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
(
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(
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)
)
[COL.COLO4_19083] => Array
(
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(
[HOMFAM] => HOM05D002404
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)
)
[Phvul.006G137800] => Array
(
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(
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)
)
[unitig_747.g22020] => Array
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(
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)
)
[PGR102G0182] => Array
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(
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)
)
[THA.LOC104826301] => Array
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(
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)
)
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(
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)
)
[CANSAT54G2750] => Array
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(
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)
)
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(
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)
)
[HanXRQChr01g0011001] => Array
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(
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)
)
[Oeu049279.1] => Array
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)
)
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(
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(
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)
)
[CARHR122910] => Array
(
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(
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)
)
[Cfa011630] => Array
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(
[HOMFAM] => HOM05D002404
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)
)
[PRCOL_00005339] => Array
(
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(
[HOMFAM] => HOM05D002404
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)
)
[Hund18869] => Array
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(
[HOMFAM] => HOM05D002404
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)
)
[TAR636G2785] => Array
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(
[HOMFAM] => HOM05D002404
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)
)
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(
[HOMFAM] => HOM05D002404
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)
)
[Actinidia33951] => Array
(
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(
[HOMFAM] => HOM05D002404
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)
)
[Migut.D02143] => Array
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(
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)
)
[Eucgr.J01951] => Array
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(
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)
)
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)
)
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(
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)
)
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)
)
[Ca_14888_v3] => Array
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)
)
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(
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)
)
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(
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)
)
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)
)
[Lj6g0014589] => Array
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(
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)
)
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)
)
[MSTRG.21172] => Array
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(
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)
)
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)
)
[Glyma.18G067800] => Array
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(
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)
)
[CSS0029507] => Array
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(
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)
)
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)
)
[Lsat_1_v5_gn_8_12580] => Array
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(
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)
)
[Sc12g0001020] => Array
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[species] => sci
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(
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)
)
[CiPaw.13G083600] => Array
(
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(
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)
)
[SEGI_13348] => Array
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(
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)
)
[TWI31G0565] => Array
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(
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)
)
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[species] => aly
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(
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)
)
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(
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)
)
[CSS0001422] => Array
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(
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)
)
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(
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)
)
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(
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)
)
[Lj2A1074T37] => Array
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(
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)
)
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(
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)
)
[PSO384G1519] => Array
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(
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)
)
[PSO585G0022] => Array
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(
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)
)
[Rhsim01G0234200] => Array
(
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(
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)
)
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[species] => sed
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(
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)
[vmacro14574] => Array
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(
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)
)
[Zm00001eb192050] => Array
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(
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)
)
[Carub.0004s1063] => Array
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[species] => cru
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[gf] => Array
(
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)
)
[MELO3C025879.2] => Array
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[species] => cme
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(
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)
)
[Duzib150G0009] => Array
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[alignment_length] => 267
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[species] => dzi
[common_name] => Durio zibethinus
[gf] => Array
(
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)
)
[Manes.02G123000] => Array
(
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[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
(
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[species] => mtr
[common_name] => Medicago truncatula
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(
[HOMFAM] => HOM05D002404
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)
)
[PGR119G1764] => Array
(
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[species] => pgr
[common_name] => Punica granatum
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(
[HOMFAM] => HOM05D002404
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)
)
[Sed0018009] => Array
(
[gene_id] => Sed0018009
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[species] => sed
[common_name] => Sechium edule
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(
[HOMFAM] => HOM05D002404
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)
)
[Ah.14g082670] => Array
(
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[species] => amhyb
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(
[HOMFAM] => HOM05D002404
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)
)
[ATR0680G321] => Array
(
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[species] => atr
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(
[HOMFAM] => HOM05D002404
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)
)
[CsaV3_6G016510] => Array
(
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[species] => csa
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(
[HOMFAM] => HOM05D002404
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)
)
[Duzib170G0557] => Array
(
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[species] => dzi
[common_name] => Durio zibethinus
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[Lsat_1_v5_gn_8_72200] => Array
(
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[species] => lsa
[common_name] => Lactuca sativa
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[PGR044G0110] => Array
(
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[identity_percentage] => 61.3
[species] => pgr
[common_name] => Punica granatum
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(
[HOMFAM] => HOM05D002404
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)
)
[TAR633G0461] => Array
(
[gene_id] => TAR633G0461
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[species] => tar
[common_name] => Trochodendron aralioides
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[vmacro07002] => Array
(
[gene_id] => vmacro07002
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[species] => vma
[common_name] => Vaccinium macrocarpon
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(
[HOMFAM] => HOM05D002404
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)
)
[AL4G24290] => Array
(
[gene_id] => AL4G24290
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[species] => aly
[common_name] => Arabidopsis lyrata
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[CARHR007080] => Array
(
[gene_id] => CARHR007080
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[alignment_length] => 259
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[species] => chi
[common_name] => Cardamine hirsuta
[gf] => Array
(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[AUR62001707] => Array
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[gene_id] => AUR62001707
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[species] => cqu
[common_name] => Chenopodium quinoa
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(
[HOMFAM] => HOM05D002404
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)
)
[AUR62020074] => Array
(
[gene_id] => AUR62020074
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[species] => cqu
[common_name] => Chenopodium quinoa
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[MBI14_g32930_MAGBIO] => Array
(
[gene_id] => MBI14_g32930_MAGBIO
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[bit_score] => 349.4
[alignment_length] => 266
[identity_percentage] => 59.8
[species] => mbi
[common_name] => Magnolia biondii
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[Nitab4.5_0000744g0120] => Array
(
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[alignment_length] => 260
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[species] => nta
[common_name] => Nicotiana tabacum
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(
[HOMFAM] => HOM05D002404
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)
)
[Peaxi162Scf01058g00150] => Array
(
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[alignment_length] => 260
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[species] => pax
[common_name] => Petunia axillaris
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(
[HOMFAM] => HOM05D002404
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)
)
[SMO172G0020] => Array
(
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[species] => smo
[common_name] => Selaginella moellendorffii
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(
[HOMFAM] => HOM05D002404
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)
)
[TPR.G30115] => Array
(
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[species] => tpr
[common_name] => Trifolium pratense
[gf] => Array
(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[C04p21270] => Array
(
[gene_id] => C04p21270
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[species] => bna
[common_name] => Brassica napus
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(
[HOMFAM] => HOM05D002404
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)
)
[BolC4t23656H] => Array
(
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[species] => bol
[common_name] => Brassica oleracea
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[ECA233G2070] => Array
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[species] => eca
[common_name] => Erigeron canadensis
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(
[HOMFAM] => HOM05D002404
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)
)
[Lalb_Chr15g0082601] => Array
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[species] => lal
[common_name] => Lupinus albus
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(
[HOMFAM] => HOM05D002404
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)
)
[Nitab4.5_0011134g0030] => Array
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[species] => nta
[common_name] => Nicotiana tabacum
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(
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)
)
[Pp3c12_18160] => Array
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[species] => ppa
[common_name] => Physcomitrium patens
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(
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)
)
[THA.LOC104815801] => Array
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[species] => tha
[common_name] => Tarenaya hassleriana
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)
)
[TWI75G1109] => Array
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[species] => twi
[common_name] => Tripterygium wilfordii
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(
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)
)
[QL01p029015] => Array
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(
[HOMFAM] => HOM05D002404
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)
)
[AT2G29570] => Array
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[species] => ath
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)
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[BcaB02g10263] => Array
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[HOMFAM] => HOM05D002404
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)
)
[Lalb_Chr18g0050611] => Array
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[species] => lal
[common_name] => Lupinus albus
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)
)
[Sp4g12300] => Array
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[species] => spa
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(
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)
)
[SGA_v2.0_scaffold77G25326] => Array
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[species] => sas
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(
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)
)
[Ah.08g220430] => Array
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(
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)
)
[A05p15830] => Array
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[species] => bna
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(
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)
[BraA05t20496Z] => Array
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[species] => bra
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(
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)
)
[ClCG02G019790] => Array
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[species] => cla
[common_name] => Citrullus lanatus
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(
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)
)
[Prupe.6G063300] => Array
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[species] => ppe
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(
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)
)
[Thhalv10017099m.g] => Array
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[species] => esa
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(
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)
)
[Psat5g162720] => Array
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[species] => psa
[common_name] => Pisum sativum
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(
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)
)
[Zm00001eb258230] => Array
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[species] => zma
[common_name] => Zea mays
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(
[HOMFAM] => HOM05D002404
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)
)
[FvH4_3g37710] => Array
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[species] => fve
[common_name] => Fragaria vesca
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(
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)
)
[FAN16G1397] => Array
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[species] => fan
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(
[HOMFAM] => HOM05D002404
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)
)
[FAN21G0265] => Array
(
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[species] => fan
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(
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)
)
[Sp1g06120] => Array
(
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[alignment_length] => 259
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[species] => spa
[common_name] => Schrenkiella parvula
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[BcaC07g42462] => Array
(
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[species] => bca
[common_name] => Brassica carinata
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[FAN11G3986] => Array
(
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[alignment_length] => 260
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[species] => fan
[common_name] => Fragaria x ananassa
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[ATR0618G446] => Array
(
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[bit_score] => 345.9
[alignment_length] => 258
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[species] => atr
[common_name] => Amborella trichopoda
[gf] => Array
(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[Thhalv10008509m.g] => Array
(
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[bit_score] => 345.9
[alignment_length] => 259
[identity_percentage] => 60.2
[species] => esa
[common_name] => Eutrema salsugineum
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(
[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
)
[Hma1.2p1_0710F.1_g207410] => Array
(
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[bit_score] => 345.9
[alignment_length] => 267
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[species] => hma
[common_name] => Hydrangea macrophylla
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[RcHm_v2.0_Chr5g0067981] => Array
(
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[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
(
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[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
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[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
(
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[bit_score] => 345.5
[alignment_length] => 260
[identity_percentage] => 59.6
[species] => bol
[common_name] => Brassica oleracea
[gf] => Array
(
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)
)
[BraA09t41985Z] => Array
(
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[species] => bra
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(
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)
)
[Solyc06g076660.3] => Array
(
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[species] => sly
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(
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)
)
[Sopen06g033050] => Array
(
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[species] => spe
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(
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)
)
[PGSC0003DMG400030432] => Array
(
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[species] => stu
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(
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)
)
[CAN.G394.99] => Array
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[species] => can
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)
)
[Cc02_g07010] => Array
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)
)
[DCAR_007406] => Array
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[species] => dca
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(
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)
)
[Dinv34434] => Array
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[species] => din
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)
)
[FvH4_6g24870] => Array
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)
)
[FAN05G4258] => Array
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)
)
[Sabra16G0150400] => Array
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[species] => sbr
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(
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)
)
[Cc01_g13700] => Array
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[species] => ccan
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(
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)
)
[MD03G1078300] => Array
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[species] => mdo
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(
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)
)
[Rhsim03G0139300] => Array
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(
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)
)
[Aa31LG5G6890] => Array
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[species] => aar
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(
[HOMFAM] => HOM05D002404
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)
)
[FAN25G0398] => Array
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[species] => fan
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)
)
[MBI18_g09770_MAGBIO] => Array
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[species] => mbi
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(
[HOMFAM] => HOM05D002404
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)
)
[MD11G1083000] => Array
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[species] => mdo
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(
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)
)
[MD13G1227300] => Array
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(
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)
)
[FAN14G3520] => Array
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[species] => fan
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(
[HOMFAM] => HOM05D002404
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)
)
[SGA_v2.0_scaffold95G28680] => Array
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(
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)
)
[arahy.Tifrunner.gnm1.ann1.6QL4ST] => Array
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[species] => arhy
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(
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)
)
[arahy.Tifrunner.gnm1.ann1.L4PA5N] => Array
(
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(
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)
)
[arahy.Tifrunner.gnm1.ann1.U7GG8I] => Array
(
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)
)
[Mapoly0075s0032] => Array
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[species] => mpo
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)
)
[ClCG07G003870] => Array
(
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[species] => cla
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)
)
[CsaV3_5G008820] => Array
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[species] => csa
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(
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)
)
[DCAR_011777] => Array
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(
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)
)
[Potri.009G040900] => Array
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[species] => ptr
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(
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)
)
[Oeu032673.1] => Array
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[species] => oeu
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(
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)
)
[Sc10g0002110] => Array
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[species] => sci
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(
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)
)
[SGA_v2.0_scaffold2G01058] => Array
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(
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)
)
[arahy.Tifrunner.gnm1.ann1.PUR3G8] => Array
(
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[alignment_length] => 265
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(
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)
)
[Mapoly0086s0078] => Array
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[species] => mpo
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(
[HOMFAM] => HOM05D002404
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)
)
[Sed0017261] => Array
(
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[species] => sed
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(
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)
)
[Lj1A143T40] => Array
(
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[identity_percentage] => 59.2
[species] => lonja
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(
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)
)
[EL10Ac7g16103] => Array
(
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[alignment_length] => 295
[identity_percentage] => 53.2
[species] => bvu
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(
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)
)
[AUR62022826] => Array
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[alignment_length] => 259
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[species] => cqu
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(
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)
)
[AUR62012192] => Array
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[alignment_length] => 258
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[species] => cqu
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(
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)
)
[Rhsim01G0234300] => Array
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[alignment_length] => 259
[identity_percentage] => 59.1
[species] => rsi
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(
[HOMFAM] => HOM05D002404
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)
)
[Ah.10g036710] => Array
(
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[alignment_length] => 268
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[species] => amhyb
[common_name] => Amaranthus hybridus
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(
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)
)
[MELO3C025142.2] => Array
(
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[alignment_length] => 260
[identity_percentage] => 58.1
[species] => cme
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(
[HOMFAM] => HOM05D002404
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)
)
[QL08p062470] => Array
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[alignment_length] => 322
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[species] => qlo
[common_name] => Quercus lobata
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(
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)
)
[TPR.G15751] => Array
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[alignment_length] => 259
[identity_percentage] => 57.9
[species] => tpr
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[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[Dinv14480] => Array
(
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[alignment_length] => 222
[identity_percentage] => 64.4
[species] => din
[common_name] => Davidia involucrata
[gf] => Array
(
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)
)
[GSVIVG01024815001] => Array
(
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[bit_score] => 307.8
[alignment_length] => 227
[identity_percentage] => 62.1
[species] => vvi
[common_name] => Vitis vinifera
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[EL10Ac2g04771] => Array
(
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[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
(
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[bit_score] => 303.5
[alignment_length] => 221
[identity_percentage] => 63.8
[species] => mbi
[common_name] => Magnolia biondii
[gf] => Array
(
[HOMFAM] => HOM05D002404
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)
)
[unitig_0.g1546] => Array
(
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[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
(
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[bit_score] => 300.4
[alignment_length] => 222
[identity_percentage] => 60.4
[species] => ppa
[common_name] => Physcomitrium patens
[gf] => Array
(
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[ORTHOFAM] => ORTHO05D003647
)
)
[Lj1A949T60] => Array
(
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[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
(
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[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
(
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[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
(
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[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
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[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
(
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[species] => cav
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(
[HOMFAM] => HOM05D002404
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[AagrBONN_evm.TU.Sc2ySwM_368.185] => Array
(
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(
[HOMFAM] => HOM05D002404
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)
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[CiPaw.01G294900] => Array
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(
[HOMFAM] => HOM05D002404
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)
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[Cc01_g09170] => Array
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(
[HOMFAM] => HOM05D002404
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)
)
[Gorai.012G075000] => Array
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[species] => gra
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(
[HOMFAM] => HOM05D002404
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[HanXRQChr12g0369341] => Array
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[HOMFAM] => HOM05D002404
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)
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[FAN12G0397] => Array
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[HOMFAM] => HOM05D002404
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)
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[CBR_g8027] => Array
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[HOMFAM] => HOM05D002404
[ORTHOFAM] => ORTHO05D003647
)
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[CDE02G0969] => Array
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[HOMFAM] => HOM05D002404
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)
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[FAN17G2398] => Array
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[HOMFAM] => HOM05D002404
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)
)
[Migut.F01240] => Array
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[HOMFAM] => HOM05D002404
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)
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[HOMFAM] => HOM05D002404
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[species] => ccan
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[HOMFAM] => HOM05D002404
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)
)
[Migut.F01239] => Array
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[HOMFAM] => HOM05D002404
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[AL4G24280] => Array
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[HOMFAM] => HOM05D002404
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)
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[arahy.Tifrunner.gnm1.ann1.7KT8N3] => Array
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[HOMFAM] => HOM05D002404
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)
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[FAN22G0348] => Array
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[species] => fan
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[HOMFAM] => HOM05D002404
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)
)
[Hund13825] => Array
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[species] => sun
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[HOMFAM] => HOM05D002404
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)
)
[Phvul.008G283900] => Array
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[species] => pvu
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[HOMFAM] => HOM05D002404
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)
[C05p05420] => Array
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[HOMFAM] => HOM05D002404
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)
)
[Phvul.L010543] => Array
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[HOMFAM] => HOM05D002404
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[TWI81G0926] => Array
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[HOMFAM] => HOM05D002404
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[HOMFAM] => HOM05D002404
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)
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[Duzib114G1052] => Array
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[HOMFAM] => HOM05D002404
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)
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[species] => din
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[HOMFAM] => HOM05D002404
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[GSVIVG01024814001] => Array
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[HOMFAM] => HOM05D002404
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)
[MBI05_g34805_MAGBIO] => Array
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[HOMFAM] => HOM05D002404
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)
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[HOMFAM] => HOM05D002404
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[HOMFAM] => HOM05D002404
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[SEGI_20540] => Array
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[PGR091G0001] => Array
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[SalBow5G5047] => Array
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[HOMFAM] => HOM05D002404
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[CiPaw.15G124600] => Array
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[QL93p0331_0124] => Array
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[species] => qlo
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(
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(
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[Migut.F01527] => Array
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[species] => egut
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(
[HOMFAM] => HOM05D002404
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[Dinv29454] => Array
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[species] => din
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(
[HOMFAM] => HOM05D002404
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[Ciclev10030011m.g] => Array
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[alignment_length] => 65
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[species] => ccl
[common_name] => Citrus clementina
[gf] => Array
(
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[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
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(
)
)
[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
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(
)
)
[FormUtils] => Array
(
[class] => FormUtils
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(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
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(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
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(
)
)
[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
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*RECURSION*
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[components] => Array
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[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
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[_componentMap:protected] => Array
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[FunctionalUtils] => Array
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*RECURSION*
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[components] => Array
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[_componentMap:protected] => Array
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[Organism] => OrganismComponent Object
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[_Collection:protected] => ComponentCollection Object
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[_componentMap:protected] => Array
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[GenomeBrowser] => Array
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[Blast] => BlastComponent Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
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[components] => Array
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[_componentMap:protected] => Array
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[WorkbenchUtils] => WorkbenchUtilsComponent Object
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[_componentMap:protected] => Array
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[ExternalPrograms] => Array
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[_componentMap:protected] => Array
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[Sequence] => Array
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[ExternalPrograms] => ExternalProgramsComponent Object
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[program_paths:ExternalProgramsComponent:private] => Array
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[java] => Array
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[command] => java -Djava.awt.headless=true
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[perl] => Array
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[bash] => Array
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[modules] => Array
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[command] =>
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[local_settings] =>
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[bedops] => Array
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[command] =>
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[muscle] => Array
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[mafft] => Array
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[modules] => Array
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[phyml] => Array
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[modules] => Array
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[fasttree] => Array
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[iqtree] => Array
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[_Collection:protected] => ComponentCollection Object
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[_componentMap:protected] => Array
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[FastaUtils] => FastaUtilsComponent Object
(
[name] => FastaUtils
[controller] => AnalysisController Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
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[_componentMap:protected] => Array
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[MsaUtils] => MsaUtilsComponent Object
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[name] => MsaUtils
[controller] => AnalysisController Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
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[_componentMap:protected] => Array
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[PhylogeneticUtils] => PhylogeneticUtilsComponent Object
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[controller] => AnalysisController Object
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[components] => Array
(
[0] => ExternalPrograms
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[_componentMap:protected] => Array
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[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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(
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[Sequence] => SequenceComponent Object
(
[name] => Sequence
[components] => Array
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[1] => Coordinates
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[_Collection:protected] => ComponentCollection Object
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[settings] => Array
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[_componentMap:protected] => Array
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[Blast] => Array
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[class] => Blast
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[Coordinates] => Array
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[class] => Coordinates
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[ExternalPrograms] => Array
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[controller] => AnalysisController Object
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[RequestHandler] => RequestHandlerComponent Object
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[ajaxLayout] => ajax
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[request] => CakeRequest Object
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[params] => Array
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[plugin] =>
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[data] => Array
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[_detectors:protected] => Array
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[get] => Array
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[env] => REQUEST_METHOD
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[patch] => Array
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[post] => Array
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[put] => Array
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[flash] => Array
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[1] => AvantGo
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[8] => iPad
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[11] => NetFront
[12] => Nokia
[13] => Opera Mini
[14] => Opera Mobi
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[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
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[_input:protected] =>
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[_mimeTypes:protected] => Array
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[html] => Array
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[1] => */*
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[rpm] => audio/x-pn-realaudio-plugin
[snd] => audio/basic
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[aac] => audio/aac
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[c] => text/plain
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[1] => */*
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[ics] => text/calendar
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[sgml] => text/sgml
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[tpl] => text/template
[txt] => text/plain
[text] => text/plain
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[fli] => video/x-fli
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[mpeg] => video/mpeg
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[viv] => video/vnd.vivo
[vivo] => video/vnd.vivo
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[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
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[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
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[1] => text/vnd.wap.wmlscript
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[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
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[_protocol:protected] => HTTP/1.1
[_status:protected] => 200
[_contentType:protected] => text/html
[_headers:protected] => Array
(
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[_body:protected] =>
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[_fileRange:protected] =>
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[_cacheDirectives:protected] => Array
(
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[_cookies:protected] => Array
(
)
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[ext] =>
[_renderType:protected] =>
[_inputTypeMap:protected] => Array
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[json] => Array
(
[0] => json_decode
[1] => 1
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[xml] => Array
(
[0] => Array
(
[0] => RequestHandlerComponent Object
*RECURSION*
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[_viewClassMap:protected] => Array
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[json] => Json
[xml] => Xml
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
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[checkHttpCache] => 1
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[components] => Array
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[_componentMap:protected] => Array
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)
[params] => CakeRequest Object
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[params] => Array
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[plugin] =>
[controller] => analysis
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[named] => Array
(
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[isAjax] =>
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[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
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[delete] => Array
(
[env] => REQUEST_METHOD
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)
[head] => Array
(
[env] => REQUEST_METHOD
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[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
)
[ssl] => Array
(
[env] => HTTPS
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)
[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
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[skp] => application/x-koan
[skt] => application/x-koan
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[smil] => application/smil
[sol] => application/solids
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[src] => application/x-wais-source
[step] => application/STEP
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[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
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[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
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[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
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[5] => Fennec
[6] => iPod
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[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
)
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)
[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
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[command] =>
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[local_settings] =>
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[blastdbcmd] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
)
[command] => blastdbcmd
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[local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
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[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
(
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)
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[mafft] => Array
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[cluster_settings] => Array
(
[modules] => Array
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[0] => mafft/x86_64/7.187
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)
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[phyml] => Array
(
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[modules] => Array
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)
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[fasttree] => Array
(
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(
[modules] => Array
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[modules] => Array
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[iqtree] => Array
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[modules] => Array
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[FastaUtils] => Array
(
[class] => FastaUtils
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(
)
)
)
)
[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
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)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[Blast] => Array
(
[class] => Blast
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(
)
)
[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
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)
[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
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[post] => Array
(
[env] => REQUEST_METHOD
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[put] => Array
(
[env] => REQUEST_METHOD
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[delete] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
(
[env] => REQUEST_METHOD
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[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
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[ssl] => Array
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[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
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(
[0] => Android
[1] => AvantGo
[2] => BB10
[3] => BlackBerry
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[5] => Fennec
[6] => iPod
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[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
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
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)
)
[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
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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
*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
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[mkv] => video/x-matroska
[pkpass] => application/vnd.apple.pkpass
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)
[_protocol:protected] => HTTP/1.1
[_status:protected] => 200
[_contentType:protected] => text/html
[_headers:protected] => Array
(
)
[_body:protected] =>
[_file:protected] =>
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[_cookies:protected] => Array
(
)
)
[ext] =>
[_renderType:protected] =>
[_inputTypeMap:protected] => Array
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[_viewClassMap:protected] => Array
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[_Collection:protected] => ComponentCollection Object
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[settings] => Array
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[checkHttpCache] => 1
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[components] => Array
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[params] => CakeRequest Object
(
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(
[plugin] =>
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(
)
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(
[get] => Array
(
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[put] => Array
(
[env] => REQUEST_METHOD
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[delete] => Array
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[env] => REQUEST_METHOD
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[head] => Array
(
[env] => REQUEST_METHOD
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(
[env] => REQUEST_METHOD
[value] => OPTIONS
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[ssl] => Array
(
[env] => HTTPS
[value] => 1
)
[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
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(
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[json] => Array
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)
[param] => ext
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)
[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
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[components] => Array
(
[0] => FunctionalUtils
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[_Collection:protected] => ComponentCollection Object
(
[_Controller:protected] => AnalysisController Object
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[_enabled:protected] => Array
(
[Session] => Array
(
[0] => 10
[1] => 1
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[DataUtils] => Array
(
[0] => 10
[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
[0] => 10
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)
[GeneFamilies] => Array
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[0] => 10
[1] => 4
)
[Organism] => Array
(
[0] => 10
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[Blast] => Array
(
[0] => 10
[1] => 6
)
[WorkbenchUtils] => Array
(
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[1] => 7
)
[PhylogeneticModuleUtils] => Array
(
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[1] => 8
)
[ExternalPrograms] => Array
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[0] => 10
[1] => 9
)
[FastaUtils] => Array
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[0] => 10
[1] => 10
)
[MsaUtils] => Array
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[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
(
)
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[DataUtils] => DataUtilsComponent Object
(
[name] => DataUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FunctionalUtils
[2] => GeneFamilies
[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
(
[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
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[components] => Array
(
[0] => ExternalPrograms
[1] => FormUtils
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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
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
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[ExternalPrograms] => Array
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[class] => ExternalPrograms
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)
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[class] => FastaUtils
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)
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(
)
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[PhylogeneticUtils] => Array
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[class] => PhylogeneticUtils
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(
)
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[Sequence] => Array
(
[class] => Sequence
[settings] => Array
(
)
)
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[ExternalPrograms] => ExternalProgramsComponent Object
(
[name] => ExternalPrograms
[components] => Array
(
[0] => FastaUtils
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[program_paths:ExternalProgramsComponent:private] => Array
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[java] => Array
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[cluster_settings] => Array
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[modules] => Array
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)
[command] => java -Djava.awt.headless=true
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)
[perl] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[0] => perl
)
[command] => perl -w
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[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
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[modules] => Array
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[command] =>
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[local_settings] =>
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[blastdbcmd] => Array
(
[cluster_settings] => Array
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[modules] => Array
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[0] => blast
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[command] => blastdbcmd
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[blast] => Array
(
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[modules] => Array
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[0] => blast
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[command] =>
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[muscle] => Array
(
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(
[modules] => Array
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[mafft] => Array
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[modules] => Array
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[phyml] => Array
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[modules] => Array
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[0] => phyml/x86_64/20150219
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)
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[fasttree] => Array
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[modules] => Array
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[raxml] => Array
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[modules] => Array
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[modules] => Array
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)
[_componentMap:protected] => Array
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[FastaUtils] => Array
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[class] => FastaUtils
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(
)
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[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
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[class] => Blast
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)
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[Coordinates] => Array
(
[class] => Coordinates
[settings] => Array
(
)
)
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
)
[controller] => AnalysisController Object
*RECURSION*
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[RequestHandler] => RequestHandlerComponent Object
(
[ajaxLayout] => ajax
[enabled] => 1
[request] => CakeRequest Object
(
[params] => Array
(
[plugin] =>
[controller] => analysis
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[named] => Array
(
)
[pass] => Array
(
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[isAjax] =>
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[data] => Array
(
)
[query] => Array
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)
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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
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[patch] => Array
(
[env] => REQUEST_METHOD
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[post] => Array
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[put] => Array
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[delete] => Array
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[mobile] => Array
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[20] => SonyEricsson
[21] => Symbian
[22] => UP\.Browser
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[25] => Windows Phone OS
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[json] => Array
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[param] => ext
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[xml] => Array
(
[accept] => Array
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[param] => ext
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[_input:protected] =>
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[response] => CakeResponse Object
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[303] => See Other
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[305] => Use Proxy
[307] => Temporary Redirect
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[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
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[_mimeTypes:protected] => Array
(
[html] => Array
(
[0] => text/html
[1] => */*
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[json] => application/json
[xml] => Array
(
[0] => application/xml
[1] => text/xml
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[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
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[dcr] => application/x-director
[dir] => application/x-director
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[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
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[pdf] => application/pdf
[pgn] => application/x-chess-pgn
[pot] => application/vnd.ms-powerpoint
[pps] => application/vnd.ms-powerpoint
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[sit] => application/x-stuffit
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[src] => application/x-wais-source
[step] => application/STEP
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[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
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[tex] => application/x-tex
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[ttf] => font/ttf
[unv] => application/i-deas
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[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
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[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
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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
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[put] => Array
(
[env] => REQUEST_METHOD
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[delete] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
(
[env] => REQUEST_METHOD
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[options] => Array
(
[env] => REQUEST_METHOD
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[ssl] => Array
(
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)
[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
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)
[flash] => Array
(
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[mobile] => Array
(
[env] => HTTP_USER_AGENT
[options] => Array
(
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[1] => AvantGo
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[3] => BlackBerry
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[12] => Nokia
[13] => Opera Mini
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[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
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[json] => Array
(
[accept] => Array
(
[0] => application/json
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[param] => ext
[value] => json
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[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
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[param] => ext
[value] => xml
)
)
[_input:protected] =>
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[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
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[doc] => application/msword
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[drw] => application/drafting
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[dxr] => application/x-director
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[eps] => application/postscript
[exe] => application/octet-stream
[ez] => application/andrew-inset
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[gz] => application/x-gzip
[bz2] => application/x-bzip
[7z] => application/x-7z-compressed
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[ico] => image/x-icon
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[me] => application/x-troff-me
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[pdf] => application/pdf
[pgn] => application/x-chess-pgn
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[pptx] => application/vnd.openxmlformats-officedocument.presentationml.presentation
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[prt] => application/pro_eng
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[scm] => application/x-lotusscreencam
[set] => application/set
[sh] => application/x-sh
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[sit] => application/x-stuffit
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[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
(
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)
)
[raxml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
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)
)
[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
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[0] => gene_id
[1] => Cre12.g515850
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[isAjax] =>
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[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
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[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
(
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[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
(
)
)
[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
[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
(
)
)
[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
(
[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
(
)
)
[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
(
[_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
*RECURSION*
[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
(
[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
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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
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)
[head] => Array
(
[env] => REQUEST_METHOD
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[options] => Array
(
[env] => REQUEST_METHOD
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)
[ssl] => Array
(
[env] => HTTPS
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)
[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
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[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
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[sit] => application/x-stuffit
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[skp] => application/x-koan
[skt] => application/x-koan
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[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
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[5] => Fennec
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[10] => MIDP
[11] => NetFront
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[13] => Opera Mini
[14] => Opera Mobi
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[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
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[local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
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[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
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)
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[phyml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => phyml/x86_64/20150219
)
)
)
[fasttree] => Array
(
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(
[modules] => Array
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)
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[modules] => Array
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)
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[iqtree] => Array
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(
[modules] => Array
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[0] => iqtree/x86_64/1.5.5
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*RECURSION*
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(
)
[_componentMap:protected] => Array
(
[FastaUtils] => Array
(
[class] => FastaUtils
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(
)
)
)
)
[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
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(
)
)
[Coordinates] => Array
(
[class] => Coordinates
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(
)
)
[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
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)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[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
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)
[put] => Array
(
[env] => REQUEST_METHOD
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)
[delete] => Array
(
[env] => REQUEST_METHOD
[value] => DELETE
)
[head] => Array
(
[env] => REQUEST_METHOD
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)
[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
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[ssl] => Array
(
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[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
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[flash] => Array
(
[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
)
[mobile] => Array
(
[env] => HTTP_USER_AGENT
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(
[0] => Android
[1] => AvantGo
[2] => BB10
[3] => BlackBerry
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[5] => Fennec
[6] => iPod
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[10] => MIDP
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[13] => Opera Mini
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[18] => Plucker
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[20] => SonyEricsson
[21] => Symbian
[22] => UP\.Browser
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[24] => Windows CE
[25] => Windows Phone OS
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)
)
[requested] => Array
(
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[value] => 1
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[json] => Array
(
[accept] => Array
(
[0] => application/json
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[param] => ext
[value] => json
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[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
)
)
)
[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
)
[passParams] =>
)
[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] =>
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[collate] => latin1_swedish_ci
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[_associationKeys:protected] => Array
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[_associations:protected] => Array
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[__backAssociation] => Array
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[__backOriginalAssociation] => Array
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[__backContainableAssociation] => Array
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[__safeUpdateMode] =>
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[_insertID:protected] =>
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[_eventManager:protected] => CakeEventManager Object
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[Model.afterSave] => Array
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[_isGlobal:protected] =>
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[GeneFamilyTypes] => GeneFamilyTypes Object
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[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
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[id] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 10
[key] => primary
[collate] => latin1_swedish_ci
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[name] => Array
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[type] => string
[null] =>
[default] =>
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[prefix] => Array
(
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[default] =>
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[collate] => latin1_swedish_ci
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[gene_type] => Array
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[type] => enum('coding','rna','pseudo','te')
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[method] => Array
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[default] =>
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[ancestry] => Array
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[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
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)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
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[tableToModel] => Array
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[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
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)
[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
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)
[_mappedMethods:protected] => Array
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)
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(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
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)
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(
)
[_associationKeys:protected] => Array
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)
[hasMany] => Array
(
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[hasAndBelongsToMany] => Array
(
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)
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[_associations:protected] => Array
(
[0] => belongsTo
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[2] => hasMany
[3] => hasAndBelongsToMany
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[__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
(
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(
[10] => Array
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[0] => Array
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(
)
[_mappedMethods:protected] => Array
(
)
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(
)
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(
)
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[1] => Array
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(
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(
)
[_loaded:protected] => Array
(
)
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[1] => trigger
)
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[1] => Array
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[Model.beforeValidate] => Array
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(
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(
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[1] => Array
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[Similarities] => Similarities Object
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[id] =>
[data] => Array
(
)
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(
[species] => Array
(
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(
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[hits] => Array
(
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[null] =>
[default] =>
[length] =>
)
)
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
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[tableToModel] => Array
(
[similarities] => Similarities
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[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
(
)
[actsAs] =>
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(
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(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
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(
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(
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(
)
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[hasMany] => Array
(
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[9] => finderQuery
[10] => counterQuery
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[hasAndBelongsToMany] => Array
(
[0] => className
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[2] => with
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[4] => associationForeignKey
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[10] => unique
[11] => finderQuery
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[_associations:protected] => Array
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[3] => hasAndBelongsToMany
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[__backAssociation] => Array
(
)
[__backInnerAssociation] => Array
(
)
[__backOriginalAssociation] => Array
(
)
[__backContainableAssociation] => Array
(
)
[__safeUpdateMode] =>
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[_insertID:protected] =>
[_sourceConfigured:protected] => 1
[findMethods] => Array
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[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
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[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
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[1] => beforeFind
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[passParams] => 1
)
)
)
[Model.afterFind] => Array
(
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[0] => Array
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[callable] => Array
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[0] => BehaviorCollection Object
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(
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[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
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[1] => trigger
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[passParams] =>
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[1] => Array
(
[callable] => Array
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[passParams] => 1
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[Model.beforeValidate] => Array
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(
[0] => Array
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[callable] => Array
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[0] => BehaviorCollection Object
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[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
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[1] => trigger
)
[passParams] =>
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[1] => Array
(
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[passParams] => 1
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[Model.afterValidate] => Array
(
[10] => Array
(
[0] => Array
(
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controller Notice (8) : Trying to get property 'Configuration' of non-object [APP/Controller/Component/GenomeBrowserComponent.php , line 105 ]Code Context
//Construct url for synteny-scores
$species_tree = $this -> controller -> Configuration -> getBasicSpeciesTree ();
$species = 'cre'
$configuration_settings = array(
'annotation_directory' => 'GFF/%SPECIES%/',
'annotation_file_compressed' => 'true',
'annotation_file_extension' => 'gff3',
'annotation_file_prefix' => 'annotation.all_transcripts.all_features',
'data_url' => 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/',
'genomes_directory' => 'Genomes',
'genomes_file_compressed' => 'true',
'genomes_file_extension' => 'fasta'
)
$base_data_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/'
$genome_dir_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/Genomes/'
$annotation_dir_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/GFF/cre/'
$genome_file_name = 'cre.fasta.gz'
$annotation_file_name = 'annotation.all_transcripts.all_features.cre.gff3.gz'
$genome_file_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/Genomes/cre.fasta.gz'
$annotation_file_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/GFF/cre/annotation.all_transcripts.all_features.cre.gff3.gz' GenomeBrowserComponent::getValidatedDataSettings() - APP/Controller/Component/GenomeBrowserComponent.php, line 105
DataUtilsComponent::getSidebarToolsInfo() - APP/Controller/Component/DataUtilsComponent.php, line 65
AppController::beforeRender() - APP/Controller/AppController.php, line 94
CakeEventManager::dispatch() - CORE/Cake/Event/CakeEventManager.php, line 243
Controller::render() - CORE/Cake/Controller/Controller.php, line 936
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151
Errors
Call to a member function getBasicSpeciesTree() on null
Error:
An Internal Error Has Occurred.
Stack Trace
APP/Controller/Component/DataUtilsComponent.php line 65 → GenomeBrowserComponent->getValidatedDataSettings() $default_hom_gf_type_id = $this -> GeneFamilies -> getHomologyCodingGeneFamilyType ();
$full_gene_info = $AnnotationModel -> getFullGeneInfo ( $gene_id );
pr ( $this -> controller );
$igv_genome_browser_info = $this -> GenomeBrowser -> getValidatedDataSettings ( $full_gene_info [ 'species' ],);
APP/Controller/AppController.php line 94 → DataUtilsComponent->getSidebarToolsInfo() $identifier = isset(( $this -> viewVars )[ "sidebar_information" ][ "id" ])?( $this -> viewVars )[ "sidebar_information" ][ "id" ]: null ;
if( $type === "gene_id" ){
$this -> set ( "sidebar" , "gene_sidebar" );
$this -> set ( "sidebar_info" , $this -> DataUtils -> getSidebarToolsInfo ( $identifier ));
}
CORE/Cake/Event/CakeEventManager.php line 243 → AppController->beforeRender() if ( $listener [ 'passParams' ] === true ) {
$result = call_user_func_array ( $listener [ 'callable' ], $event -> data );
} else {
$result = call_user_func ( $listener [ 'callable' ], $event );
}
CORE/Cake/Controller/Controller.php line 936 → CakeEventManager->dispatch() */
public function render ( $view = null , $layout = null ) {
$event = new CakeEvent ( 'Controller.beforeRender' , $this );
$this -> getEventManager ()-> dispatch ( $event );
if ( $event -> isStopped ()) {
CORE/Cake/Routing/Dispatcher.php line 200 → Controller->render() }
if ( $render && $controller -> autoRender ) {
$response = $controller -> render ();
} elseif (!( $result instanceof CakeResponse ) && $response -> body () === null ) {
CORE/Cake/Routing/Dispatcher.php line 167 → Dispatcher->_invoke() ));
}
$response = $this -> _invoke ( $controller , $request );
if (isset( $request -> params [ 'return' ])) {
APP/webroot/index.php line 151 → Dispatcher->dispatch() App :: uses ( 'Dispatcher' , 'Routing' );
$Dispatcher = new Dispatcher ();
$Dispatcher -> dispatch (new CakeRequest (), new CakeResponse (array( 'charset' => Configure :: read ( 'App.encoding' ))));