [htm] => Array
                                                                                                (
                                                                                                    [0] => text/html
                                                                                                    [1] => */*
                                                                                                )

                                                                                            [ics] => text/calendar
                                                                                            [m] => text/plain
                                                                                            [rtf] => text/rtf
                                                                                            [rtx] => text/richtext
                                                                                            [sgm] => text/sgml
                                                                                            [sgml] => text/sgml
                                                                                            [tsv] => text/tab-separated-values
                                                                                            [tpl] => text/template
                                                                                            [txt] => text/plain
                                                                                            [text] => text/plain
                                                                                            [avi] => video/x-msvideo
                                                                                            [fli] => video/x-fli
                                                                                            [mov] => video/quicktime
                                                                                            [movie] => video/x-sgi-movie
                                                                                            [mpe] => video/mpeg
                                                                                            [mpeg] => video/mpeg
                                                                                            [mpg] => video/mpeg
                                                                                            [qt] => video/quicktime
                                                                                            [viv] => video/vnd.vivo
                                                                                            [vivo] => video/vnd.vivo
                                                                                            [ogv] => video/ogg
                                                                                            [webm] => video/webm
                                                                                            [mp4] => video/mp4
                                                                                            [m4v] => video/mp4
                                                                                            [f4v] => video/mp4
                                                                                            [f4p] => video/mp4
                                                                                            [m4a] => audio/mp4
                                                                                            [f4a] => audio/mp4
                                                                                            [f4b] => audio/mp4
                                                                                            [gif] => image/gif
                                                                                            [ief] => image/ief
                                                                                            [jpg] => image/jpeg
                                                                                            [jpeg] => image/jpeg
                                                                                            [jpe] => image/jpeg
                                                                                            [pbm] => image/x-portable-bitmap
                                                                                            [pgm] => image/x-portable-graymap
                                                                                            [png] => image/png
                                                                                            [pnm] => image/x-portable-anymap
                                                                                            [ppm] => image/x-portable-pixmap
                                                                                            [ras] => image/cmu-raster
                                                                                            [rgb] => image/x-rgb
                                                                                            [tif] => image/tiff
                                                                                            [tiff] => image/tiff
                                                                                            [xbm] => image/x-xbitmap
                                                                                            [xpm] => image/x-xpixmap
                                                                                            [xwd] => image/x-xwindowdump
                                                                                            [psd] => Array
                                                                                                (
                                                                                                    [0] => application/photoshop
                                                                                                    [1] => application/psd
                                                                                                    [2] => image/psd
                                                                                                    [3] => image/x-photoshop
                                                                                                    [4] => image/photoshop
                                                                                                    [5] => zz-application/zz-winassoc-psd
                                                                                                )

                                                                                            [ice] => x-conference/x-cooltalk
                                                                                            [iges] => model/iges
                                                                                            [igs] => model/iges
                                                                                            [mesh] => model/mesh
                                                                                            [msh] => model/mesh
                                                                                            [silo] => model/mesh
                                                                                            [vrml] => model/vrml
                                                                                            [wrl] => model/vrml
                                                                                            [mime] => www/mime
                                                                                            [pdb] => chemical/x-pdb
                                                                                            [xyz] => chemical/x-pdb
                                                                                            [javascript] => application/javascript
                                                                                            [form] => application/x-www-form-urlencoded
                                                                                            [file] => multipart/form-data
                                                                                            [xhtml] => Array
                                                                                                (
                                                                                                    [0] => application/xhtml+xml
                                                                                                    [1] => application/xhtml
                                                                                                    [2] => text/xhtml
                                                                                                )

                                                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                                                            [atom] => application/atom+xml
                                                                                            [amf] => application/x-amf
                                                                                            [wap] => Array
                                                                                                (
                                                                                                    [0] => text/vnd.wap.wml
                                                                                                    [1] => text/vnd.wap.wmlscript
                                                                                                    [2] => image/vnd.wap.wbmp
                                                                                                )

                                                                                            [wml] => text/vnd.wap.wml
                                                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                                                            [wbmp] => image/vnd.wap.wbmp
                                                                                            [woff] => application/x-font-woff
                                                                                            [webp] => image/webp
                                                                                            [appcache] => text/cache-manifest
                                                                                            [manifest] => text/cache-manifest
                                                                                            [htc] => text/x-component
                                                                                            [rdf] => application/xml
                                                                                            [crx] => application/x-chrome-extension
                                                                                            [oex] => application/x-opera-extension
                                                                                            [xpi] => application/x-xpinstall
                                                                                            [safariextz] => application/octet-stream
                                                                                            [webapp] => application/x-web-app-manifest+json
                                                                                            [vcf] => text/x-vcard
                                                                                            [vtt] => text/vtt
                                                                                            [mkv] => video/x-matroska
                                                                                            [pkpass] => application/vnd.apple.pkpass
                                                                                            [ajax] => text/html
                                                                                        )

                                                                                    [_protocol:protected] => HTTP/1.1
                                                                                    [_status:protected] => 200
                                                                                    [_contentType:protected] => text/html
                                                                                    [_headers:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_body:protected] => 
                                                                                    [_file:protected] => 
                                                                                    [_fileRange:protected] => 
                                                                                    [_charset:protected] => UTF-8
                                                                                    [_cacheDirectives:protected] => Array
                                                                                        (
                                                                                        )

                                                                                    [_cookies:protected] => Array
                                                                                        (
                                                                                        )

                                                                                )

                                                                            [ext] => 
                                                                            [_renderType:protected] => 
                                                                            [_inputTypeMap:protected] => Array
                                                                                (
                                                                                    [json] => Array
                                                                                        (
                                                                                            [0] => json_decode
                                                                                            [1] => 1
                                                                                        )

                                                                                    [xml] => Array
                                                                                        (
                                                                                            [0] => Array
                                                                                                (
                                                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                                                    [1] => convertXml
                                                                                                )

                                                                                        )

                                                                                )

                                                                            [_viewClassMap:protected] => Array
                                                                                (
                                                                                    [json] => Json
                                                                                    [xml] => Xml
                                                                                )

                                                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                                                            [settings] => Array
                                                                                (
                                                                                    [checkHttpCache] => 1
                                                                                )

                                                                            [components] => Array
                                                                                (
                                                                                )

                                                                            [_componentMap:protected] => Array
                                                                                (
                                                                                )

                                                                            [params] => CakeRequest Object
                                                                                (
                                                                                    [params] => Array
                                                                                        (
                                                                                            [plugin] => 
                                                                                            [controller] => analysis
                                                                                            [action] => custom_tree_creation
                                                                                            [named] => Array
                                                                                                (
                                                                                                )

                                                                                            [pass] => Array
                                                                                                (
                                                                                                    [0] => gene_id
                                                                                                    [1] => Cre12.g515850
                                                                                                )

                                                                                            [isAjax] => 
                                                                                        )

                                                                                    [data] => Array
                                                                                        (
                                                                                        )

                                                                                    [query] => Array
                                                                                        (
                                                                                        )

                                                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                                                    [_detectors:protected] => Array
                                                                                        (
                                                                                            [get] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => GET
                                                                                                )

                                                                                            [patch] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PATCH
                                                                                                )

                                                                                            [post] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => POST
                                                                                                )

                                                                                            [put] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => PUT
                                                                                                )

                                                                                            [delete] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => DELETE
                                                                                                )

                                                                                            [head] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => HEAD
                                                                                                )

                                                                                            [options] => Array
                                                                                                (
                                                                                                    [env] => REQUEST_METHOD
                                                                                                    [value] => OPTIONS
                                                                                                )

                                                                                            [ssl] => Array
                                                                                                (
                                                                                                    [env] => HTTPS
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [ajax] => Array
                                                                                                (
                                                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                                                    [value] => XMLHttpRequest
                                                                                                )

                                                                                            [flash] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                                                )

                                                                                            [mobile] => Array
                                                                                                (
                                                                                                    [env] => HTTP_USER_AGENT
                                                                                                    [options] => Array
                                                                                                        (
                                                                                                            [0] => Android
                                                                                                            [1] => AvantGo
                                                                                                            [2] => BB10
                                                                                                            [3] => BlackBerry
                                                                                                            [4] => DoCoMo
                                                                                                            [5] => Fennec
                                                                                                            [6] => iPod
                                                                                                            [7] => iPhone
                                                                                                            [8] => iPad
                                                                                                            [9] => J2ME
                                                                                                            [10] => MIDP
                                                                                                            [11] => NetFront
                                                                                                            [12] => Nokia
                                                                                                            [13] => Opera Mini
                                                                                                            [14] => Opera Mobi
                                                                                                            [15] => PalmOS
                                                                                                            [16] => PalmSource
                                                                                                            [17] => portalmmm
                                                                                                            [18] => Plucker
                                                                                                            [19] => ReqwirelessWeb
                                                                                                            [20] => SonyEricsson
                                                                                                            [21] => Symbian
                                                                                                            [22] => UP\.Browser
                                                                                                            [23] => webOS
                                                                                                            [24] => Windows CE
                                                                                                            [25] => Windows Phone OS
                                                                                                            [26] => Xiino
                                                                                                        )

                                                                                                )

                                                                                            [requested] => Array
                                                                                                (
                                                                                                    [param] => requested
                                                                                                    [value] => 1
                                                                                                )

                                                                                            [json] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/json
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => json
                                                                                                )

                                                                                            [xml] => Array
                                                                                                (
                                                                                                    [accept] => Array
                                                                                                        (
                                                                                                            [0] => application/xml
                                                                                                            [1] => text/xml
                                                                                                        )

                                                                                                    [param] => ext
                                                                                                    [value] => xml
                                                                                                )

                                                                                        )

                                                                                    [_input:protected] => 
                                                                                )

                                                                        )

                                                                )

                                                            [defaultPriority] => 10
                                                        )

                                                    [1] => trigger
                                                )

                                            [passParams] => 
                                        )

                                    [1] => Array
                                        (
                                            [callable] => Array
                                                (
                                                    [0] => AnalysisController Object
 *RECURSION*
                                                    [1] => afterFilter
                                                )

                                            [passParams] => 
                                        )

                                )

                        )

                )

            [_isGlobal:protected] => 
        )

    [Session] => SessionComponent Object
        (
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
 *RECURSION*
                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [DataUtils] => DataUtilsComponent Object
        (
            [name] => DataUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FunctionalUtils
                    [2] => GeneFamilies
                    [3] => GenomeBrowser
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
 *RECURSION*
                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                    [GeneFamilies] => Array
                        (
                            [class] => GeneFamilies
                            [settings] => Array
                                (
                                )

                        )

                    [GenomeBrowser] => Array
                        (
                            [class] => GenomeBrowser
                            [settings] => Array
                                (
                                )

                        )

                )

            [GeneFamilies] => GeneFamiliesComponent Object
                (
                    [name] => GeneFamilies
                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                    [_Collection:protected] => ComponentCollection Object
                        (
                            [_Controller:protected] => AnalysisController Object
 *RECURSION*
                            [_enabled:protected] => Array
                                (
                                    [Session] => Array
                                        (
                                            [0] => 10
                                            [1] => 1
                                        )

                                    [DataUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 2
                                        )

                                    [FunctionalAnnotationUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 3
                                        )

                                    [GeneFamilies] => Array
                                        (
                                            [0] => 10
                                            [1] => 4
                                        )

                                    [Organism] => Array
                                        (
                                            [0] => 10
                                            [1] => 5
                                        )

                                    [Blast] => Array
                                        (
                                            [0] => 10
                                            [1] => 6
                                        )

                                    [WorkbenchUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 7
                                        )

                                    [PhylogeneticModuleUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 8
                                        )

                                    [ExternalPrograms] => Array
                                        (
                                            [0] => 10
                                            [1] => 9
                                        )

                                    [FastaUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 10
                                        )

                                    [MsaUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 11
                                        )

                                    [PhylogeneticUtils] => Array
                                        (
                                            [0] => 10
                                            [1] => 12
                                        )

                                    [Sequence] => Array
                                        (
                                            [0] => 10
                                            [1] => 13
                                        )

                                    [RequestHandler] => Array
                                        (
                                            [0] => 10
                                            [1] => 14
                                        )

                                )

                            [_loaded:protected] => Array
                                (
                                    [Session] => SessionComponent Object
                                        (
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [DataUtils] => DataUtilsComponent Object
 *RECURSION*
                                    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                        (
                                            [name] => FunctionalAnnotationUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => FunctionalUtils
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [FunctionalUtils] => Array
                                                        (
                                                            [class] => FunctionalUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                                    [Organism] => OrganismComponent Object
                                        (
                                            [name] => Organism
                                            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => GenomeBrowser
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [GenomeBrowser] => Array
                                                        (
                                                            [class] => GenomeBrowser
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [Blast] => BlastComponent Object
                                        (
                                            [name] => Blast
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                        (
                                            [name] => WorkbenchUtils
                                            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                    [1] => FormUtils
                                                    [2] => FunctionalUtils
                                                    [3] => GeneFamilies
                                                    [4] => WorkbenchSharedAccessRights
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FormUtils] => Array
                                                        (
                                                            [class] => FormUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FunctionalUtils] => Array
                                                        (
                                                            [class] => FunctionalUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [GeneFamilies] => Array
                                                        (
                                                            [class] => GeneFamilies
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [WorkbenchSharedAccessRights] => Array
                                                        (
                                                            [class] => WorkbenchSharedAccessRights
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                        (
                                            [name] => PhylogeneticModuleUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                    [1] => FastaUtils
                                                    [2] => MsaUtils
                                                    [3] => PhylogeneticUtils
                                                    [4] => Sequence
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [FastaUtils] => Array
                                                        (
                                                            [class] => FastaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [MsaUtils] => Array
                                                        (
                                                            [class] => MsaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [PhylogeneticUtils] => Array
                                                        (
                                                            [class] => PhylogeneticUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [Sequence] => Array
                                                        (
                                                            [class] => Sequence
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [ExternalPrograms] => ExternalProgramsComponent Object
                                        (
                                            [name] => ExternalPrograms
                                            [components] => Array
                                                (
                                                    [0] => FastaUtils
                                                )

                                            [program_paths:ExternalProgramsComponent:private] => Array
                                                (
                                                    [java] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => java/x86_64/21.0.2
                                                                        )

                                                                    [command] => java -Djava.awt.headless=true
                                                                )

                                                            [local_settings] => java -Djava.awt.headless=true
                                                            [db_connector] => mysql-connector-java-8.0.21.jar
                                                        )

                                                    [perl] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => perl
                                                                        )

                                                                    [command] => perl -w
                                                                )

                                                            [local_settings] => /usr/bin/perl
                                                        )

                                                    [bash] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => 
                                                        )

                                                    [bedops] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => bedops/x86_64/2.4.37
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => 
                                                        )

                                                    [blastdbcmd] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => blast
                                                                        )

                                                                    [command] => blastdbcmd
                                                                )

                                                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                        )

                                                    [blast] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => blast
                                                                        )

                                                                    [command] => 
                                                                )

                                                            [local_settings] => /usr/local/blast/2.2.24/bin/
                                                        )

                                                    [muscle] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => muscle/x86_64/3.8.31
                                                                        )

                                                                )

                                                        )

                                                    [mafft] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => mafft/x86_64/7.187
                                                                        )

                                                                )

                                                        )

                                                    [phyml] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => phyml/x86_64/20150219
                                                                        )

                                                                )

                                                        )

                                                    [fasttree] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => fasttree/x86_64/2.1.7
                                                                        )

                                                                )

                                                        )

                                                    [raxml] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => raxml/x86_64/8.2.8
                                                                        )

                                                                )

                                                        )

                                                    [iqtree] => Array
                                                        (
                                                            [cluster_settings] => Array
                                                                (
                                                                    [modules] => Array
                                                                        (
                                                                            [0] => iqtree/x86_64/1.5.5
                                                                        )

                                                                )

                                                        )

                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [FastaUtils] => Array
                                                        (
                                                            [class] => FastaUtils
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [FastaUtils] => FastaUtilsComponent Object
                                        (
                                            [name] => FastaUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [MsaUtils] => MsaUtilsComponent Object
                                        (
                                            [name] => MsaUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                        (
                                            [name] => PhylogeneticUtils
                                            [controller] => AnalysisController Object
 *RECURSION*
                                            [components] => Array
                                                (
                                                    [0] => ExternalPrograms
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                        )

                                    [Sequence] => SequenceComponent Object
                                        (
                                            [name] => Sequence
                                            [components] => Array
                                                (
                                                    [0] => Blast
                                                    [1] => Coordinates
                                                    [2] => ExternalPrograms
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                    [Blast] => Array
                                                        (
                                                            [class] => Blast
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [Coordinates] => Array
                                                        (
                                                            [class] => Coordinates
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                    [ExternalPrograms] => Array
                                                        (
                                                            [class] => ExternalPrograms
                                                            [settings] => Array
                                                                (
                                                                )

                                                        )

                                                )

                                            [controller] => AnalysisController Object
 *RECURSION*
                                        )

                                    [RequestHandler] => RequestHandlerComponent Object
                                        (
                                            [ajaxLayout] => ajax
                                            [enabled] => 1
                                            [request] => CakeRequest Object
                                                (
                                                    [params] => Array
                                                        (
                                                            [plugin] => 
                                                            [controller] => analysis
                                                            [action] => custom_tree_creation
                                                            [named] => Array
                                                                (
                                                                )

                                                            [pass] => Array
                                                                (
                                                                    [0] => gene_id
                                                                    [1] => Cre12.g515850
                                                                )

                                                            [isAjax] => 
                                                        )

                                                    [data] => Array
                                                        (
                                                        )

                                                    [query] => Array
                                                        (
                                                        )

                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                    [_detectors:protected] => Array
                                                        (
                                                            [get] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => GET
                                                                )

                                                            [patch] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PATCH
                                                                )

                                                            [post] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => POST
                                                                )

                                                            [put] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PUT
                                                                )

                                                            [delete] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => DELETE
                                                                )

                                                            [head] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => HEAD
                                                                )

                                                            [options] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => OPTIONS
                                                                )

                                                            [ssl] => Array
                                                                (
                                                                    [env] => HTTPS
                                                                    [value] => 1
                                                                )

                                                            [ajax] => Array
                                                                (
                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                    [value] => XMLHttpRequest
                                                                )

                                                            [flash] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                )

                                                            [mobile] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [options] => Array
                                                                        (
                                                                            [0] => Android
                                                                            [1] => AvantGo
                                                                            [2] => BB10
                                                                            [3] => BlackBerry
                                                                            [4] => DoCoMo
                                                                            [5] => Fennec
                                                                            [6] => iPod
                                                                            [7] => iPhone
                                                                            [8] => iPad
                                                                            [9] => J2ME
                                                                            [10] => MIDP
                                                                            [11] => NetFront
                                                                            [12] => Nokia
                                                                            [13] => Opera Mini
                                                                            [14] => Opera Mobi
                                                                            [15] => PalmOS
                                                                            [16] => PalmSource
                                                                            [17] => portalmmm
                                                                            [18] => Plucker
                                                                            [19] => ReqwirelessWeb
                                                                            [20] => SonyEricsson
                                                                            [21] => Symbian
                                                                            [22] => UP\.Browser
                                                                            [23] => webOS
                                                                            [24] => Windows CE
                                                                            [25] => Windows Phone OS
                                                                            [26] => Xiino
                                                                        )

                                                                )

                                                            [requested] => Array
                                                                (
                                                                    [param] => requested
                                                                    [value] => 1
                                                                )

                                                            [json] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/json
                                                                        )

                                                                    [param] => ext
                                                                    [value] => json
                                                                )

                                                            [xml] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/xml
                                                                            [1] => text/xml
                                                                        )

                                                                    [param] => ext
                                                                    [value] => xml
                                                                )

                                                        )

                                                    [_input:protected] => 
                                                )

                                            [response] => CakeResponse Object
                                                (
                                                    [_statusCodes:protected] => Array
                                                        (
                                                            [100] => Continue
                                                            [101] => Switching Protocols
                                                            [200] => OK
                                                            [201] => Created
                                                            [202] => Accepted
                                                            [203] => Non-Authoritative Information
                                                            [204] => No Content
                                                            [205] => Reset Content
                                                            [206] => Partial Content
                                                            [300] => Multiple Choices
                                                            [301] => Moved Permanently
                                                            [302] => Found
                                                            [303] => See Other
                                                            [304] => Not Modified
                                                            [305] => Use Proxy
                                                            [307] => Temporary Redirect
                                                            [400] => Bad Request
                                                            [401] => Unauthorized
                                                            [402] => Payment Required
                                                            [403] => Forbidden
                                                            [404] => Not Found
                                                            [405] => Method Not Allowed
                                                            [406] => Not Acceptable
                                                            [407] => Proxy Authentication Required
                                                            [408] => Request Time-out
                                                            [409] => Conflict
                                                            [410] => Gone
                                                            [411] => Length Required
                                                            [412] => Precondition Failed
                                                            [413] => Request Entity Too Large
                                                            [414] => Request-URI Too Large
                                                            [415] => Unsupported Media Type
                                                            [416] => Requested range not satisfiable
                                                            [417] => Expectation Failed
                                                            [429] => Too Many Requests
                                                            [500] => Internal Server Error
                                                            [501] => Not Implemented
                                                            [502] => Bad Gateway
                                                            [503] => Service Unavailable
                                                            [504] => Gateway Time-out
                                                            [505] => Unsupported Version
                                                        )

                                                    [_mimeTypes:protected] => Array
                                                        (
                                                            [html] => Array
                                                                (
                                                                    [0] => text/html
                                                                    [1] => */*
                                                                )

                                                            [json] => application/json
                                                            [xml] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [rss] => application/rss+xml
                                                            [ai] => application/postscript
                                                            [bcpio] => application/x-bcpio
                                                            [bin] => application/octet-stream
                                                            [ccad] => application/clariscad
                                                            [cdf] => application/x-netcdf
                                                            [class] => application/octet-stream
                                                            [cpio] => application/x-cpio
                                                            [cpt] => application/mac-compactpro
                                                            [csh] => application/x-csh
                                                            [csv] => Array
                                                                (
                                                                    [0] => text/csv
                                                                    [1] => application/vnd.ms-excel
                                                                )

                                                            [dcr] => application/x-director
                                                            [dir] => application/x-director
                                                            [dms] => application/octet-stream
                                                            [doc] => application/msword
                                                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                            [drw] => application/drafting
                                                            [dvi] => application/x-dvi
                                                            [dwg] => application/acad
                                                            [dxf] => application/dxf
                                                            [dxr] => application/x-director
                                                            [eot] => application/vnd.ms-fontobject
                                                            [eps] => application/postscript
                                                            [exe] => application/octet-stream
                                                            [ez] => application/andrew-inset
                                                            [flv] => video/x-flv
                                                            [gtar] => application/x-gtar
                                                            [gz] => application/x-gzip
                                                            [bz2] => application/x-bzip
                                                            [7z] => application/x-7z-compressed
                                                            [hdf] => application/x-hdf
                                                            [hqx] => application/mac-binhex40
                                                            [ico] => image/x-icon
                                                            [ips] => application/x-ipscript
                                                            [ipx] => application/x-ipix
                                                            [js] => application/javascript
                                                            [jsonapi] => application/vnd.api+json
                                                            [latex] => application/x-latex
                                                            [lha] => application/octet-stream
                                                            [lsp] => application/x-lisp
                                                            [lzh] => application/octet-stream
                                                            [man] => application/x-troff-man
                                                            [me] => application/x-troff-me
                                                            [mif] => application/vnd.mif
                                                            [ms] => application/x-troff-ms
                                                            [nc] => application/x-netcdf
                                                            [oda] => application/oda
                                                            [otf] => font/otf
                                                            [pdf] => application/pdf
                                                            [pgn] => application/x-chess-pgn
                                                            [pot] => application/vnd.ms-powerpoint
                                                            [pps] => application/vnd.ms-powerpoint
                                                            [ppt] => application/vnd.ms-powerpoint
                                                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                            [ppz] => application/vnd.ms-powerpoint
                                                            [pre] => application/x-freelance
                                                            [prt] => application/pro_eng
                                                            [ps] => application/postscript
                                                            [roff] => application/x-troff
                                                            [scm] => application/x-lotusscreencam
                                                            [set] => application/set
                                                            [sh] => application/x-sh
                                                            [shar] => application/x-shar
                                                            [sit] => application/x-stuffit
                                                            [skd] => application/x-koan
                                                            [skm] => application/x-koan
                                                            [skp] => application/x-koan
                                                            [skt] => application/x-koan
                                                            [smi] => application/smil
                                                            [smil] => application/smil
                                                            [sol] => application/solids
                                                            [spl] => application/x-futuresplash
                                                            [src] => application/x-wais-source
                                                            [step] => application/STEP
                                                            [stl] => application/SLA
                                                            [stp] => application/STEP
                                                            [sv4cpio] => application/x-sv4cpio
                                                            [sv4crc] => application/x-sv4crc
                                                            [svg] => image/svg+xml
                                                            [svgz] => image/svg+xml
                                                            [swf] => application/x-shockwave-flash
                                                            [t] => application/x-troff
                                                            [tar] => application/x-tar
                                                            [tcl] => application/x-tcl
                                                            [tex] => application/x-tex
                                                            [texi] => application/x-texinfo
                                                            [texinfo] => application/x-texinfo
                                                            [tr] => application/x-troff
                                                            [tsp] => application/dsptype
                                                            [ttc] => font/ttf
                                                            [ttf] => font/ttf
                                                            [unv] => application/i-deas
                                                            [ustar] => application/x-ustar
                                                            [vcd] => application/x-cdlink
                                                            [vda] => application/vda
                                                            [xlc] => application/vnd.ms-excel
                                                            [xll] => application/vnd.ms-excel
                                                            [xlm] => application/vnd.ms-excel
                                                            [xls] => application/vnd.ms-excel
                                                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                            [xlw] => application/vnd.ms-excel
                                                            [zip] => application/zip
                                                            [aif] => audio/x-aiff
                                                            [aifc] => audio/x-aiff
                                                            [aiff] => audio/x-aiff
                                                            [au] => audio/basic
                                                            [kar] => audio/midi
                                                            [mid] => audio/midi
                                                            [midi] => audio/midi
                                                            [mp2] => audio/mpeg
                                                            [mp3] => audio/mpeg
                                                            [mpga] => audio/mpeg
                                                            [ogg] => audio/ogg
                                                            [oga] => audio/ogg
                                                            [spx] => audio/ogg
                                                            [ra] => audio/x-realaudio
                                                            [ram] => audio/x-pn-realaudio
                                                            [rm] => audio/x-pn-realaudio
                                                            [rpm] => audio/x-pn-realaudio-plugin
                                                            [snd] => audio/basic
                                                            [tsi] => audio/TSP-audio
                                                            [wav] => audio/x-wav
                                                            [aac] => audio/aac
                                                            [asc] => text/plain
                                                            [c] => text/plain
                                                            [cc] => text/plain
                                                            [css] => text/css
                                                            [etx] => text/x-setext
                                                            [f] => text/plain
                                                            [f90] => text/plain
                                                            [h] => text/plain
                                                            [hh] => text/plain
                                                            [htm] => Array
                                                                (
                                                                    [0] => text/html
                                                                    [1] => */*
                                                                )

                                                            [ics] => text/calendar
                                                            [m] => text/plain
                                                            [rtf] => text/rtf
                                                            [rtx] => text/richtext
                                                            [sgm] => text/sgml
                                                            [sgml] => text/sgml
                                                            [tsv] => text/tab-separated-values
                                                            [tpl] => text/template
                                                            [txt] => text/plain
                                                            [text] => text/plain
                                                            [avi] => video/x-msvideo
                                                            [fli] => video/x-fli
                                                            [mov] => video/quicktime
                                                            [movie] => video/x-sgi-movie
                                                            [mpe] => video/mpeg
                                                            [mpeg] => video/mpeg
                                                            [mpg] => video/mpeg
                                                            [qt] => video/quicktime
                                                            [viv] => video/vnd.vivo
                                                            [vivo] => video/vnd.vivo
                                                            [ogv] => video/ogg
                                                            [webm] => video/webm
                                                            [mp4] => video/mp4
                                                            [m4v] => video/mp4
                                                            [f4v] => video/mp4
                                                            [f4p] => video/mp4
                                                            [m4a] => audio/mp4
                                                            [f4a] => audio/mp4
                                                            [f4b] => audio/mp4
                                                            [gif] => image/gif
                                                            [ief] => image/ief
                                                            [jpg] => image/jpeg
                                                            [jpeg] => image/jpeg
                                                            [jpe] => image/jpeg
                                                            [pbm] => image/x-portable-bitmap
                                                            [pgm] => image/x-portable-graymap
                                                            [png] => image/png
                                                            [pnm] => image/x-portable-anymap
                                                            [ppm] => image/x-portable-pixmap
                                                            [ras] => image/cmu-raster
                                                            [rgb] => image/x-rgb
                                                            [tif] => image/tiff
                                                            [tiff] => image/tiff
                                                            [xbm] => image/x-xbitmap
                                                            [xpm] => image/x-xpixmap
                                                            [xwd] => image/x-xwindowdump
                                                            [psd] => Array
                                                                (
                                                                    [0] => application/photoshop
                                                                    [1] => application/psd
                                                                    [2] => image/psd
                                                                    [3] => image/x-photoshop
                                                                    [4] => image/photoshop
                                                                    [5] => zz-application/zz-winassoc-psd
                                                                )

                                                            [ice] => x-conference/x-cooltalk
                                                            [iges] => model/iges
                                                            [igs] => model/iges
                                                            [mesh] => model/mesh
                                                            [msh] => model/mesh
                                                            [silo] => model/mesh
                                                            [vrml] => model/vrml
                                                            [wrl] => model/vrml
                                                            [mime] => www/mime
                                                            [pdb] => chemical/x-pdb
                                                            [xyz] => chemical/x-pdb
                                                            [javascript] => application/javascript
                                                            [form] => application/x-www-form-urlencoded
                                                            [file] => multipart/form-data
                                                            [xhtml] => Array
                                                                (
                                                                    [0] => application/xhtml+xml
                                                                    [1] => application/xhtml
                                                                    [2] => text/xhtml
                                                                )

                                                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                            [atom] => application/atom+xml
                                                            [amf] => application/x-amf
                                                            [wap] => Array
                                                                (
                                                                    [0] => text/vnd.wap.wml
                                                                    [1] => text/vnd.wap.wmlscript
                                                                    [2] => image/vnd.wap.wbmp
                                                                )

                                                            [wml] => text/vnd.wap.wml
                                                            [wmlscript] => text/vnd.wap.wmlscript
                                                            [wbmp] => image/vnd.wap.wbmp
                                                            [woff] => application/x-font-woff
                                                            [webp] => image/webp
                                                            [appcache] => text/cache-manifest
                                                            [manifest] => text/cache-manifest
                                                            [htc] => text/x-component
                                                            [rdf] => application/xml
                                                            [crx] => application/x-chrome-extension
                                                            [oex] => application/x-opera-extension
                                                            [xpi] => application/x-xpinstall
                                                            [safariextz] => application/octet-stream
                                                            [webapp] => application/x-web-app-manifest+json
                                                            [vcf] => text/x-vcard
                                                            [vtt] => text/vtt
                                                            [mkv] => video/x-matroska
                                                            [pkpass] => application/vnd.apple.pkpass
                                                            [ajax] => text/html
                                                        )

                                                    [_protocol:protected] => HTTP/1.1
                                                    [_status:protected] => 200
                                                    [_contentType:protected] => text/html
                                                    [_headers:protected] => Array
                                                        (
                                                        )

                                                    [_body:protected] => 
                                                    [_file:protected] => 
                                                    [_fileRange:protected] => 
                                                    [_charset:protected] => UTF-8
                                                    [_cacheDirectives:protected] => Array
                                                        (
                                                        )

                                                    [_cookies:protected] => Array
                                                        (
                                                        )

                                                )

                                            [ext] => 
                                            [_renderType:protected] => 
                                            [_inputTypeMap:protected] => Array
                                                (
                                                    [json] => Array
                                                        (
                                                            [0] => json_decode
                                                            [1] => 1
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [0] => Array
                                                                (
                                                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                                                    [1] => convertXml
                                                                )

                                                        )

                                                )

                                            [_viewClassMap:protected] => Array
                                                (
                                                    [json] => Json
                                                    [xml] => Xml
                                                )

                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                    [checkHttpCache] => 1
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                            [params] => CakeRequest Object
                                                (
                                                    [params] => Array
                                                        (
                                                            [plugin] => 
                                                            [controller] => analysis
                                                            [action] => custom_tree_creation
                                                            [named] => Array
                                                                (
                                                                )

                                                            [pass] => Array
                                                                (
                                                                    [0] => gene_id
                                                                    [1] => Cre12.g515850
                                                                )

                                                            [isAjax] => 
                                                        )

                                                    [data] => Array
                                                        (
                                                        )

                                                    [query] => Array
                                                        (
                                                        )

                                                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                    [base] => /plaza.dev/_dev_instances/feedback
                                                    [webroot] => /plaza.dev/_dev_instances/feedback/
                                                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                                    [_detectors:protected] => Array
                                                        (
                                                            [get] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => GET
                                                                )

                                                            [patch] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PATCH
                                                                )

                                                            [post] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => POST
                                                                )

                                                            [put] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => PUT
                                                                )

                                                            [delete] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => DELETE
                                                                )

                                                            [head] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => HEAD
                                                                )

                                                            [options] => Array
                                                                (
                                                                    [env] => REQUEST_METHOD
                                                                    [value] => OPTIONS
                                                                )

                                                            [ssl] => Array
                                                                (
                                                                    [env] => HTTPS
                                                                    [value] => 1
                                                                )

                                                            [ajax] => Array
                                                                (
                                                                    [env] => HTTP_X_REQUESTED_WITH
                                                                    [value] => XMLHttpRequest
                                                                )

                                                            [flash] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                                                )

                                                            [mobile] => Array
                                                                (
                                                                    [env] => HTTP_USER_AGENT
                                                                    [options] => Array
                                                                        (
                                                                            [0] => Android
                                                                            [1] => AvantGo
                                                                            [2] => BB10
                                                                            [3] => BlackBerry
                                                                            [4] => DoCoMo
                                                                            [5] => Fennec
                                                                            [6] => iPod
                                                                            [7] => iPhone
                                                                            [8] => iPad
                                                                            [9] => J2ME
                                                                            [10] => MIDP
                                                                            [11] => NetFront
                                                                            [12] => Nokia
                                                                            [13] => Opera Mini
                                                                            [14] => Opera Mobi
                                                                            [15] => PalmOS
                                                                            [16] => PalmSource
                                                                            [17] => portalmmm
                                                                            [18] => Plucker
                                                                            [19] => ReqwirelessWeb
                                                                            [20] => SonyEricsson
                                                                            [21] => Symbian
                                                                            [22] => UP\.Browser
                                                                            [23] => webOS
                                                                            [24] => Windows CE
                                                                            [25] => Windows Phone OS
                                                                            [26] => Xiino
                                                                        )

                                                                )

                                                            [requested] => Array
                                                                (
                                                                    [param] => requested
                                                                    [value] => 1
                                                                )

                                                            [json] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/json
                                                                        )

                                                                    [param] => ext
                                                                    [value] => json
                                                                )

                                                            [xml] => Array
                                                                (
                                                                    [accept] => Array
                                                                        (
                                                                            [0] => application/xml
                                                                            [1] => text/xml
                                                                        )

                                                                    [param] => ext
                                                                    [value] => xml
                                                                )

                                                        )

                                                    [_input:protected] => 
                                                )

                                        )

                                )

                            [defaultPriority] => 10
                        )

                    [settings] => Array
                        (
                        )

                    [components] => Array
                        (
                        )

                    [_componentMap:protected] => Array
                        (
                        )

                )

        )

    [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
        (
            [name] => FunctionalAnnotationUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => FunctionalUtils
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
 *RECURSION*
                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [GeneFamilies] => GeneFamiliesComponent Object
        (
            [name] => GeneFamilies
            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
 *RECURSION*
                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [Organism] => OrganismComponent Object
        (
            [name] => Organism
            [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => GenomeBrowser
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
 *RECURSION*
                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [GenomeBrowser] => Array
                        (
                            [class] => GenomeBrowser
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [Blast] => BlastComponent Object
        (
            [name] => Blast
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
 *RECURSION*
                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
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                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
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                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
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                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [WorkbenchUtils] => WorkbenchUtilsComponent Object
        (
            [name] => WorkbenchUtils
            [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FormUtils
                    [2] => FunctionalUtils
                    [3] => GeneFamilies
                    [4] => WorkbenchSharedAccessRights
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
 *RECURSION*
                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
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                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
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                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FormUtils] => Array
                        (
                            [class] => FormUtils
                            [settings] => Array
                                (
                                )

                        )

                    [FunctionalUtils] => Array
                        (
                            [class] => FunctionalUtils
                            [settings] => Array
                                (
                                )

                        )

                    [GeneFamilies] => Array
                        (
                            [class] => GeneFamilies
                            [settings] => Array
                                (
                                )

                        )

                    [WorkbenchSharedAccessRights] => Array
                        (
                            [class] => WorkbenchSharedAccessRights
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
        (
            [name] => PhylogeneticModuleUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                    [1] => FastaUtils
                    [2] => MsaUtils
                    [3] => PhylogeneticUtils
                    [4] => Sequence
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
 *RECURSION*
                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
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                                                    [isAjax] => 
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                                            [data] => Array
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                                                )

                                            [query] => Array
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                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
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                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
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                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
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                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
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                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
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                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
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                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
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                                                    [ajax] => Array
                                                        (
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                                                            [value] => XMLHttpRequest
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                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
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                                                                    [1] => AvantGo
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                                                                    [8] => iPad
                                                                    [9] => J2ME
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                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
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                                                                    [20] => SonyEricsson
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                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                    [FastaUtils] => Array
                        (
                            [class] => FastaUtils
                            [settings] => Array
                                (
                                )

                        )

                    [MsaUtils] => Array
                        (
                            [class] => MsaUtils
                            [settings] => Array
                                (
                                )

                        )

                    [PhylogeneticUtils] => Array
                        (
                            [class] => PhylogeneticUtils
                            [settings] => Array
                                (
                                )

                        )

                    [Sequence] => Array
                        (
                            [class] => Sequence
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [ExternalPrograms] => ExternalProgramsComponent Object
        (
            [name] => ExternalPrograms
            [components] => Array
                (
                    [0] => FastaUtils
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            [program_paths:ExternalProgramsComponent:private] => Array
                (
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                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => java/x86_64/21.0.2
                                        )

                                    [command] => java -Djava.awt.headless=true
                                )

                            [local_settings] => java -Djava.awt.headless=true
                            [db_connector] => mysql-connector-java-8.0.21.jar
                        )

                    [perl] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => perl
                                        )

                                    [command] => perl -w
                                )

                            [local_settings] => /usr/bin/perl
                        )

                    [bash] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                        )

                                    [command] => 
                                )

                            [local_settings] => 
                        )

                    [bedops] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => bedops/x86_64/2.4.37
                                        )

                                    [command] => 
                                )

                            [local_settings] => 
                        )

                    [blastdbcmd] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => blast
                                        )

                                    [command] => blastdbcmd
                                )

                            [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
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                    [blast] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => blast
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                                    [command] => 
                                )

                            [local_settings] => /usr/local/blast/2.2.24/bin/
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                    [muscle] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => muscle/x86_64/3.8.31
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                                )

                        )

                    [mafft] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => mafft/x86_64/7.187
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                                )

                        )

                    [phyml] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => phyml/x86_64/20150219
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                                )

                        )

                    [fasttree] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => fasttree/x86_64/2.1.7
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                                )

                        )

                    [raxml] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => raxml/x86_64/8.2.8
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                                )

                        )

                    [iqtree] => Array
                        (
                            [cluster_settings] => Array
                                (
                                    [modules] => Array
                                        (
                                            [0] => iqtree/x86_64/1.5.5
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                                )

                        )

                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
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                                            [3] => GenomeBrowser
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                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
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                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
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                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
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                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
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                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
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                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

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                            [ExternalPrograms] => ExternalProgramsComponent Object
 *RECURSION*
                            [FastaUtils] => FastaUtilsComponent Object
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                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
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                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
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                                        (
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                                            [1] => Coordinates
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                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
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                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
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                            [RequestHandler] => RequestHandlerComponent Object
                                (
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                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
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                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
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                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [FastaUtils] => Array
                        (
                            [class] => FastaUtils
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [FastaUtils] => FastaUtilsComponent Object
        (
            [name] => FastaUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
 *RECURSION*
                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [MsaUtils] => MsaUtilsComponent Object
        (
            [name] => MsaUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
 *RECURSION*
                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

        )

    [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
        (
            [name] => PhylogeneticUtils
            [controller] => AnalysisController Object
 *RECURSION*
            [components] => Array
                (
                    [0] => ExternalPrograms
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
 *RECURSION*
                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                )

        )

    [Sequence] => SequenceComponent Object
        (
            [name] => Sequence
            [components] => Array
                (
                    [0] => Blast
                    [1] => Coordinates
                    [2] => ExternalPrograms
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
 *RECURSION*
                            [RequestHandler] => RequestHandlerComponent Object
                                (
                                    [ajaxLayout] => ajax
                                    [enabled] => 1
                                    [request] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                    [response] => CakeResponse Object
                                        (
                                            [_statusCodes:protected] => Array
                                                (
                                                    [100] => Continue
                                                    [101] => Switching Protocols
                                                    [200] => OK
                                                    [201] => Created
                                                    [202] => Accepted
                                                    [203] => Non-Authoritative Information
                                                    [204] => No Content
                                                    [205] => Reset Content
                                                    [206] => Partial Content
                                                    [300] => Multiple Choices
                                                    [301] => Moved Permanently
                                                    [302] => Found
                                                    [303] => See Other
                                                    [304] => Not Modified
                                                    [305] => Use Proxy
                                                    [307] => Temporary Redirect
                                                    [400] => Bad Request
                                                    [401] => Unauthorized
                                                    [402] => Payment Required
                                                    [403] => Forbidden
                                                    [404] => Not Found
                                                    [405] => Method Not Allowed
                                                    [406] => Not Acceptable
                                                    [407] => Proxy Authentication Required
                                                    [408] => Request Time-out
                                                    [409] => Conflict
                                                    [410] => Gone
                                                    [411] => Length Required
                                                    [412] => Precondition Failed
                                                    [413] => Request Entity Too Large
                                                    [414] => Request-URI Too Large
                                                    [415] => Unsupported Media Type
                                                    [416] => Requested range not satisfiable
                                                    [417] => Expectation Failed
                                                    [429] => Too Many Requests
                                                    [500] => Internal Server Error
                                                    [501] => Not Implemented
                                                    [502] => Bad Gateway
                                                    [503] => Service Unavailable
                                                    [504] => Gateway Time-out
                                                    [505] => Unsupported Version
                                                )

                                            [_mimeTypes:protected] => Array
                                                (
                                                    [html] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [json] => application/json
                                                    [xml] => Array
                                                        (
                                                            [0] => application/xml
                                                            [1] => text/xml
                                                        )

                                                    [rss] => application/rss+xml
                                                    [ai] => application/postscript
                                                    [bcpio] => application/x-bcpio
                                                    [bin] => application/octet-stream
                                                    [ccad] => application/clariscad
                                                    [cdf] => application/x-netcdf
                                                    [class] => application/octet-stream
                                                    [cpio] => application/x-cpio
                                                    [cpt] => application/mac-compactpro
                                                    [csh] => application/x-csh
                                                    [csv] => Array
                                                        (
                                                            [0] => text/csv
                                                            [1] => application/vnd.ms-excel
                                                        )

                                                    [dcr] => application/x-director
                                                    [dir] => application/x-director
                                                    [dms] => application/octet-stream
                                                    [doc] => application/msword
                                                    [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                                                    [drw] => application/drafting
                                                    [dvi] => application/x-dvi
                                                    [dwg] => application/acad
                                                    [dxf] => application/dxf
                                                    [dxr] => application/x-director
                                                    [eot] => application/vnd.ms-fontobject
                                                    [eps] => application/postscript
                                                    [exe] => application/octet-stream
                                                    [ez] => application/andrew-inset
                                                    [flv] => video/x-flv
                                                    [gtar] => application/x-gtar
                                                    [gz] => application/x-gzip
                                                    [bz2] => application/x-bzip
                                                    [7z] => application/x-7z-compressed
                                                    [hdf] => application/x-hdf
                                                    [hqx] => application/mac-binhex40
                                                    [ico] => image/x-icon
                                                    [ips] => application/x-ipscript
                                                    [ipx] => application/x-ipix
                                                    [js] => application/javascript
                                                    [jsonapi] => application/vnd.api+json
                                                    [latex] => application/x-latex
                                                    [lha] => application/octet-stream
                                                    [lsp] => application/x-lisp
                                                    [lzh] => application/octet-stream
                                                    [man] => application/x-troff-man
                                                    [me] => application/x-troff-me
                                                    [mif] => application/vnd.mif
                                                    [ms] => application/x-troff-ms
                                                    [nc] => application/x-netcdf
                                                    [oda] => application/oda
                                                    [otf] => font/otf
                                                    [pdf] => application/pdf
                                                    [pgn] => application/x-chess-pgn
                                                    [pot] => application/vnd.ms-powerpoint
                                                    [pps] => application/vnd.ms-powerpoint
                                                    [ppt] => application/vnd.ms-powerpoint
                                                    [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                                                    [ppz] => application/vnd.ms-powerpoint
                                                    [pre] => application/x-freelance
                                                    [prt] => application/pro_eng
                                                    [ps] => application/postscript
                                                    [roff] => application/x-troff
                                                    [scm] => application/x-lotusscreencam
                                                    [set] => application/set
                                                    [sh] => application/x-sh
                                                    [shar] => application/x-shar
                                                    [sit] => application/x-stuffit
                                                    [skd] => application/x-koan
                                                    [skm] => application/x-koan
                                                    [skp] => application/x-koan
                                                    [skt] => application/x-koan
                                                    [smi] => application/smil
                                                    [smil] => application/smil
                                                    [sol] => application/solids
                                                    [spl] => application/x-futuresplash
                                                    [src] => application/x-wais-source
                                                    [step] => application/STEP
                                                    [stl] => application/SLA
                                                    [stp] => application/STEP
                                                    [sv4cpio] => application/x-sv4cpio
                                                    [sv4crc] => application/x-sv4crc
                                                    [svg] => image/svg+xml
                                                    [svgz] => image/svg+xml
                                                    [swf] => application/x-shockwave-flash
                                                    [t] => application/x-troff
                                                    [tar] => application/x-tar
                                                    [tcl] => application/x-tcl
                                                    [tex] => application/x-tex
                                                    [texi] => application/x-texinfo
                                                    [texinfo] => application/x-texinfo
                                                    [tr] => application/x-troff
                                                    [tsp] => application/dsptype
                                                    [ttc] => font/ttf
                                                    [ttf] => font/ttf
                                                    [unv] => application/i-deas
                                                    [ustar] => application/x-ustar
                                                    [vcd] => application/x-cdlink
                                                    [vda] => application/vda
                                                    [xlc] => application/vnd.ms-excel
                                                    [xll] => application/vnd.ms-excel
                                                    [xlm] => application/vnd.ms-excel
                                                    [xls] => application/vnd.ms-excel
                                                    [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                                                    [xlw] => application/vnd.ms-excel
                                                    [zip] => application/zip
                                                    [aif] => audio/x-aiff
                                                    [aifc] => audio/x-aiff
                                                    [aiff] => audio/x-aiff
                                                    [au] => audio/basic
                                                    [kar] => audio/midi
                                                    [mid] => audio/midi
                                                    [midi] => audio/midi
                                                    [mp2] => audio/mpeg
                                                    [mp3] => audio/mpeg
                                                    [mpga] => audio/mpeg
                                                    [ogg] => audio/ogg
                                                    [oga] => audio/ogg
                                                    [spx] => audio/ogg
                                                    [ra] => audio/x-realaudio
                                                    [ram] => audio/x-pn-realaudio
                                                    [rm] => audio/x-pn-realaudio
                                                    [rpm] => audio/x-pn-realaudio-plugin
                                                    [snd] => audio/basic
                                                    [tsi] => audio/TSP-audio
                                                    [wav] => audio/x-wav
                                                    [aac] => audio/aac
                                                    [asc] => text/plain
                                                    [c] => text/plain
                                                    [cc] => text/plain
                                                    [css] => text/css
                                                    [etx] => text/x-setext
                                                    [f] => text/plain
                                                    [f90] => text/plain
                                                    [h] => text/plain
                                                    [hh] => text/plain
                                                    [htm] => Array
                                                        (
                                                            [0] => text/html
                                                            [1] => */*
                                                        )

                                                    [ics] => text/calendar
                                                    [m] => text/plain
                                                    [rtf] => text/rtf
                                                    [rtx] => text/richtext
                                                    [sgm] => text/sgml
                                                    [sgml] => text/sgml
                                                    [tsv] => text/tab-separated-values
                                                    [tpl] => text/template
                                                    [txt] => text/plain
                                                    [text] => text/plain
                                                    [avi] => video/x-msvideo
                                                    [fli] => video/x-fli
                                                    [mov] => video/quicktime
                                                    [movie] => video/x-sgi-movie
                                                    [mpe] => video/mpeg
                                                    [mpeg] => video/mpeg
                                                    [mpg] => video/mpeg
                                                    [qt] => video/quicktime
                                                    [viv] => video/vnd.vivo
                                                    [vivo] => video/vnd.vivo
                                                    [ogv] => video/ogg
                                                    [webm] => video/webm
                                                    [mp4] => video/mp4
                                                    [m4v] => video/mp4
                                                    [f4v] => video/mp4
                                                    [f4p] => video/mp4
                                                    [m4a] => audio/mp4
                                                    [f4a] => audio/mp4
                                                    [f4b] => audio/mp4
                                                    [gif] => image/gif
                                                    [ief] => image/ief
                                                    [jpg] => image/jpeg
                                                    [jpeg] => image/jpeg
                                                    [jpe] => image/jpeg
                                                    [pbm] => image/x-portable-bitmap
                                                    [pgm] => image/x-portable-graymap
                                                    [png] => image/png
                                                    [pnm] => image/x-portable-anymap
                                                    [ppm] => image/x-portable-pixmap
                                                    [ras] => image/cmu-raster
                                                    [rgb] => image/x-rgb
                                                    [tif] => image/tiff
                                                    [tiff] => image/tiff
                                                    [xbm] => image/x-xbitmap
                                                    [xpm] => image/x-xpixmap
                                                    [xwd] => image/x-xwindowdump
                                                    [psd] => Array
                                                        (
                                                            [0] => application/photoshop
                                                            [1] => application/psd
                                                            [2] => image/psd
                                                            [3] => image/x-photoshop
                                                            [4] => image/photoshop
                                                            [5] => zz-application/zz-winassoc-psd
                                                        )

                                                    [ice] => x-conference/x-cooltalk
                                                    [iges] => model/iges
                                                    [igs] => model/iges
                                                    [mesh] => model/mesh
                                                    [msh] => model/mesh
                                                    [silo] => model/mesh
                                                    [vrml] => model/vrml
                                                    [wrl] => model/vrml
                                                    [mime] => www/mime
                                                    [pdb] => chemical/x-pdb
                                                    [xyz] => chemical/x-pdb
                                                    [javascript] => application/javascript
                                                    [form] => application/x-www-form-urlencoded
                                                    [file] => multipart/form-data
                                                    [xhtml] => Array
                                                        (
                                                            [0] => application/xhtml+xml
                                                            [1] => application/xhtml
                                                            [2] => text/xhtml
                                                        )

                                                    [xhtml-mobile] => application/vnd.wap.xhtml+xml
                                                    [atom] => application/atom+xml
                                                    [amf] => application/x-amf
                                                    [wap] => Array
                                                        (
                                                            [0] => text/vnd.wap.wml
                                                            [1] => text/vnd.wap.wmlscript
                                                            [2] => image/vnd.wap.wbmp
                                                        )

                                                    [wml] => text/vnd.wap.wml
                                                    [wmlscript] => text/vnd.wap.wmlscript
                                                    [wbmp] => image/vnd.wap.wbmp
                                                    [woff] => application/x-font-woff
                                                    [webp] => image/webp
                                                    [appcache] => text/cache-manifest
                                                    [manifest] => text/cache-manifest
                                                    [htc] => text/x-component
                                                    [rdf] => application/xml
                                                    [crx] => application/x-chrome-extension
                                                    [oex] => application/x-opera-extension
                                                    [xpi] => application/x-xpinstall
                                                    [safariextz] => application/octet-stream
                                                    [webapp] => application/x-web-app-manifest+json
                                                    [vcf] => text/x-vcard
                                                    [vtt] => text/vtt
                                                    [mkv] => video/x-matroska
                                                    [pkpass] => application/vnd.apple.pkpass
                                                    [ajax] => text/html
                                                )

                                            [_protocol:protected] => HTTP/1.1
                                            [_status:protected] => 200
                                            [_contentType:protected] => text/html
                                            [_headers:protected] => Array
                                                (
                                                )

                                            [_body:protected] => 
                                            [_file:protected] => 
                                            [_fileRange:protected] => 
                                            [_charset:protected] => UTF-8
                                            [_cacheDirectives:protected] => Array
                                                (
                                                )

                                            [_cookies:protected] => Array
                                                (
                                                )

                                        )

                                    [ext] => 
                                    [_renderType:protected] => 
                                    [_inputTypeMap:protected] => Array
                                        (
                                            [json] => Array
                                                (
                                                    [0] => json_decode
                                                    [1] => 1
                                                )

                                            [xml] => Array
                                                (
                                                    [0] => Array
                                                        (
                                                            [0] => RequestHandlerComponent Object
 *RECURSION*
                                                            [1] => convertXml
                                                        )

                                                )

                                        )

                                    [_viewClassMap:protected] => Array
                                        (
                                            [json] => Json
                                            [xml] => Xml
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                            [checkHttpCache] => 1
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                    [params] => CakeRequest Object
                                        (
                                            [params] => Array
                                                (
                                                    [plugin] => 
                                                    [controller] => analysis
                                                    [action] => custom_tree_creation
                                                    [named] => Array
                                                        (
                                                        )

                                                    [pass] => Array
                                                        (
                                                            [0] => gene_id
                                                            [1] => Cre12.g515850
                                                        )

                                                    [isAjax] => 
                                                )

                                            [data] => Array
                                                (
                                                )

                                            [query] => Array
                                                (
                                                )

                                            [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [base] => /plaza.dev/_dev_instances/feedback
                                            [webroot] => /plaza.dev/_dev_instances/feedback/
                                            [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                                            [_detectors:protected] => Array
                                                (
                                                    [get] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => GET
                                                        )

                                                    [patch] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PATCH
                                                        )

                                                    [post] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => POST
                                                        )

                                                    [put] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => PUT
                                                        )

                                                    [delete] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => DELETE
                                                        )

                                                    [head] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => HEAD
                                                        )

                                                    [options] => Array
                                                        (
                                                            [env] => REQUEST_METHOD
                                                            [value] => OPTIONS
                                                        )

                                                    [ssl] => Array
                                                        (
                                                            [env] => HTTPS
                                                            [value] => 1
                                                        )

                                                    [ajax] => Array
                                                        (
                                                            [env] => HTTP_X_REQUESTED_WITH
                                                            [value] => XMLHttpRequest
                                                        )

                                                    [flash] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [pattern] => /^(Shockwave|Adobe) Flash/
                                                        )

                                                    [mobile] => Array
                                                        (
                                                            [env] => HTTP_USER_AGENT
                                                            [options] => Array
                                                                (
                                                                    [0] => Android
                                                                    [1] => AvantGo
                                                                    [2] => BB10
                                                                    [3] => BlackBerry
                                                                    [4] => DoCoMo
                                                                    [5] => Fennec
                                                                    [6] => iPod
                                                                    [7] => iPhone
                                                                    [8] => iPad
                                                                    [9] => J2ME
                                                                    [10] => MIDP
                                                                    [11] => NetFront
                                                                    [12] => Nokia
                                                                    [13] => Opera Mini
                                                                    [14] => Opera Mobi
                                                                    [15] => PalmOS
                                                                    [16] => PalmSource
                                                                    [17] => portalmmm
                                                                    [18] => Plucker
                                                                    [19] => ReqwirelessWeb
                                                                    [20] => SonyEricsson
                                                                    [21] => Symbian
                                                                    [22] => UP\.Browser
                                                                    [23] => webOS
                                                                    [24] => Windows CE
                                                                    [25] => Windows Phone OS
                                                                    [26] => Xiino
                                                                )

                                                        )

                                                    [requested] => Array
                                                        (
                                                            [param] => requested
                                                            [value] => 1
                                                        )

                                                    [json] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/json
                                                                )

                                                            [param] => ext
                                                            [value] => json
                                                        )

                                                    [xml] => Array
                                                        (
                                                            [accept] => Array
                                                                (
                                                                    [0] => application/xml
                                                                    [1] => text/xml
                                                                )

                                                            [param] => ext
                                                            [value] => xml
                                                        )

                                                )

                                            [_input:protected] => 
                                        )

                                )

                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                    [Blast] => Array
                        (
                            [class] => Blast
                            [settings] => Array
                                (
                                )

                        )

                    [Coordinates] => Array
                        (
                            [class] => Coordinates
                            [settings] => Array
                                (
                                )

                        )

                    [ExternalPrograms] => Array
                        (
                            [class] => ExternalPrograms
                            [settings] => Array
                                (
                                )

                        )

                )

            [controller] => AnalysisController Object
 *RECURSION*
        )

    [RequestHandler] => RequestHandlerComponent Object
        (
            [ajaxLayout] => ajax
            [enabled] => 1
            [request] => CakeRequest Object
                (
                    [params] => Array
                        (
                            [plugin] => 
                            [controller] => analysis
                            [action] => custom_tree_creation
                            [named] => Array
                                (
                                )

                            [pass] => Array
                                (
                                    [0] => gene_id
                                    [1] => Cre12.g515850
                                )

                            [isAjax] => 
                        )

                    [data] => Array
                        (
                        )

                    [query] => Array
                        (
                        )

                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                    [base] => /plaza.dev/_dev_instances/feedback
                    [webroot] => /plaza.dev/_dev_instances/feedback/
                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                    [_detectors:protected] => Array
                        (
                            [get] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => GET
                                )

                            [patch] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PATCH
                                )

                            [post] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => POST
                                )

                            [put] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PUT
                                )

                            [delete] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => DELETE
                                )

                            [head] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => HEAD
                                )

                            [options] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => OPTIONS
                                )

                            [ssl] => Array
                                (
                                    [env] => HTTPS
                                    [value] => 1
                                )

                            [ajax] => Array
                                (
                                    [env] => HTTP_X_REQUESTED_WITH
                                    [value] => XMLHttpRequest
                                )

                            [flash] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                )

                            [mobile] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [options] => Array
                                        (
                                            [0] => Android
                                            [1] => AvantGo
                                            [2] => BB10
                                            [3] => BlackBerry
                                            [4] => DoCoMo
                                            [5] => Fennec
                                            [6] => iPod
                                            [7] => iPhone
                                            [8] => iPad
                                            [9] => J2ME
                                            [10] => MIDP
                                            [11] => NetFront
                                            [12] => Nokia
                                            [13] => Opera Mini
                                            [14] => Opera Mobi
                                            [15] => PalmOS
                                            [16] => PalmSource
                                            [17] => portalmmm
                                            [18] => Plucker
                                            [19] => ReqwirelessWeb
                                            [20] => SonyEricsson
                                            [21] => Symbian
                                            [22] => UP\.Browser
                                            [23] => webOS
                                            [24] => Windows CE
                                            [25] => Windows Phone OS
                                            [26] => Xiino
                                        )

                                )

                            [requested] => Array
                                (
                                    [param] => requested
                                    [value] => 1
                                )

                            [json] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/json
                                        )

                                    [param] => ext
                                    [value] => json
                                )

                            [xml] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/xml
                                            [1] => text/xml
                                        )

                                    [param] => ext
                                    [value] => xml
                                )

                        )

                    [_input:protected] => 
                )

            [response] => CakeResponse Object
                (
                    [_statusCodes:protected] => Array
                        (
                            [100] => Continue
                            [101] => Switching Protocols
                            [200] => OK
                            [201] => Created
                            [202] => Accepted
                            [203] => Non-Authoritative Information
                            [204] => No Content
                            [205] => Reset Content
                            [206] => Partial Content
                            [300] => Multiple Choices
                            [301] => Moved Permanently
                            [302] => Found
                            [303] => See Other
                            [304] => Not Modified
                            [305] => Use Proxy
                            [307] => Temporary Redirect
                            [400] => Bad Request
                            [401] => Unauthorized
                            [402] => Payment Required
                            [403] => Forbidden
                            [404] => Not Found
                            [405] => Method Not Allowed
                            [406] => Not Acceptable
                            [407] => Proxy Authentication Required
                            [408] => Request Time-out
                            [409] => Conflict
                            [410] => Gone
                            [411] => Length Required
                            [412] => Precondition Failed
                            [413] => Request Entity Too Large
                            [414] => Request-URI Too Large
                            [415] => Unsupported Media Type
                            [416] => Requested range not satisfiable
                            [417] => Expectation Failed
                            [429] => Too Many Requests
                            [500] => Internal Server Error
                            [501] => Not Implemented
                            [502] => Bad Gateway
                            [503] => Service Unavailable
                            [504] => Gateway Time-out
                            [505] => Unsupported Version
                        )

                    [_mimeTypes:protected] => Array
                        (
                            [html] => Array
                                (
                                    [0] => text/html
                                    [1] => */*
                                )

                            [json] => application/json
                            [xml] => Array
                                (
                                    [0] => application/xml
                                    [1] => text/xml
                                )

                            [rss] => application/rss+xml
                            [ai] => application/postscript
                            [bcpio] => application/x-bcpio
                            [bin] => application/octet-stream
                            [ccad] => application/clariscad
                            [cdf] => application/x-netcdf
                            [class] => application/octet-stream
                            [cpio] => application/x-cpio
                            [cpt] => application/mac-compactpro
                            [csh] => application/x-csh
                            [csv] => Array
                                (
                                    [0] => text/csv
                                    [1] => application/vnd.ms-excel
                                )

                            [dcr] => application/x-director
                            [dir] => application/x-director
                            [dms] => application/octet-stream
                            [doc] => application/msword
                            [docx] => application/vnd.openxmlformats-officedocument.wordprocessingml.document
                            [drw] => application/drafting
                            [dvi] => application/x-dvi
                            [dwg] => application/acad
                            [dxf] => application/dxf
                            [dxr] => application/x-director
                            [eot] => application/vnd.ms-fontobject
                            [eps] => application/postscript
                            [exe] => application/octet-stream
                            [ez] => application/andrew-inset
                            [flv] => video/x-flv
                            [gtar] => application/x-gtar
                            [gz] => application/x-gzip
                            [bz2] => application/x-bzip
                            [7z] => application/x-7z-compressed
                            [hdf] => application/x-hdf
                            [hqx] => application/mac-binhex40
                            [ico] => image/x-icon
                            [ips] => application/x-ipscript
                            [ipx] => application/x-ipix
                            [js] => application/javascript
                            [jsonapi] => application/vnd.api+json
                            [latex] => application/x-latex
                            [lha] => application/octet-stream
                            [lsp] => application/x-lisp
                            [lzh] => application/octet-stream
                            [man] => application/x-troff-man
                            [me] => application/x-troff-me
                            [mif] => application/vnd.mif
                            [ms] => application/x-troff-ms
                            [nc] => application/x-netcdf
                            [oda] => application/oda
                            [otf] => font/otf
                            [pdf] => application/pdf
                            [pgn] => application/x-chess-pgn
                            [pot] => application/vnd.ms-powerpoint
                            [pps] => application/vnd.ms-powerpoint
                            [ppt] => application/vnd.ms-powerpoint
                            [pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
                            [ppz] => application/vnd.ms-powerpoint
                            [pre] => application/x-freelance
                            [prt] => application/pro_eng
                            [ps] => application/postscript
                            [roff] => application/x-troff
                            [scm] => application/x-lotusscreencam
                            [set] => application/set
                            [sh] => application/x-sh
                            [shar] => application/x-shar
                            [sit] => application/x-stuffit
                            [skd] => application/x-koan
                            [skm] => application/x-koan
                            [skp] => application/x-koan
                            [skt] => application/x-koan
                            [smi] => application/smil
                            [smil] => application/smil
                            [sol] => application/solids
                            [spl] => application/x-futuresplash
                            [src] => application/x-wais-source
                            [step] => application/STEP
                            [stl] => application/SLA
                            [stp] => application/STEP
                            [sv4cpio] => application/x-sv4cpio
                            [sv4crc] => application/x-sv4crc
                            [svg] => image/svg+xml
                            [svgz] => image/svg+xml
                            [swf] => application/x-shockwave-flash
                            [t] => application/x-troff
                            [tar] => application/x-tar
                            [tcl] => application/x-tcl
                            [tex] => application/x-tex
                            [texi] => application/x-texinfo
                            [texinfo] => application/x-texinfo
                            [tr] => application/x-troff
                            [tsp] => application/dsptype
                            [ttc] => font/ttf
                            [ttf] => font/ttf
                            [unv] => application/i-deas
                            [ustar] => application/x-ustar
                            [vcd] => application/x-cdlink
                            [vda] => application/vda
                            [xlc] => application/vnd.ms-excel
                            [xll] => application/vnd.ms-excel
                            [xlm] => application/vnd.ms-excel
                            [xls] => application/vnd.ms-excel
                            [xlsx] => application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
                            [xlw] => application/vnd.ms-excel
                            [zip] => application/zip
                            [aif] => audio/x-aiff
                            [aifc] => audio/x-aiff
                            [aiff] => audio/x-aiff
                            [au] => audio/basic
                            [kar] => audio/midi
                            [mid] => audio/midi
                            [midi] => audio/midi
                            [mp2] => audio/mpeg
                            [mp3] => audio/mpeg
                            [mpga] => audio/mpeg
                            [ogg] => audio/ogg
                            [oga] => audio/ogg
                            [spx] => audio/ogg
                            [ra] => audio/x-realaudio
                            [ram] => audio/x-pn-realaudio
                            [rm] => audio/x-pn-realaudio
                            [rpm] => audio/x-pn-realaudio-plugin
                            [snd] => audio/basic
                            [tsi] => audio/TSP-audio
                            [wav] => audio/x-wav
                            [aac] => audio/aac
                            [asc] => text/plain
                            [c] => text/plain
                            [cc] => text/plain
                            [css] => text/css
                            [etx] => text/x-setext
                            [f] => text/plain
                            [f90] => text/plain
                            [h] => text/plain
                            [hh] => text/plain
                            [htm] => Array
                                (
                                    [0] => text/html
                                    [1] => */*
                                )

                            [ics] => text/calendar
                            [m] => text/plain
                            [rtf] => text/rtf
                            [rtx] => text/richtext
                            [sgm] => text/sgml
                            [sgml] => text/sgml
                            [tsv] => text/tab-separated-values
                            [tpl] => text/template
                            [txt] => text/plain
                            [text] => text/plain
                            [avi] => video/x-msvideo
                            [fli] => video/x-fli
                            [mov] => video/quicktime
                            [movie] => video/x-sgi-movie
                            [mpe] => video/mpeg
                            [mpeg] => video/mpeg
                            [mpg] => video/mpeg
                            [qt] => video/quicktime
                            [viv] => video/vnd.vivo
                            [vivo] => video/vnd.vivo
                            [ogv] => video/ogg
                            [webm] => video/webm
                            [mp4] => video/mp4
                            [m4v] => video/mp4
                            [f4v] => video/mp4
                            [f4p] => video/mp4
                            [m4a] => audio/mp4
                            [f4a] => audio/mp4
                            [f4b] => audio/mp4
                            [gif] => image/gif
                            [ief] => image/ief
                            [jpg] => image/jpeg
                            [jpeg] => image/jpeg
                            [jpe] => image/jpeg
                            [pbm] => image/x-portable-bitmap
                            [pgm] => image/x-portable-graymap
                            [png] => image/png
                            [pnm] => image/x-portable-anymap
                            [ppm] => image/x-portable-pixmap
                            [ras] => image/cmu-raster
                            [rgb] => image/x-rgb
                            [tif] => image/tiff
                            [tiff] => image/tiff
                            [xbm] => image/x-xbitmap
                            [xpm] => image/x-xpixmap
                            [xwd] => image/x-xwindowdump
                            [psd] => Array
                                (
                                    [0] => application/photoshop
                                    [1] => application/psd
                                    [2] => image/psd
                                    [3] => image/x-photoshop
                                    [4] => image/photoshop
                                    [5] => zz-application/zz-winassoc-psd
                                )

                            [ice] => x-conference/x-cooltalk
                            [iges] => model/iges
                            [igs] => model/iges
                            [mesh] => model/mesh
                            [msh] => model/mesh
                            [silo] => model/mesh
                            [vrml] => model/vrml
                            [wrl] => model/vrml
                            [mime] => www/mime
                            [pdb] => chemical/x-pdb
                            [xyz] => chemical/x-pdb
                            [javascript] => application/javascript
                            [form] => application/x-www-form-urlencoded
                            [file] => multipart/form-data
                            [xhtml] => Array
                                (
                                    [0] => application/xhtml+xml
                                    [1] => application/xhtml
                                    [2] => text/xhtml
                                )

                            [xhtml-mobile] => application/vnd.wap.xhtml+xml
                            [atom] => application/atom+xml
                            [amf] => application/x-amf
                            [wap] => Array
                                (
                                    [0] => text/vnd.wap.wml
                                    [1] => text/vnd.wap.wmlscript
                                    [2] => image/vnd.wap.wbmp
                                )

                            [wml] => text/vnd.wap.wml
                            [wmlscript] => text/vnd.wap.wmlscript
                            [wbmp] => image/vnd.wap.wbmp
                            [woff] => application/x-font-woff
                            [webp] => image/webp
                            [appcache] => text/cache-manifest
                            [manifest] => text/cache-manifest
                            [htc] => text/x-component
                            [rdf] => application/xml
                            [crx] => application/x-chrome-extension
                            [oex] => application/x-opera-extension
                            [xpi] => application/x-xpinstall
                            [safariextz] => application/octet-stream
                            [webapp] => application/x-web-app-manifest+json
                            [vcf] => text/x-vcard
                            [vtt] => text/vtt
                            [mkv] => video/x-matroska
                            [pkpass] => application/vnd.apple.pkpass
                            [ajax] => text/html
                        )

                    [_protocol:protected] => HTTP/1.1
                    [_status:protected] => 200
                    [_contentType:protected] => text/html
                    [_headers:protected] => Array
                        (
                        )

                    [_body:protected] => 
                    [_file:protected] => 
                    [_fileRange:protected] => 
                    [_charset:protected] => UTF-8
                    [_cacheDirectives:protected] => Array
                        (
                        )

                    [_cookies:protected] => Array
                        (
                        )

                )

            [ext] => 
            [_renderType:protected] => 
            [_inputTypeMap:protected] => Array
                (
                    [json] => Array
                        (
                            [0] => json_decode
                            [1] => 1
                        )

                    [xml] => Array
                        (
                            [0] => Array
                                (
                                    [0] => RequestHandlerComponent Object
 *RECURSION*
                                    [1] => convertXml
                                )

                        )

                )

            [_viewClassMap:protected] => Array
                (
                    [json] => Json
                    [xml] => Xml
                )

            [_Collection:protected] => ComponentCollection Object
                (
                    [_Controller:protected] => AnalysisController Object
 *RECURSION*
                    [_enabled:protected] => Array
                        (
                            [Session] => Array
                                (
                                    [0] => 10
                                    [1] => 1
                                )

                            [DataUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 2
                                )

                            [FunctionalAnnotationUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 3
                                )

                            [GeneFamilies] => Array
                                (
                                    [0] => 10
                                    [1] => 4
                                )

                            [Organism] => Array
                                (
                                    [0] => 10
                                    [1] => 5
                                )

                            [Blast] => Array
                                (
                                    [0] => 10
                                    [1] => 6
                                )

                            [WorkbenchUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 7
                                )

                            [PhylogeneticModuleUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 8
                                )

                            [ExternalPrograms] => Array
                                (
                                    [0] => 10
                                    [1] => 9
                                )

                            [FastaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 10
                                )

                            [MsaUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 11
                                )

                            [PhylogeneticUtils] => Array
                                (
                                    [0] => 10
                                    [1] => 12
                                )

                            [Sequence] => Array
                                (
                                    [0] => 10
                                    [1] => 13
                                )

                            [RequestHandler] => Array
                                (
                                    [0] => 10
                                    [1] => 14
                                )

                        )

                    [_loaded:protected] => Array
                        (
                            [Session] => SessionComponent Object
                                (
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [DataUtils] => DataUtilsComponent Object
                                (
                                    [name] => DataUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FunctionalUtils
                                            [2] => GeneFamilies
                                            [3] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [GeneFamilies] => GeneFamiliesComponent Object
                                        (
                                            [name] => GeneFamilies
                                            [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                            [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                            [settings] => Array
                                                (
                                                )

                                            [components] => Array
                                                (
                                                )

                                            [_componentMap:protected] => Array
                                                (
                                                )

                                        )

                                )

                            [FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
                                (
                                    [name] => FunctionalAnnotationUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => FunctionalUtils
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [GeneFamilies] => GeneFamiliesComponent Object
                                (
                                    [name] => GeneFamilies
                                    [controller:GeneFamiliesComponent:private] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [Organism] => OrganismComponent Object
                                (
                                    [name] => Organism
                                    [controller:OrganismComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => GenomeBrowser
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [GenomeBrowser] => Array
                                                (
                                                    [class] => GenomeBrowser
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Blast] => BlastComponent Object
                                (
                                    [name] => Blast
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [WorkbenchUtils] => WorkbenchUtilsComponent Object
                                (
                                    [name] => WorkbenchUtils
                                    [controller:WorkbenchUtilsComponent:private] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FormUtils
                                            [2] => FunctionalUtils
                                            [3] => GeneFamilies
                                            [4] => WorkbenchSharedAccessRights
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FormUtils] => Array
                                                (
                                                    [class] => FormUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FunctionalUtils] => Array
                                                (
                                                    [class] => FunctionalUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [GeneFamilies] => Array
                                                (
                                                    [class] => GeneFamilies
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [WorkbenchSharedAccessRights] => Array
                                                (
                                                    [class] => WorkbenchSharedAccessRights
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
                                (
                                    [name] => PhylogeneticModuleUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                            [1] => FastaUtils
                                            [2] => MsaUtils
                                            [3] => PhylogeneticUtils
                                            [4] => Sequence
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [MsaUtils] => Array
                                                (
                                                    [class] => MsaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [PhylogeneticUtils] => Array
                                                (
                                                    [class] => PhylogeneticUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Sequence] => Array
                                                (
                                                    [class] => Sequence
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [ExternalPrograms] => ExternalProgramsComponent Object
                                (
                                    [name] => ExternalPrograms
                                    [components] => Array
                                        (
                                            [0] => FastaUtils
                                        )

                                    [program_paths:ExternalProgramsComponent:private] => Array
                                        (
                                            [java] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => java/x86_64/21.0.2
                                                                )

                                                            [command] => java -Djava.awt.headless=true
                                                        )

                                                    [local_settings] => java -Djava.awt.headless=true
                                                    [db_connector] => mysql-connector-java-8.0.21.jar
                                                )

                                            [perl] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => perl
                                                                )

                                                            [command] => perl -w
                                                        )

                                                    [local_settings] => /usr/bin/perl
                                                )

                                            [bash] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [bedops] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => bedops/x86_64/2.4.37
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => 
                                                )

                                            [blastdbcmd] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => blastdbcmd
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
                                                )

                                            [blast] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => blast
                                                                )

                                                            [command] => 
                                                        )

                                                    [local_settings] => /usr/local/blast/2.2.24/bin/
                                                )

                                            [muscle] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => muscle/x86_64/3.8.31
                                                                )

                                                        )

                                                )

                                            [mafft] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => mafft/x86_64/7.187
                                                                )

                                                        )

                                                )

                                            [phyml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => phyml/x86_64/20150219
                                                                )

                                                        )

                                                )

                                            [fasttree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => fasttree/x86_64/2.1.7
                                                                )

                                                        )

                                                )

                                            [raxml] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => raxml/x86_64/8.2.8
                                                                )

                                                        )

                                                )

                                            [iqtree] => Array
                                                (
                                                    [cluster_settings] => Array
                                                        (
                                                            [modules] => Array
                                                                (
                                                                    [0] => iqtree/x86_64/1.5.5
                                                                )

                                                        )

                                                )

                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [FastaUtils] => Array
                                                (
                                                    [class] => FastaUtils
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [FastaUtils] => FastaUtilsComponent Object
                                (
                                    [name] => FastaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [MsaUtils] => MsaUtilsComponent Object
                                (
                                    [name] => MsaUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [components] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                        )

                                )

                            [PhylogeneticUtils] => PhylogeneticUtilsComponent Object
                                (
                                    [name] => PhylogeneticUtils
                                    [controller] => AnalysisController Object
 *RECURSION*
                                    [components] => Array
                                        (
                                            [0] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                )

                            [Sequence] => SequenceComponent Object
                                (
                                    [name] => Sequence
                                    [components] => Array
                                        (
                                            [0] => Blast
                                            [1] => Coordinates
                                            [2] => ExternalPrograms
                                        )

                                    [_Collection:protected] => ComponentCollection Object
 *RECURSION*
                                    [settings] => Array
                                        (
                                        )

                                    [_componentMap:protected] => Array
                                        (
                                            [Blast] => Array
                                                (
                                                    [class] => Blast
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [Coordinates] => Array
                                                (
                                                    [class] => Coordinates
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                            [ExternalPrograms] => Array
                                                (
                                                    [class] => ExternalPrograms
                                                    [settings] => Array
                                                        (
                                                        )

                                                )

                                        )

                                    [controller] => AnalysisController Object
 *RECURSION*
                                )

                            [RequestHandler] => RequestHandlerComponent Object
 *RECURSION*
                        )

                    [defaultPriority] => 10
                )

            [settings] => Array
                (
                    [checkHttpCache] => 1
                )

            [components] => Array
                (
                )

            [_componentMap:protected] => Array
                (
                )

            [params] => CakeRequest Object
                (
                    [params] => Array
                        (
                            [plugin] => 
                            [controller] => analysis
                            [action] => custom_tree_creation
                            [named] => Array
                                (
                                )

                            [pass] => Array
                                (
                                    [0] => gene_id
                                    [1] => Cre12.g515850
                                )

                            [isAjax] => 
                        )

                    [data] => Array
                        (
                        )

                    [query] => Array
                        (
                        )

                    [url] => analysis/custom_tree_creation/gene_id/Cre12.g515850
                    [base] => /plaza.dev/_dev_instances/feedback
                    [webroot] => /plaza.dev/_dev_instances/feedback/
                    [here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/Cre12.g515850
                    [_detectors:protected] => Array
                        (
                            [get] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => GET
                                )

                            [patch] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PATCH
                                )

                            [post] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => POST
                                )

                            [put] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => PUT
                                )

                            [delete] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => DELETE
                                )

                            [head] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => HEAD
                                )

                            [options] => Array
                                (
                                    [env] => REQUEST_METHOD
                                    [value] => OPTIONS
                                )

                            [ssl] => Array
                                (
                                    [env] => HTTPS
                                    [value] => 1
                                )

                            [ajax] => Array
                                (
                                    [env] => HTTP_X_REQUESTED_WITH
                                    [value] => XMLHttpRequest
                                )

                            [flash] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [pattern] => /^(Shockwave|Adobe) Flash/
                                )

                            [mobile] => Array
                                (
                                    [env] => HTTP_USER_AGENT
                                    [options] => Array
                                        (
                                            [0] => Android
                                            [1] => AvantGo
                                            [2] => BB10
                                            [3] => BlackBerry
                                            [4] => DoCoMo
                                            [5] => Fennec
                                            [6] => iPod
                                            [7] => iPhone
                                            [8] => iPad
                                            [9] => J2ME
                                            [10] => MIDP
                                            [11] => NetFront
                                            [12] => Nokia
                                            [13] => Opera Mini
                                            [14] => Opera Mobi
                                            [15] => PalmOS
                                            [16] => PalmSource
                                            [17] => portalmmm
                                            [18] => Plucker
                                            [19] => ReqwirelessWeb
                                            [20] => SonyEricsson
                                            [21] => Symbian
                                            [22] => UP\.Browser
                                            [23] => webOS
                                            [24] => Windows CE
                                            [25] => Windows Phone OS
                                            [26] => Xiino
                                        )

                                )

                            [requested] => Array
                                (
                                    [param] => requested
                                    [value] => 1
                                )

                            [json] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/json
                                        )

                                    [param] => ext
                                    [value] => json
                                )

                            [xml] => Array
                                (
                                    [accept] => Array
                                        (
                                            [0] => application/xml
                                            [1] => text/xml
                                        )

                                    [param] => ext
                                    [value] => xml
                                )

                        )

                    [_input:protected] => 
                )

        )

    [Annotation] => Annotation Object
        (
            [name] => Annotation
            [useTable] => annotation
            [primaryKey] => gene_id
            [cacheQueries] => 
            [cacheSources] => 
            [belongsTo] => Array
                (
                    [AnnotSource] => Array
                        (
                            [foreignKey] => species
                            [className] => AnnotSource
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                )

            [hasMany] => Array
                (
                    [GfDatum] => Array
                        (
                            [foreignKey] => gene_id
                            [className] => GfDatum
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [limit] => 
                            [offset] => 
                            [dependent] => 
                            [exclusive] => 
                            [finderQuery] => 
                            [counterQuery] => 
                        )

                )

            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => annotation
            [_schema:protected] => Array
                (
                    [gene_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [transcript] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [coord_cds] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [start] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [stop] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [coord_transcript] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [seq] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [strand] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 1
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [chr] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [type] => Array
                        (
                            [type] => enum('coding','rna','te','pseudo')
                            [null] => 
                            [default] => coding
                            [length] => 6
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [check_transcript] => Array
                        (
                            [type] => enum('none','ne','eq')
                            [null] => 
                            [default] => none
                            [length] => 4
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [check_protein] => Array
                        (
                            [type] => enum('none','ne','eq')
                            [null] => 
                            [default] => none
                            [length] => 4
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [transl_table] => Array
                        (
                            [type] => tinyinteger
                            [null] => 
                            [default] => 1
                            [length] => 
                            [unsigned] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Annotation
            [tableToModel] => Array
                (
                    [annotation] => Annotation
                )

            [hasOne] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Annotation
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
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                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
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                                                    [passParams] => 
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                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Annotation
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Annotation Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [Configuration] => Configuration Object
        (
            [name] => Configuration
            [useTable] => configuration
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => configuration
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [method] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [key] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 255
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [value] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [comment] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Configuration
            [tableToModel] => Array
                (
                    [configuration] => Configuration
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Configuration
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Configuration
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Configuration Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [AnnotSource] => AnnotSource Object
        (
            [name] => AnnotSource
            [useTable] => annot_sources
            [primaryKey] => species
            [displayField] => common_name
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => annot_sources
            [_schema:protected] => Array
                (
                    [source] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 255
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [url] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 250
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [common_name] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 100
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [eco_type] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 100
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [description] => Array
                        (
                            [type] => text
                            [null] => 
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [paper] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [pubmed_id] => Array
                        (
                            [type] => integer
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [tax_id] => Array
                        (
                            [type] => integer
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                    [mitochondrion] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 15
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [chloroplast] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 15
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [disclaimer] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => AnnotSource
            [tableToModel] => Array
                (
                    [annot_sources] => AnnotSource
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => AnnotSource
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => AnnotSource
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => AnnotSource Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [GeneFamilyTypes] => GeneFamilyTypes Object
        (
            [name] => GeneFamilyTypes
            [useTable] => gene_family_types
            [primaryKey] => id
            [displayField] => name
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => gene_family_types
            [_schema:protected] => Array
                (
                    [id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [comment] => unique identifier for this gene family type. foreign key to other GF tables
                            [charset] => latin1
                        )

                    [name] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [collate] => latin1_swedish_ci
                            [comment] => description of gene family type
                            [charset] => latin1
                        )

                    [prefix] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [collate] => latin1_swedish_ci
                            [comment] => prefix used for building the gf type. for compatibility reasons. shouldn't be used.
                            [charset] => latin1
                        )

                    [gene_type] => Array
                        (
                            [type] => enum('coding','rna','pseudo','te')
                            [null] => 
                            [default] => coding
                            [length] => 6
                            [collate] => latin1_swedish_ci
                            [comment] => should match type from table annotation
                            [charset] => latin1
                        )

                    [method] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 500
                            [collate] => latin1_swedish_ci
                            [comment] => JSON style information of the building method+parameters used
                            [charset] => latin1
                        )

                    [ancestry] => Array
                        (
                            [type] => enum('homology','orthology','homeology','other')
                            [null] => 
                            [default] => homology
                            [length] => 9
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [comment] => type of gene family content
                            [charset] => latin1
                        )

                    [parent_id] => Array
                        (
                            [type] => string
                            [null] => 1
                            [default] => 
                            [length] => 10
                            [collate] => latin1_swedish_ci
                            [comment] => link to the parent id if appropriate
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => GeneFamilyTypes
            [tableToModel] => Array
                (
                    [gene_family_types] => GeneFamilyTypes
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => GeneFamilyTypes
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GeneFamilyTypes
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GeneFamilyTypes Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [Similarities] => Similarities Object
        (
            [name] => Similarities
            [useTable] => similarities
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => similarities
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [query] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [hits] => Array
                        (
                            [type] => binary
                            [null] => 
                            [default] => 
                            [length] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => Similarities
            [tableToModel] => Array
                (
                    [similarities] => Similarities
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Similarities
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => Similarities
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => Similarities Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [GfDatum] => GfDatum Object
        (
            [name] => GfDatum
            [useTable] => gf_data
            [belongsTo] => Array
                (
                    [Annotation] => Array
                        (
                            [className] => Annotation
                            [foreignKey] => gene_id
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                    [Genefamily] => Array
                        (
                            [className] => GeneFamily
                            [foreignKey] => gf_id
                            [conditions] => 
                            [fields] => 
                            [order] => 
                            [counterCache] => 
                        )

                )

            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => gf_data
            [primaryKey] => id
            [_schema:protected] => Array
                (
                    [gf_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [gf_type] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 10
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [comment] => links to gene_family_types id
                            [charset] => latin1
                        )

                    [species] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 21
                            [key] => index
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [gene_id] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 50
                            [key] => primary
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [synteny_data] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [cluster_data] => Array
                        (
                            [type] => float
                            [null] => 1
                            [default] => 
                            [length] => 
                            [unsigned] => 
                        )

                    [outlier] => Array
                        (
                            [type] => smallinteger
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => GfDatum
            [tableToModel] => Array
                (
                    [gf_data] => GfDatum
                )

            [cacheQueries] => 
            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => GfDatum
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => beforeFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => afterFind
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => beforeValidate
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterValidate] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => afterValidate
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                            [Model.beforeSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => beforeSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterSave] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => afterSave
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.beforeDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => beforeDelete
                                                        )

                                                    [passParams] => 1
                                                )

                                        )

                                )

                            [Model.afterDelete] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => BehaviorCollection Object
                                                                (
                                                                    [modelName] => GfDatum
                                                                    [_methods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_mappedMethods:protected] => Array
                                                                        (
                                                                        )

                                                                    [_enabled:protected] => Array
                                                                        (
                                                                        )

                                                                    [_loaded:protected] => Array
                                                                        (
                                                                        )

                                                                    [defaultPriority] => 10
                                                                )

                                                            [1] => trigger
                                                        )

                                                    [passParams] => 
                                                )

                                            [1] => Array
                                                (
                                                    [callable] => Array
                                                        (
                                                            [0] => GfDatum Object
 *RECURSION*
                                                            [1] => afterDelete
                                                        )

                                                    [passParams] => 
                                                )

                                        )

                                )

                        )

                    [_isGlobal:protected] => 
                )

            [_validator:protected] => 
        )

    [AdExperiments] => AdExperiments Object
        (
            [name] => AdExperiments
            [useTable] => ad_experiments
            [primaryKey] => exp_id
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => db_plaza_public_dicots_05
            [table] => ad_experiments
            [_schema:protected] => Array
                (
                    [exp_id] => Array
                        (
                            [type] => smallinteger
                            [null] => 
                            [default] => 0
                            [length] => 
                            [unsigned] => 1
                            [key] => primary
                        )

                    [description] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 255
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [description_advanced] => Array
                        (
                            [type] => text
                            [null] => 1
                            [default] => 
                            [length] => 
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [organisms] => Array
                        (
                            [type] => string
                            [null] => 
                            [default] => 
                            [length] => 512
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                    [to_show] => Array
                        (
                            [type] => enum('true','false')
                            [null] => 
                            [default] => false
                            [length] => 5
                            [collate] => latin1_swedish_ci
                            [charset] => latin1
                        )

                )

            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [tablePrefix] => 
            [plugin] => 
            [alias] => AdExperiments
            [tableToModel] => Array
                (
                    [ad_experiments] => AdExperiments
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => AdExperiments
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 1
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => CakeEventManager Object
                (
                    [_listeners:protected] => Array
                        (
                            [Model.beforeFind] => Array
                                (
                                    [10] => Array
                                        (
                                            [0] => Array
                                                (
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            [schemaName] => db_plaza_public_dicots_05
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            [actsAs] => 
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                )

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            [_associations:protected] => Array
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            [_eventManager:protected] => CakeEventManager Object
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                                                            [1] => trigger
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                                                                    [_loaded:protected] => Array
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                                                                        )

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                                                            [1] => trigger
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                                            [1] => Array
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                                                    [passParams] => 
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    [Msa] => Msa Object
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            [schemaName] => 
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            [validationErrors] => Array
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            [validationDomain] => 
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            [hasAndBelongsToMany] => Array
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            [actsAs] => 
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            [_associations:protected] => Array
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                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => 
            [_validator:protected] => 
        )

    [Trees] => Trees Object
        (
            [name] => Trees
            [useTable] => trees
            [useDbConfig] => default
            [id] => 
            [data] => Array
                (
                )

            [schemaName] => 
            [table] => trees
            [primaryKey] => id
            [_schema:protected] => 
            [validate] => Array
                (
                )

            [validationErrors] => Array
                (
                )

            [validationDomain] => 
            [plugin] => 
            [alias] => Trees
            [tableToModel] => Array
                (
                    [trees] => Trees
                )

            [cacheQueries] => 
            [belongsTo] => Array
                (
                )

            [hasOne] => Array
                (
                )

            [hasMany] => Array
                (
                )

            [hasAndBelongsToMany] => Array
                (
                )

            [actsAs] => 
            [Behaviors] => BehaviorCollection Object
                (
                    [modelName] => Trees
                    [_methods:protected] => Array
                        (
                        )

                    [_mappedMethods:protected] => Array
                        (
                        )

                    [_enabled:protected] => Array
                        (
                        )

                    [_loaded:protected] => Array
                        (
                        )

                    [defaultPriority] => 10
                )

            [whitelist] => Array
                (
                )

            [cacheSources] => 1
            [findQueryType] => 
            [recursive] => 1
            [order] => 
            [virtualFields] => Array
                (
                )

            [_associationKeys:protected] => Array
                (
                    [belongsTo] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => counterCache
                        )

                    [hasOne] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => dependent
                        )

                    [hasMany] => Array
                        (
                            [0] => className
                            [1] => foreignKey
                            [2] => conditions
                            [3] => fields
                            [4] => order
                            [5] => limit
                            [6] => offset
                            [7] => dependent
                            [8] => exclusive
                            [9] => finderQuery
                            [10] => counterQuery
                        )

                    [hasAndBelongsToMany] => Array
                        (
                            [0] => className
                            [1] => joinTable
                            [2] => with
                            [3] => foreignKey
                            [4] => associationForeignKey
                            [5] => conditions
                            [6] => fields
                            [7] => order
                            [8] => limit
                            [9] => offset
                            [10] => unique
                            [11] => finderQuery
                        )

                )

            [_associations:protected] => Array
                (
                    [0] => belongsTo
                    [1] => hasOne
                    [2] => hasMany
                    [3] => hasAndBelongsToMany
                )

            [__backAssociation] => Array
                (
                )

            [__backInnerAssociation] => Array
                (
                )

            [__backOriginalAssociation] => Array
                (
                )

            [__backContainableAssociation] => Array
                (
                )

            [__safeUpdateMode] => 
            [useConsistentAfterFind] => 1
            [_insertID:protected] => 
            [_sourceConfigured:protected] => 
            [findMethods] => Array
                (
                    [all] => 1
                    [first] => 1
                    [count] => 1
                    [neighbors] => 1
                    [list] => 1
                    [threaded] => 1
                )

            [_eventManager:protected] => 
            [_validator:protected] => 
        )

)
controller
Notice (8): Trying to get property 'Configuration' of non-object [APP/Controller/Component/GenomeBrowserComponent.php, line 105]
Errors

Call to a member function getBasicSpeciesTree() on null

Error: An Internal Error Has Occurred.

Stack Trace

  • APP/Controller/Component/DataUtilsComponent.php line 65GenomeBrowserComponent->getValidatedDataSettings()
  • APP/Controller/AppController.php line 94DataUtilsComponent->getSidebarToolsInfo()
  • CORE/Cake/Event/CakeEventManager.php line 243AppController->beforeRender()
  • CORE/Cake/Controller/Controller.php line 936CakeEventManager->dispatch()
  • CORE/Cake/Routing/Dispatcher.php line 200Controller->render()
  • CORE/Cake/Routing/Dispatcher.php line 167Dispatcher->_invoke()
  • APP/webroot/index.php line 151Dispatcher->dispatch()