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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
(
[arahy.Tifrunner.gnm1.ann1.87PAU8] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.87PAU8
[e_value] => 1.4e-182
[bit_score] => 642.9
[alignment_length] => 343
[identity_percentage] => 100.0
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.GW23Z6] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.GW23Z6
[e_value] => 1.3e-132
[bit_score] => 476.9
[alignment_length] => 370
[identity_percentage] => 75.4
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.T41GG2] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.T41GG2
[e_value] => 1.7e-127
[bit_score] => 459.9
[alignment_length] => 316
[identity_percentage] => 75.6
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.625I4R] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.625I4R
[e_value] => 6.4e-127
[bit_score] => 458.0
[alignment_length] => 373
[identity_percentage] => 67.3
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.LDA4IK] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.LDA4IK
[e_value] => 3.2e-126
[bit_score] => 455.7
[alignment_length] => 316
[identity_percentage] => 75.0
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.3AR30J] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.3AR30J
[e_value] => 4.2e-126
[bit_score] => 455.3
[alignment_length] => 316
[identity_percentage] => 75.3
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.ZY293U] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.ZY293U
[e_value] => 7.1e-126
[bit_score] => 454.5
[alignment_length] => 316
[identity_percentage] => 75.0
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.9T44NN] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.9T44NN
[e_value] => 9.3e-126
[bit_score] => 454.1
[alignment_length] => 316
[identity_percentage] => 75.0
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.JB5G6S] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.JB5G6S
[e_value] => 9.3e-126
[bit_score] => 454.1
[alignment_length] => 316
[identity_percentage] => 74.7
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.4R1N6H] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.4R1N6H
[e_value] => 1.2e-125
[bit_score] => 453.8
[alignment_length] => 316
[identity_percentage] => 74.7
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.7UIB1D] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.7UIB1D
[e_value] => 2.1e-125
[bit_score] => 453.0
[alignment_length] => 316
[identity_percentage] => 74.4
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.390B12] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.390B12
[e_value] => 1.3e-124
[bit_score] => 450.3
[alignment_length] => 316
[identity_percentage] => 74.4
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.HIWB5S] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.HIWB5S
[e_value] => 1.3e-124
[bit_score] => 450.3
[alignment_length] => 316
[identity_percentage] => 74.4
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.86RVGQ] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.86RVGQ
[e_value] => 2.3e-124
[bit_score] => 449.5
[alignment_length] => 316
[identity_percentage] => 73.7
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.HQL5ZH] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.HQL5ZH
[e_value] => 2.3e-124
[bit_score] => 449.5
[alignment_length] => 316
[identity_percentage] => 77.8
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.44H41D] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.44H41D
[e_value] => 3.9e-124
[bit_score] => 448.7
[alignment_length] => 316
[identity_percentage] => 73.7
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.NZ73MH] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.NZ73MH
[e_value] => 3.9e-124
[bit_score] => 448.7
[alignment_length] => 316
[identity_percentage] => 74.4
[species] => arhy
[common_name] => Arachis hypogaea
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.PTE4RY] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.PTE4RY
[e_value] => 5.1e-124
[bit_score] => 448.4
[alignment_length] => 316
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)
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(
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)
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[alignment_length] => 234
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(
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(
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(
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[ORTHOFAM] => ORTHO05D000197
)
)
[Sopen10g016530] => Array
(
[gene_id] => Sopen10g016530
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[species] => spe
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[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.VAKC15] => Array
(
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[CiPaw.02G081200] => Array
(
[gene_id] => CiPaw.02G081200
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[alignment_length] => 59
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[species] => cil
[common_name] => Carya illinoinensis
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Lj2g0026023] => Array
(
[gene_id] => Lj2g0026023
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[species] => lja
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Oeu050619.1] => Array
(
[gene_id] => Oeu050619.1
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[species] => oeu
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(
[HOMFAM] => HOM05D004680
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)
)
[CAN.G150.7] => Array
(
[gene_id] => CAN.G150.7
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[species] => can
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(
[HOMFAM] => HOM05D000158
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)
)
[arahy.Tifrunner.gnm1.ann1.X91M1R] => Array
(
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[alignment_length] => 79
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
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)
)
[Sopen01g025440] => Array
(
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[species] => spe
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(
[HOMFAM] => HOM05D000158
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)
)
[Sopen09g015140] => Array
(
[gene_id] => Sopen09g015140
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[species] => spe
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(
[HOMFAM] => HOM05D000158
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)
)
[Sopen05g019960] => Array
(
[gene_id] => Sopen05g019960
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[species] => spe
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[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Sopen09g015650] => Array
(
[gene_id] => Sopen09g015650
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[species] => spe
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.EDY1F1] => Array
(
[gene_id] => arahy.Tifrunner.gnm1.ann1.EDY1F1
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[bit_score] => 59.3
[alignment_length] => 131
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Oeu064487.1] => Array
(
[gene_id] => Oeu064487.1
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[species] => oeu
[common_name] => Olea europaea
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D010634
)
)
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(
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
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)
)
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(
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[alignment_length] => 78
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[MELO3C030509.2] => Array
(
[gene_id] => MELO3C030509.2
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[species] => cme
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D015087
)
)
[Manes.10G066150] => Array
(
[gene_id] => Manes.10G066150
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[species] => mes
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Nitab4.5_0000274g0170] => Array
(
[gene_id] => Nitab4.5_0000274g0170
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[alignment_length] => 78
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(
[HOMFAM] => HOM05D009165
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)
)
[Sopen05g024500] => Array
(
[gene_id] => Sopen05g024500
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[species] => spe
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
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(
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
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(
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
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)
)
[Thhalv10022480m.g] => Array
(
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(
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[ORTHOFAM] => ORTHO05D000197
)
)
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(
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[species] => spe
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[gf] => Array
(
[HOMFAM] => HOM05D000158
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)
)
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(
[gene_id] => Sopen12g012480
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[species] => spe
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[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Nitab4.5_0003796g0110] => Array
(
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[species] => nta
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(
[HOMFAM] => HOM05D009165
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)
)
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(
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[species] => spe
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(
[HOMFAM] => HOM05D000004
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)
)
[Sopen11g007830] => Array
(
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[species] => spe
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[MELO3C026406.2] => Array
(
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[alignment_length] => 266
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[species] => cme
[common_name] => Cucumis melo
[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Nitab4.5_0008503g0020] => Array
(
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[alignment_length] => 81
[identity_percentage] => 38.3
[species] => nta
[common_name] => Nicotiana tabacum
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(
[HOMFAM] => HOM05D009165
[ORTHOFAM] => ORTHO05D011118
)
)
[arahy.Tifrunner.gnm1.ann1.C5B7DM] => Array
(
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[alignment_length] => 84
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[arahy.Tifrunner.gnm1.ann1.SI7STU] => Array
(
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[alignment_length] => 38
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[species] => arhy
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(
[HOMFAM] => HOM05D000158
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)
)
[arahy.Tifrunner.gnm1.ann1.X0U8Y0] => Array
(
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[alignment_length] => 53
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[gf] => Array
(
[HOMFAM] => HOM05D000158
[ORTHOFAM] => ORTHO05D000197
)
)
[Nitab4.5_0000125g0390] => Array
(
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[alignment_length] => 72
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[species] => nta
[common_name] => Nicotiana tabacum
[gf] => Array
(
[HOMFAM] => HOM05D009165
[ORTHOFAM] => ORTHO05D011118
)
)
)
[similarity_hits_species] => Array
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[99] => arahy.Tifrunner.gnm1.ann1.AXU1GU
[100] => arahy.Tifrunner.gnm1.ann1.VHLD2J
[101] => arahy.Tifrunner.gnm1.ann1.EVFR00
[102] => arahy.Tifrunner.gnm1.ann1.DBEW1J
[103] => arahy.Tifrunner.gnm1.ann1.DUA4ZE
[104] => arahy.Tifrunner.gnm1.ann1.Q9UUMB
[105] => arahy.Tifrunner.gnm1.ann1.217P67
[106] => arahy.Tifrunner.gnm1.ann1.SPE56M
[107] => arahy.Tifrunner.gnm1.ann1.YRHH3L
[108] => arahy.Tifrunner.gnm1.ann1.IE1D11
[109] => arahy.Tifrunner.gnm1.ann1.6U6G8M
[110] => arahy.Tifrunner.gnm1.ann1.C593YE
[111] => arahy.Tifrunner.gnm1.ann1.31ESZ9
[112] => arahy.Tifrunner.gnm1.ann1.UQ4A0Q
[113] => arahy.Tifrunner.gnm1.ann1.FHGQ5B
[114] => arahy.Tifrunner.gnm1.ann1.AR04AZ
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[159] => arahy.Tifrunner.gnm1.ann1.DWAY4T
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[171] => arahy.Tifrunner.gnm1.ann1.XS5DYX
[172] => arahy.Tifrunner.gnm1.ann1.IRD4WN
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[175] => arahy.Tifrunner.gnm1.ann1.HZWW81
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[179] => arahy.Tifrunner.gnm1.ann1.E2IS3L
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[181] => arahy.Tifrunner.gnm1.ann1.A3328F
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[184] => arahy.Tifrunner.gnm1.ann1.Y4Y8ET
[185] => arahy.Tifrunner.gnm1.ann1.IA7WGU
[186] => arahy.Tifrunner.gnm1.ann1.APK0NP
[187] => arahy.Tifrunner.gnm1.ann1.2SA9QW
[188] => arahy.Tifrunner.gnm1.ann1.3L2L0Y
[189] => arahy.Tifrunner.gnm1.ann1.2EH0QW
[190] => arahy.Tifrunner.gnm1.ann1.CLW9FC
[191] => arahy.Tifrunner.gnm1.ann1.QI581D
[192] => arahy.Tifrunner.gnm1.ann1.U4M58P
[193] => arahy.Tifrunner.gnm1.ann1.0G7P3D
[194] => arahy.Tifrunner.gnm1.ann1.HB2SP5
[195] => arahy.Tifrunner.gnm1.ann1.0UKE70
[196] => arahy.Tifrunner.gnm1.ann1.WSML5L
[197] => arahy.Tifrunner.gnm1.ann1.71573I
[198] => arahy.Tifrunner.gnm1.ann1.0G5FLV
[199] => arahy.Tifrunner.gnm1.ann1.IQR40G
[200] => arahy.Tifrunner.gnm1.ann1.C99TYC
[201] => arahy.Tifrunner.gnm1.ann1.F0AUH3
[202] => arahy.Tifrunner.gnm1.ann1.90XE5V
[203] => arahy.Tifrunner.gnm1.ann1.QD41U6
[204] => arahy.Tifrunner.gnm1.ann1.G2V00H
[205] => arahy.Tifrunner.gnm1.ann1.Q6MQNA
[206] => arahy.Tifrunner.gnm1.ann1.KU6KXV
[207] => arahy.Tifrunner.gnm1.ann1.R7CRBK
[208] => arahy.Tifrunner.gnm1.ann1.JFJ878
[209] => arahy.Tifrunner.gnm1.ann1.K0EZJ4
[210] => arahy.Tifrunner.gnm1.ann1.659L4B
[211] => arahy.Tifrunner.gnm1.ann1.AV92MX
[212] => arahy.Tifrunner.gnm1.ann1.VHU47D
[213] => arahy.Tifrunner.gnm1.ann1.JNB467
[214] => arahy.Tifrunner.gnm1.ann1.XN6NS8
[215] => arahy.Tifrunner.gnm1.ann1.1P3WRE
[216] => arahy.Tifrunner.gnm1.ann1.W04P42
[217] => arahy.Tifrunner.gnm1.ann1.Y1KF2B
[218] => arahy.Tifrunner.gnm1.ann1.BEX5HG
[219] => arahy.Tifrunner.gnm1.ann1.Q72NH6
[220] => arahy.Tifrunner.gnm1.ann1.S1Q5XH
[221] => arahy.Tifrunner.gnm1.ann1.18PYUZ
[222] => arahy.Tifrunner.gnm1.ann1.8K0ZU0
[223] => arahy.Tifrunner.gnm1.ann1.I3DMP8
[224] => arahy.Tifrunner.gnm1.ann1.9Y4FQ2
[225] => arahy.Tifrunner.gnm1.ann1.I7E4L8
[226] => arahy.Tifrunner.gnm1.ann1.IW28EF
[227] => arahy.Tifrunner.gnm1.ann1.GD7WFM
[228] => arahy.Tifrunner.gnm1.ann1.N3555V
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[230] => arahy.Tifrunner.gnm1.ann1.V0BAMU
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[237] => arahy.Tifrunner.gnm1.ann1.N7R8CX
[238] => arahy.Tifrunner.gnm1.ann1.YL2BBV
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[240] => arahy.Tifrunner.gnm1.ann1.5S8HU1
[241] => arahy.Tifrunner.gnm1.ann1.6U09DB
[242] => arahy.Tifrunner.gnm1.ann1.CIR6XW
[243] => arahy.Tifrunner.gnm1.ann1.FHI9NT
[244] => arahy.Tifrunner.gnm1.ann1.JCQ008
[245] => arahy.Tifrunner.gnm1.ann1.7I5EIZ
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[248] => arahy.Tifrunner.gnm1.ann1.M97NZA
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[255] => arahy.Tifrunner.gnm1.ann1.RZIJ2L
[256] => arahy.Tifrunner.gnm1.ann1.ZPS03P
[257] => arahy.Tifrunner.gnm1.ann1.EUAW6M
[258] => arahy.Tifrunner.gnm1.ann1.GIY5N5
[259] => arahy.Tifrunner.gnm1.ann1.UC4KU4
[260] => arahy.Tifrunner.gnm1.ann1.ZIM2T0
[261] => arahy.Tifrunner.gnm1.ann1.9F14AA
[262] => arahy.Tifrunner.gnm1.ann1.EKYZ7W
[263] => arahy.Tifrunner.gnm1.ann1.GCX1C5
[264] => arahy.Tifrunner.gnm1.ann1.GJ1AII
[265] => arahy.Tifrunner.gnm1.ann1.HUSQ38
[266] => arahy.Tifrunner.gnm1.ann1.QV2FY5
[267] => arahy.Tifrunner.gnm1.ann1.SEYZ0I
[268] => arahy.Tifrunner.gnm1.ann1.3V14JX
[269] => arahy.Tifrunner.gnm1.ann1.IUXR99
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[271] => arahy.Tifrunner.gnm1.ann1.M2MFDB
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[273] => arahy.Tifrunner.gnm1.ann1.C39H2M
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[275] => arahy.Tifrunner.gnm1.ann1.DQ3ZQE
[276] => arahy.Tifrunner.gnm1.ann1.ZMN0FL
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[284] => arahy.Tifrunner.gnm1.ann1.V4TPZ0
[285] => arahy.Tifrunner.gnm1.ann1.8UCL89
[286] => arahy.Tifrunner.gnm1.ann1.848KF4
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[290] => arahy.Tifrunner.gnm1.ann1.P57W7I
[291] => arahy.Tifrunner.gnm1.ann1.9IG2T4
[292] => arahy.Tifrunner.gnm1.ann1.LSKZ83
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[295] => arahy.Tifrunner.gnm1.ann1.S13B92
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[305] => arahy.Tifrunner.gnm1.ann1.7A5GZE
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[362] => arahy.Tifrunner.gnm1.ann1.SI7STU
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)
[gma] => Array
(
[0] => Glyma.15G177300
[1] => Glyma.20G037200
[2] => Glyma.19G068000
[3] => Glyma.20G060800
[4] => Glyma.15G210800
[5] => Glyma.18G122400
[6] => Glyma.18G150700
[7] => Glyma.03G079900
[8] => Glyma.14G146500
[9] => Glyma.20G059900
[10] => Glyma.07G119600
[11] => Glyma.14G141100
[12] => Glyma.06G232700
[13] => Glyma.09G096400
[14] => Glyma.19G100300
[15] => Glyma.14G146600
[16] => Glyma.11G160800
[17] => Glyma.05G072900
[18] => Glyma.08G289400
[19] => Glyma.09G151100
[20] => Glyma.01G094300
[21] => Glyma.07G173200
[22] => Glyma.18G122300
[23] => Glyma.06G202700
[24] => Glyma.20G030000
[25] => Glyma.18G156400
[26] => Glyma.01G130900
)
[lja] => Array
(
[0] => Lj4g0013407
[1] => Lj1g0013168
[2] => Lj2g0018729
[3] => Lj6g0014333
[4] => Lj2g0014614
[5] => Lj1g0020144
[6] => Lj5g0006538
[7] => LjContig00408g0026416
[8] => LjContig00562g0026224
[9] => Lj4g0023820
[10] => Lj1g0013324
[11] => Lj1g0019916
[12] => Lj3g0009331
[13] => Lj3g0014470
[14] => Lj1g0004876
[15] => Lj3g0017745
[16] => Lj6g0009158
[17] => LjContig00080g0019961
[18] => Lj3g0020463
[19] => LjContig00506g0000245
[20] => Lj5g0012305
[21] => Lj3g0021112
[22] => Lj3g0024906
[23] => Lj6g0015358
[24] => Lj2g0025940
[25] => Lj2g0009501
[26] => Lj1g0002293
[27] => Lj1g0015392
[28] => Lj2g0002189
[29] => Lj3g0001164
[30] => Lj5g0017108
[31] => Lj2g0019716
[32] => Lj4g0018844
[33] => Lj2g0012339
[34] => Lj1g0000788
[35] => LjContig00155g0016901
[36] => Lj5g0027822
[37] => Lj1g0026464
[38] => LjContig00272g0003804
[39] => Lj1g0016672
[40] => Lj2g0004387
[41] => Lj4g0023280
[42] => Lj2g0028079
[43] => Lj1g0005560
[44] => Lj2g0010792
[45] => Lj2g0026449
[46] => Lj3g0011191
[47] => Lj4g0027308
[48] => Lj6g0006038
[49] => Lj2g0026023
)
[tpr] => Array
(
[0] => TPR.G22094
[1] => TPR.G9238
[2] => TPR.G39902
[3] => TPR.G16515
[4] => TPR.G30711
[5] => TPR.G39624
[6] => TPR.G10845
[7] => TPR.G40709
[8] => TPR.G35396
[9] => TPR.G3937
[10] => TPR.G40697
)
[gra] => Array
(
[0] => Gorai.003G148400
[1] => Gorai.003G159900
[2] => Gorai.005G169400
[3] => Gorai.013G120300
[4] => Gorai.008G129700
[5] => Gorai.001G201500
[6] => Gorai.005G226600
[7] => Gorai.007G262100
[8] => Gorai.013G103100
[9] => Gorai.009G307900
[10] => Gorai.012G096500
[11] => Gorai.007G206600
[12] => Gorai.003G115300
[13] => Gorai.013G130000
[14] => Gorai.001G087300
[15] => Gorai.010G157800
[16] => Gorai.008G169100
[17] => Gorai.001G115800
[18] => Gorai.002G201500
[19] => Gorai.003G084600
[20] => Gorai.010G130200
[21] => Gorai.004G224200
[22] => Gorai.006G001200
[23] => Gorai.001G169900
[24] => Gorai.011G163800
[25] => Gorai.005G125200
)
[ama] => Array
(
[0] => MSTRG.8973
[1] => MSTRG.23897
)
[esa] => Array
(
[0] => Thhalv10024098m.g
[1] => Thhalv10012334m.g
[2] => Thhalv10024111m.g
[3] => Thhalv10002268m.g
[4] => Thhalv10002329m.g
[5] => Thhalv10001275m.g
[6] => Thhalv10009827m.g
[7] => Thhalv10023048m.g
[8] => Thhalv10023798m.g
[9] => Thhalv10022480m.g
)
[oeu] => Array
(
[0] => Oeu015188.1
[1] => Oeu022516.1
[2] => Oeu007102.1
[3] => Oeu008148.1
[4] => Oeu064343.1
[5] => Oeu064527.1
[6] => Oeu048057.1
[7] => Oeu045360.1
[8] => Oeu050619.1
[9] => Oeu064487.1
)
[car] => Array
(
[0] => Ca_22769_v3
[1] => Ca_07003_v3
[2] => Ca_26786_v3
[3] => Ca_18984_v3
[4] => Ca_04070_v3
[5] => Ca_23932_v3
[6] => Ca_03828_v3
[7] => Ca_19597_v3
[8] => Ca_03988_v3
)
[cil] => Array
(
[0] => CiPaw.04G053800
[1] => CiPaw.08G029600
[2] => CiPaw.03G092700
[3] => CiPaw.01G104600
[4] => CiPaw.03G066400
[5] => CiPaw.02G081200
)
[egut] => Array
(
[0] => Migut.O00086
[1] => Migut.O00085
[2] => Migut.O00084
[3] => Migut.O00081
[4] => Migut.H01165
)
[bna] => Array
(
[0] => C05p32790
)
[han] => Array
(
[0] => HanXRQChr02g0042331
[1] => HanXRQChr11g0333631
)
[sly] => Array
(
[0] => Solyc07g025280.1
)
[cme] => Array
(
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[1] => MELO3C004850.2
[2] => MELO3C013380.2
[3] => MELO3C028612.2
[4] => MELO3C008564.2
[5] => MELO3C022767.2
[6] => MELO3C032329.2
[7] => MELO3C003851.2
[8] => MELO3C002890.2
[9] => MELO3C031980.2
[10] => MELO3C030587.2
[11] => MELO3C027490.2
[12] => MELO3C030509.2
[13] => MELO3C026406.2
)
[can] => Array
(
[0] => CAN.G362.35
[1] => CAN.G150.7
)
[sun] => Array
(
[0] => Hund20235
[1] => Hund08072
[2] => Hund12297
[3] => Hund10648
[4] => Hund10602
[5] => Hund20332
[6] => Hund15556
)
[mes] => Array
(
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[1] => Manes.17G018812
[2] => Manes.06G001751
[3] => Manes.05G131901
[4] => Manes.16G055925
[5] => Manes.09G089621
[6] => Manes.16G057426
[7] => Manes.13G076999
[8] => Manes.S095214
[9] => Manes.10G080301
[10] => Manes.07G055364
[11] => Manes.07G055686
[12] => Manes.11G096250
[13] => Manes.10G055732
[14] => Manes.07G056008
[15] => Manes.04G156550
[16] => Manes.10G066150
)
[cla] => Array
(
[0] => ClCG03G013730
[1] => ClCG10G003450
)
[spe] => Array
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[0] => Sopen12g001100
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[2] => Sopen02g001730
[3] => Sopen10g010850
[4] => Sopen11g016230
[5] => Sopen09g014910
[6] => Sopen04g017720
[7] => Sopen07g010610
[8] => Sopen09g015640
[9] => Sopen12g012220
[10] => Sopen01g009070
[11] => Sopen09g015100
[12] => Sopen11g007840
[13] => Sopen10g016530
[14] => Sopen01g025440
[15] => Sopen09g015140
[16] => Sopen05g019960
[17] => Sopen09g015650
[18] => Sopen05g024500
[19] => Sopen11g016660
[20] => Sopen12g012480
[21] => Sopen03g014160
[22] => Sopen11g007830
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[hma] => Array
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[amhyb] => Array
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[nta] => Array
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[2] => Nitab4.5_0000218g0020
[3] => Nitab4.5_0001302g0040
[4] => Nitab4.5_0003085g0030
[5] => Nitab4.5_0000274g0170
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[7] => Nitab4.5_0008503g0020
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[mbi] => Array
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[qlo] => Array
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[acertr] => Array
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[sed] => Array
(
[0] => Sed0023676
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[stu] => Array
(
[0] => PGSC0003DMG400036915
)
)
[gene_id] => PGSC0003DMG400036915
[gf_types_information] => Array
(
[HOMFAM] => Array
(
[id] => HOMFAM
[name] => Homologous gene family
[gene_type] => coding
[parent_id] =>
[ancestry] => homology
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[ORTHOFAM] => Array
(
[id] => ORTHOFAM
[name] => Orthologous gene family
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[parent_id] => HOMFAM
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[gf_types_configuration] => Array
(
[HOMFAM] => Array
(
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[show_parentless_subfamilies] => false
[show_table] => true
[show_orphan] =>
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[ORTHOFAM] => Array
(
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[show_parentless_subfamilies] => false
[show_table] => true
[show_orphan] =>
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[all_species] => Array
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[acertr] => Array
(
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[version] => v2.0
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[ach] => Array
(
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[aar] => Array
(
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[amhyb] => Array
(
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[version] => v1.0
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[atr] => Array
(
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[common_name] => Amborella trichopoda
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[version] => JGI v1.0
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[aag] => Array
(
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[common_name] => Anthoceros agrestis
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[version] => v1.1
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[aox] => Array
(
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[common_name] => Aquilegia oxysepala
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[version] => v1.0
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[aly] => Array
(
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[common_name] => Arabidopsis lyrata
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[version] => JGI v2.1
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[ath] => Array
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[common_name] => Arabidopsis thaliana
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[version] => Araport11
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[arhy] => Array
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[version] => v1.0
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[ama] => Array
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[common_name] => Avicennia marina
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[version] => v1.1 20200527
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[bvu] => Array
(
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[common_name] => Beta vulgaris
[tax_id] => 161934
[version] => EL10_1.0
)
[bca] => Array
(
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[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
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[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
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[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
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[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
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[version] => v2.1
)
[ppa] => Array
(
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[common_name] => Physcomitrium patens
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[version] => JGI v3.3
)
[psa] => Array
(
[species] => psa
[common_name] => Pisum sativum
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[version] => V1.0a
)
[ptr] => Array
(
[species] => ptr
[common_name] => Populus trichocarpa
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[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
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[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
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[data_identifier] => arahy.Tifrunner.gnm1.ann1.87PAU8
[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
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[DataUtils] => Array
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[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
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[1] => 3
)
[GeneFamilies] => Array
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[0] => 10
[1] => 4
)
[Organism] => Array
(
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[Blast] => Array
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[1] => 6
)
[WorkbenchUtils] => Array
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[1] => 7
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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*
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[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
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[post] => Array
(
[env] => REQUEST_METHOD
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[put] => Array
(
[env] => REQUEST_METHOD
[value] => PUT
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[delete] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
(
[env] => REQUEST_METHOD
[value] => HEAD
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[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
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[ssl] => Array
(
[env] => HTTPS
[value] => 1
)
[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
[options] => Array
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[1] => AvantGo
[2] => BB10
[3] => BlackBerry
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[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
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[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] =>
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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
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[303] => See Other
[304] => Not Modified
[305] => Use Proxy
[307] => Temporary Redirect
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[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] => */*
)
[json] => application/json
[xml] => Array
(
[0] => application/xml
[1] => text/xml
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[ai] => application/postscript
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[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
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[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
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[xll] => application/vnd.ms-excel
[xlm] => application/vnd.ms-excel
[xls] => application/vnd.ms-excel
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[xlw] => application/vnd.ms-excel
[zip] => application/zip
[aif] => audio/x-aiff
[aifc] => audio/x-aiff
[aiff] => audio/x-aiff
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[kar] => audio/midi
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[midi] => audio/midi
[mp2] => audio/mpeg
[mp3] => audio/mpeg
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[ogg] => audio/ogg
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[rm] => audio/x-pn-realaudio
[rpm] => audio/x-pn-realaudio-plugin
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[tsi] => audio/TSP-audio
[wav] => audio/x-wav
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[cc] => text/plain
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[f90] => text/plain
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[htm] => Array
(
[0] => text/html
[1] => */*
)
[ics] => text/calendar
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[rtx] => text/richtext
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[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
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[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
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[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
(
[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
)
[post] => Array
(
[env] => REQUEST_METHOD
[value] => POST
)
[put] => Array
(
[env] => REQUEST_METHOD
[value] => PUT
)
[delete] => Array
(
[env] => REQUEST_METHOD
[value] => DELETE
)
[head] => Array
(
[env] => REQUEST_METHOD
[value] => HEAD
)
[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
)
[ssl] => Array
(
[env] => HTTPS
[value] => 1
)
[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
[value] => XMLHttpRequest
)
[flash] => Array
(
[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
)
[mobile] => Array
(
[env] => HTTP_USER_AGENT
[options] => Array
(
[0] => Android
[1] => AvantGo
[2] => BB10
[3] => BlackBerry
[4] => DoCoMo
[5] => Fennec
[6] => iPod
[7] => iPhone
[8] => iPad
[9] => J2ME
[10] => MIDP
[11] => NetFront
[12] => Nokia
[13] => Opera Mini
[14] => Opera Mobi
[15] => PalmOS
[16] => PalmSource
[17] => portalmmm
[18] => Plucker
[19] => ReqwirelessWeb
[20] => SonyEricsson
[21] => Symbian
[22] => UP\.Browser
[23] => webOS
[24] => Windows CE
[25] => Windows Phone OS
[26] => Xiino
)
)
[requested] => Array
(
[param] => requested
[value] => 1
)
[json] => Array
(
[accept] => Array
(
[0] => application/json
)
[param] => ext
[value] => json
)
[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
)
[param] => ext
[value] => xml
)
)
[_input:protected] =>
)
)
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnalysisController Object
*RECURSION*
[1] => beforeRender
)
[passParams] =>
)
)
)
[Controller.beforeRedirect] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => ComponentCollection Object
(
[_Controller:protected] => AnalysisController Object
*RECURSION*
[_enabled:protected] => Array
(
[Session] => Array
(
[0] => 10
[1] => 1
)
[DataUtils] => Array
(
[0] => 10
[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
[0] => 10
[1] => 3
)
[GeneFamilies] => Array
(
[0] => 10
[1] => 4
)
[Organism] => Array
(
[0] => 10
[1] => 5
)
[Blast] => Array
(
[0] => 10
[1] => 6
)
[WorkbenchUtils] => Array
(
[0] => 10
[1] => 7
)
[PhylogeneticModuleUtils] => Array
(
[0] => 10
[1] => 8
)
[ExternalPrograms] => Array
(
[0] => 10
[1] => 9
)
[FastaUtils] => Array
(
[0] => 10
[1] => 10
)
[MsaUtils] => Array
(
[0] => 10
[1] => 11
)
[PhylogeneticUtils] => Array
(
[0] => 10
[1] => 12
)
[Sequence] => Array
(
[0] => 10
[1] => 13
)
[RequestHandler] => Array
(
[0] => 10
[1] => 14
)
)
[_loaded:protected] => Array
(
[Session] => SessionComponent Object
(
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[DataUtils] => DataUtilsComponent Object
(
[name] => DataUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FunctionalUtils
[2] => GeneFamilies
[3] => GenomeBrowser
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
)
[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
(
[name] => FunctionalAnnotationUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => FunctionalUtils
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[Organism] => OrganismComponent Object
(
[name] => Organism
[controller:OrganismComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => GenomeBrowser
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
)
[Blast] => BlastComponent Object
(
[name] => Blast
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[WorkbenchUtils] => WorkbenchUtilsComponent Object
(
[name] => WorkbenchUtils
[controller:WorkbenchUtilsComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FormUtils
[2] => FunctionalUtils
[3] => GeneFamilies
[4] => WorkbenchSharedAccessRights
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FormUtils] => Array
(
[class] => FormUtils
[settings] => Array
(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[WorkbenchSharedAccessRights] => Array
(
[class] => WorkbenchSharedAccessRights
[settings] => Array
(
)
)
)
)
[PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
(
[name] => PhylogeneticModuleUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FastaUtils
[2] => MsaUtils
[3] => PhylogeneticUtils
[4] => Sequence
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FastaUtils] => Array
(
[class] => FastaUtils
[settings] => Array
(
)
)
[MsaUtils] => Array
(
[class] => MsaUtils
[settings] => Array
(
)
)
[PhylogeneticUtils] => Array
(
[class] => PhylogeneticUtils
[settings] => Array
(
)
)
[Sequence] => Array
(
[class] => Sequence
[settings] => Array
(
)
)
)
)
[ExternalPrograms] => ExternalProgramsComponent Object
(
[name] => ExternalPrograms
[components] => Array
(
[0] => FastaUtils
)
[program_paths:ExternalProgramsComponent:private] => Array
(
[java] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => java/x86_64/21.0.2
)
[command] => java -Djava.awt.headless=true
)
[local_settings] => java -Djava.awt.headless=true
[db_connector] => mysql-connector-java-8.0.21.jar
)
[perl] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => perl
)
[command] => perl -w
)
[local_settings] => /usr/bin/perl
)
[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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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
(
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[controller] => AnalysisController Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[components] => Array
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[_componentMap:protected] => Array
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[MsaUtils] => MsaUtilsComponent Object
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[controller] => AnalysisController Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[components] => Array
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[_componentMap:protected] => Array
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[PhylogeneticUtils] => PhylogeneticUtilsComponent Object
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[controller] => AnalysisController Object
*RECURSION*
[components] => Array
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[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
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[class] => ExternalPrograms
[settings] => Array
(
)
)
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[Sequence] => SequenceComponent Object
(
[name] => Sequence
[components] => Array
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[0] => Blast
[1] => Coordinates
[2] => ExternalPrograms
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[_componentMap:protected] => Array
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[Blast] => Array
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[Coordinates] => Array
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[class] => Coordinates
[settings] => Array
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[ExternalPrograms] => Array
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[class] => ExternalPrograms
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[controller] => AnalysisController Object
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[RequestHandler] => RequestHandlerComponent Object
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[ajaxLayout] => ajax
[enabled] => 1
[request] => CakeRequest Object
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[params] => Array
(
[plugin] =>
[controller] => analysis
[action] => custom_tree_creation
[named] => Array
(
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[pass] => Array
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[isAjax] =>
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[data] => Array
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[query] => Array
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[webroot] => /plaza.dev/_dev_instances/feedback/
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[_detectors:protected] => Array
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[get] => Array
(
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[patch] => Array
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[post] => Array
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[put] => Array
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[delete] => Array
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[head] => Array
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[ssl] => Array
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[ajax] => Array
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[env] => HTTP_X_REQUESTED_WITH
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[flash] => Array
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[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
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[mobile] => Array
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[env] => HTTP_USER_AGENT
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[17] => portalmmm
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[19] => ReqwirelessWeb
[20] => SonyEricsson
[21] => Symbian
[22] => UP\.Browser
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[24] => Windows CE
[25] => Windows Phone OS
[26] => Xiino
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[requested] => Array
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[param] => requested
[value] => 1
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[json] => Array
(
[accept] => Array
(
[0] => application/json
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[param] => ext
[value] => json
)
[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
)
[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
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[300] => Multiple Choices
[301] => Moved Permanently
[302] => Found
[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
)
[_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
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
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[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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[ext] =>
[_renderType:protected] =>
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[accept] => Array
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[_input:protected] =>
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[components] => Array
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[DataUtils] => DataUtilsComponent Object
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[_Controller:protected] => AnalysisController Object
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[Session] => Array
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[Sequence] => Array
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[RequestHandler] => Array
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[_componentMap:protected] => Array
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[_Collection:protected] => ComponentCollection Object
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(
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[_componentMap:protected] => Array
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[FunctionalUtils] => Array
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(
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*RECURSION*
[settings] => Array
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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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(
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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
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[settings] => Array
(
)
[components] => Array
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[_componentMap:protected] => Array
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[WorkbenchUtils] => WorkbenchUtilsComponent Object
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[ExternalPrograms] => Array
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)
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)
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[class] => WorkbenchSharedAccessRights
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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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[command] =>
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[Sequence] => SequenceComponent Object
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[controller] => AnalysisController Object
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[_mimeTypes:protected] => Array
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[html] => Array
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[mpga] => audio/mpeg
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[oga] => audio/ogg
[spx] => audio/ogg
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[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
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[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
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[4] => image/photoshop
[5] => zz-application/zz-winassoc-psd
)
[ice] => x-conference/x-cooltalk
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[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
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)
[xhtml-mobile] => application/vnd.wap.xhtml+xml
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(
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[wmlscript] => text/vnd.wap.wmlscript
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[woff] => application/x-font-woff
[webp] => image/webp
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[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
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[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
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[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
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[isAjax] =>
)
[data] => Array
(
)
[query] => Array
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)
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[webroot] => /plaza.dev/_dev_instances/feedback/
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[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
)
[post] => Array
(
[env] => REQUEST_METHOD
[value] => POST
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[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
(
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[1] => AvantGo
[2] => BB10
[3] => BlackBerry
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[5] => Fennec
[6] => iPod
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[8] => iPad
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[11] => NetFront
[12] => Nokia
[13] => Opera Mini
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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
)
)
[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
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[DataUtils] => Array
(
[0] => 10
[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
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[1] => 3
)
[GeneFamilies] => Array
(
[0] => 10
[1] => 4
)
[Organism] => Array
(
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[1] => 5
)
[Blast] => Array
(
[0] => 10
[1] => 6
)
[WorkbenchUtils] => Array
(
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[PhylogeneticModuleUtils] => Array
(
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[1] => 8
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[ExternalPrograms] => Array
(
[0] => 10
[1] => 9
)
[FastaUtils] => Array
(
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[1] => 10
)
[MsaUtils] => Array
(
[0] => 10
[1] => 11
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[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
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FormUtils] => Array
(
[class] => FormUtils
[settings] => Array
(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[WorkbenchSharedAccessRights] => Array
(
[class] => WorkbenchSharedAccessRights
[settings] => Array
(
)
)
)
)
[PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
(
[name] => PhylogeneticModuleUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FastaUtils
[2] => MsaUtils
[3] => PhylogeneticUtils
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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(
)
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[FastaUtils] => Array
(
[class] => FastaUtils
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(
)
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[MsaUtils] => Array
(
[class] => MsaUtils
[settings] => Array
(
)
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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
(
[java] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[command] => java -Djava.awt.headless=true
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)
[perl] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => perl
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[command] => perl -w
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[local_settings] => /usr/bin/perl
)
[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => bedops/x86_64/2.4.37
)
[command] =>
)
[local_settings] =>
)
[blastdbcmd] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
)
[command] => blastdbcmd
)
[local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
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[blast] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
)
[command] =>
)
[local_settings] => /usr/local/blast/2.2.24/bin/
)
[muscle] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
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)
)
)
[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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)
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[raxml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
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)
)
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[iqtree] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
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)
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[FastaUtils] => Array
(
[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
(
)
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[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*
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[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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[isAjax] =>
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[data] => Array
(
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)
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[_detectors:protected] => Array
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[get] => Array
(
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[patch] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
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[ajax] => Array
(
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[mobile] => Array
(
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[requested] => Array
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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
(
[_statusCodes:protected] => Array
(
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[201] => Created
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[305] => Use Proxy
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[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
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[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] => */*
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[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
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[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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[dxf] => application/dxf
[dxr] => application/x-director
[eot] => application/vnd.ms-fontobject
[eps] => application/postscript
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[midi] => audio/midi
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[rm] => audio/x-pn-realaudio
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[f90] => text/plain
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(
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[1] => */*
)
[ics] => text/calendar
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[sgml] => text/sgml
[tsv] => text/tab-separated-values
[tpl] => text/template
[txt] => text/plain
[text] => text/plain
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[fli] => video/x-fli
[mov] => video/quicktime
[movie] => video/x-sgi-movie
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[mpeg] => video/mpeg
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[qt] => video/quicktime
[viv] => video/vnd.vivo
[vivo] => video/vnd.vivo
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[webm] => video/webm
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[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
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[xpm] => image/x-xpixmap
[xwd] => image/x-xwindowdump
[psd] => Array
(
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[1] => application/psd
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[4] => image/photoshop
[5] => zz-application/zz-winassoc-psd
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[ice] => x-conference/x-cooltalk
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[igs] => model/iges
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[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
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(
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[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
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[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
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
[checkHttpCache] => 1
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
[params] => CakeRequest Object
(
[params] => Array
(
[plugin] =>
[controller] => analysis
[action] => custom_tree_creation
[named] => Array
(
)
[pass] => Array
(
[0] => gene_id
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[isAjax] =>
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[data] => Array
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[query] => Array
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[webroot] => /plaza.dev/_dev_instances/feedback/
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[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
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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
[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
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[1] => AvantGo
[2] => BB10
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[5] => Fennec
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[8] => iPad
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[10] => MIDP
[11] => NetFront
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[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
)
)
[requested] => Array
(
[param] => requested
[value] => 1
)
[json] => Array
(
[accept] => Array
(
[0] => application/json
)
[param] => ext
[value] => json
)
[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
)
[param] => ext
[value] => xml
)
)
[_input:protected] =>
)
)
)
[defaultPriority] => 10
)
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
)
[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
(
[name] => FunctionalAnnotationUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => FunctionalUtils
)
[_Collection:protected] => ComponentCollection Object
(
[_Controller:protected] => AnalysisController Object
*RECURSION*
[_enabled:protected] => Array
(
[Session] => Array
(
[0] => 10
[1] => 1
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[DataUtils] => Array
(
[0] => 10
[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
[0] => 10
[1] => 3
)
[GeneFamilies] => Array
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[0] => 10
[1] => 4
)
[Organism] => Array
(
[0] => 10
[1] => 5
)
[Blast] => Array
(
[0] => 10
[1] => 6
)
[WorkbenchUtils] => Array
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[0] => 10
[1] => 7
)
[PhylogeneticModuleUtils] => Array
(
[0] => 10
[1] => 8
)
[ExternalPrograms] => Array
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[0] => 10
[1] => 9
)
[FastaUtils] => Array
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[0] => 10
[1] => 10
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[MsaUtils] => Array
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[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
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(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
)
[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
*RECURSION*
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[Organism] => OrganismComponent Object
(
[name] => Organism
[controller:OrganismComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => GenomeBrowser
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
)
[Blast] => BlastComponent Object
(
[name] => Blast
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[WorkbenchUtils] => WorkbenchUtilsComponent Object
(
[name] => WorkbenchUtils
[controller:WorkbenchUtilsComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FormUtils
[2] => FunctionalUtils
[3] => GeneFamilies
[4] => WorkbenchSharedAccessRights
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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
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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(
)
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(
)
)
[MsaUtils] => Array
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[class] => MsaUtils
[settings] => Array
(
)
)
[PhylogeneticUtils] => Array
(
[class] => PhylogeneticUtils
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(
)
)
[Sequence] => Array
(
[class] => Sequence
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(
)
)
)
)
[ExternalPrograms] => ExternalProgramsComponent Object
(
[name] => ExternalPrograms
[components] => Array
(
[0] => FastaUtils
)
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[java] => Array
(
[cluster_settings] => Array
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[modules] => Array
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)
[command] => java -Djava.awt.headless=true
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[cluster_settings] => Array
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[modules] => Array
(
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[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[command] =>
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[local_settings] =>
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[blastdbcmd] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
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[command] => blastdbcmd
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(
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(
[modules] => Array
(
[0] => blast
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[command] =>
)
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[muscle] => Array
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[modules] => Array
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)
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(
)
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(
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*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
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(
)
)
)
)
[Sequence] => SequenceComponent Object
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(
[0] => Blast
[1] => Coordinates
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
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[Blast] => Array
(
[class] => Blast
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)
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[Coordinates] => Array
(
[class] => Coordinates
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(
)
)
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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(
)
)
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[controller] => AnalysisController Object
*RECURSION*
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[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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[isAjax] =>
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[data] => Array
(
)
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)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
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)
[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
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[env] => REQUEST_METHOD
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[head] => Array
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[env] => REQUEST_METHOD
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[options] => Array
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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)
)
)
[_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
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[isAjax] =>
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[data] => Array
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[query] => Array
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[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
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[post] => Array
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[env] => REQUEST_METHOD
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[put] => Array
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[env] => REQUEST_METHOD
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[delete] => Array
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[env] => REQUEST_METHOD
[value] => DELETE
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[head] => Array
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[env] => REQUEST_METHOD
[value] => HEAD
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[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
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[ssl] => Array
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[env] => HTTPS
[value] => 1
)
[ajax] => Array
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[env] => HTTP_X_REQUESTED_WITH
[value] => XMLHttpRequest
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[flash] => Array
(
[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
(
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[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
(
)
)
[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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[0] => 10
[1] => 14
)
)
[_loaded:protected] => Array
(
[Session] => SessionComponent Object
(
[_Collection:protected] => ComponentCollection Object
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[settings] => Array
(
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[components] => Array
(
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[_componentMap:protected] => Array
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[DataUtils] => DataUtilsComponent Object
(
[name] => DataUtils
[controller] => AnalysisController Object
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[components] => Array
(
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[1] => FunctionalUtils
[2] => GeneFamilies
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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)
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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
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[_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
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[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
(
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(
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[_input:protected] =>
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[Sequence] => Array
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[RequestHandler] => Array
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(
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[_componentMap:protected] => Array
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(
[class] => GeneFamilies
[settings] => Array
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)
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[GenomeBrowser] => Array
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(
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
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[_componentMap:protected] => Array
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[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
(
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[components] => Array
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
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[FunctionalUtils] => Array
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(
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*RECURSION*
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
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)
[_componentMap:protected] => Array
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[GenomeBrowser] => Array
(
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
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[components] => Array
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[_componentMap:protected] => Array
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[WorkbenchUtils] => WorkbenchUtilsComponent Object
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(
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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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[muscle] => Array
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[mafft] => Array
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[phyml] => Array
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[fasttree] => Array
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[raxml] => Array
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[iqtree] => Array
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*RECURSION*
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)
[_componentMap:protected] => Array
(
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(
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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
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)
[_componentMap:protected] => Array
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[MsaUtils] => MsaUtilsComponent Object
(
[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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)
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[PhylogeneticUtils] => PhylogeneticUtilsComponent Object
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[components] => Array
(
[0] => ExternalPrograms
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
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)
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[Sequence] => SequenceComponent Object
(
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(
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
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[Blast] => Array
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[Coordinates] => Array
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[controller] => AnalysisController Object
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[RequestHandler] => RequestHandlerComponent Object
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[request] => CakeRequest Object
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[params] => Array
(
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[_detectors:protected] => Array
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(
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[patch] => Array
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[env] => REQUEST_METHOD
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[json] => Array
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[param] => ext
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[_input:protected] =>
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[_mimeTypes:protected] => Array
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[html] => Array
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[htm] => Array
(
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[ics] => text/calendar
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[psd] => Array
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[ice] => x-conference/x-cooltalk
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[silo] => model/mesh
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[mime] => www/mime
[pdb] => chemical/x-pdb
[xyz] => chemical/x-pdb
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[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
(
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(
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(
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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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[components] => Array
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[_componentMap:protected] => Array
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[params] => CakeRequest Object
(
[params] => Array
(
[plugin] =>
[controller] => analysis
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(
)
[pass] => Array
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[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
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[patch] => Array
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[delete] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
(
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(
[env] => REQUEST_METHOD
[value] => OPTIONS
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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/
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[mobile] => Array
(
[env] => HTTP_USER_AGENT
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[25] => Windows Phone OS
[26] => Xiino
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[value] => 1
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[json] => Array
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(
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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
(
)
[_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
(
)
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[WorkbenchSharedAccessRights] => Array
(
[class] => WorkbenchSharedAccessRights
[settings] => Array
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)
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[PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
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[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FastaUtils
[2] => MsaUtils
[3] => PhylogeneticUtils
[4] => Sequence
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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
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[0] => 10
[1] => 2
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[FunctionalAnnotationUtils] => Array
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)
[GeneFamilies] => Array
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[0] => 10
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[Organism] => Array
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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
(
[0] => 10
[1] => 10
)
[MsaUtils] => Array
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[0] => 10
[1] => 11
)
[PhylogeneticUtils] => Array
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[0] => 10
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[Sequence] => Array
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[RequestHandler] => Array
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)
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[_loaded:protected] => Array
(
[Session] => SessionComponent Object
(
[_Collection:protected] => ComponentCollection Object
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[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
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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
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
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[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
(
)
)
)
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[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
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)
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[Organism] => OrganismComponent Object
(
[name] => Organism
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[components] => Array
(
[0] => GenomeBrowser
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
)
[Blast] => BlastComponent Object
(
[name] => Blast
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
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)
)
[WorkbenchUtils] => WorkbenchUtilsComponent Object
(
[name] => WorkbenchUtils
[controller:WorkbenchUtilsComponent:private] => AnalysisController Object
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[components] => Array
(
[0] => ExternalPrograms
[1] => FormUtils
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*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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[FormUtils] => Array
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[class] => FormUtils
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)
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[GeneFamilies] => Array
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[class] => GeneFamilies
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)
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[class] => WorkbenchSharedAccessRights
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)
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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
(
[cluster_settings] => Array
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[modules] => Array
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[perl] => Array
(
[cluster_settings] => Array
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[modules] => Array
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[0] => perl
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[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
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[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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(
[cluster_settings] => Array
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[modules] => Array
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[command] =>
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[muscle] => Array
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[mafft] => Array
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[phyml] => Array
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[iqtree] => Array
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)
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(
[name] => FastaUtils
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*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
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[MsaUtils] => MsaUtilsComponent Object
(
[name] => MsaUtils
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
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)
[_componentMap:protected] => Array
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)
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[PhylogeneticUtils] => PhylogeneticUtilsComponent Object
(
[name] => PhylogeneticUtils
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*RECURSION*
[components] => Array
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[0] => ExternalPrograms
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[_Collection:protected] => ComponentCollection Object
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)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
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)
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[Sequence] => SequenceComponent Object
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[name] => Sequence
[components] => Array
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[0] => Blast
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
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[Blast] => Array
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[class] => Blast
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)
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[Coordinates] => Array
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[class] => Coordinates
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)
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[ExternalPrograms] => Array
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[class] => ExternalPrograms
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(
)
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[controller] => AnalysisController Object
*RECURSION*
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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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[_detectors:protected] => Array
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[patch] => Array
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[mobile] => Array
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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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[305] => Use Proxy
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[405] => Method Not Allowed
[406] => Not Acceptable
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[408] => Request Time-out
[409] => Conflict
[410] => Gone
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[412] => Precondition Failed
[413] => Request Entity Too Large
[414] => Request-URI Too Large
[415] => Unsupported Media Type
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[417] => Expectation Failed
[429] => Too Many Requests
[500] => Internal Server Error
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[502] => Bad Gateway
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[504] => Gateway Time-out
[505] => Unsupported Version
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[_mimeTypes:protected] => Array
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[html] => Array
(
[0] => text/html
[1] => */*
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[json] => application/json
[xml] => Array
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[0] => application/xml
[1] => text/xml
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[rss] => application/rss+xml
[ai] => application/postscript
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[bin] => application/octet-stream
[ccad] => application/clariscad
[cdf] => application/x-netcdf
[class] => application/octet-stream
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[csv] => Array
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[dcr] => application/x-director
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[ez] => application/andrew-inset
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[hqx] => application/mac-binhex40
[ico] => image/x-icon
[ips] => application/x-ipscript
[ipx] => application/x-ipix
[js] => application/javascript
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[latex] => application/x-latex
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[man] => application/x-troff-man
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
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[isAjax] =>
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[data] => Array
(
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[query] => Array
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[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
)
[post] => Array
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[env] => REQUEST_METHOD
[value] => POST
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[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
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[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/
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[mobile] => Array
(
[env] => HTTP_USER_AGENT
[options] => Array
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
)
[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
)
[post] => Array
(
[env] => REQUEST_METHOD
[value] => POST
)
[put] => Array
(
[env] => REQUEST_METHOD
[value] => PUT
)
[delete] => Array
(
[env] => REQUEST_METHOD
[value] => DELETE
)
[head] => Array
(
[env] => REQUEST_METHOD
[value] => HEAD
)
[options] => Array
(
[env] => REQUEST_METHOD
[value] => OPTIONS
)
[ssl] => Array
(
[env] => HTTPS
[value] => 1
)
[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
[value] => XMLHttpRequest
)
[flash] => Array
(
[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
)
[mobile] => Array
(
[env] => HTTP_USER_AGENT
[options] => Array
(
[0] => Android
[1] => AvantGo
[2] => BB10
[3] => BlackBerry
[4] => DoCoMo
[5] => Fennec
[6] => iPod
[7] => iPhone
[8] => iPad
[9] => J2ME
[10] => MIDP
[11] => NetFront
[12] => Nokia
[13] => Opera Mini
[14] => Opera Mobi
[15] => PalmOS
[16] => PalmSource
[17] => portalmmm
[18] => Plucker
[19] => ReqwirelessWeb
[20] => SonyEricsson
[21] => Symbian
[22] => UP\.Browser
[23] => webOS
[24] => Windows CE
[25] => Windows Phone OS
[26] => Xiino
)
)
[requested] => Array
(
[param] => requested
[value] => 1
)
[json] => Array
(
[accept] => Array
(
[0] => application/json
)
[param] => ext
[value] => json
)
[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
)
[param] => ext
[value] => xml
)
)
[_input:protected] =>
)
)
)
[defaultPriority] => 10
)
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[MsaUtils] => MsaUtilsComponent Object
(
[name] => MsaUtils
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
(
[_Controller:protected] => AnalysisController Object
*RECURSION*
[_enabled:protected] => Array
(
[Session] => Array
(
[0] => 10
[1] => 1
)
[DataUtils] => Array
(
[0] => 10
[1] => 2
)
[FunctionalAnnotationUtils] => Array
(
[0] => 10
[1] => 3
)
[GeneFamilies] => Array
(
[0] => 10
[1] => 4
)
[Organism] => Array
(
[0] => 10
[1] => 5
)
[Blast] => Array
(
[0] => 10
[1] => 6
)
[WorkbenchUtils] => Array
(
[0] => 10
[1] => 7
)
[PhylogeneticModuleUtils] => Array
(
[0] => 10
[1] => 8
)
[ExternalPrograms] => Array
(
[0] => 10
[1] => 9
)
[FastaUtils] => Array
(
[0] => 10
[1] => 10
)
[MsaUtils] => Array
(
[0] => 10
[1] => 11
)
[PhylogeneticUtils] => Array
(
[0] => 10
[1] => 12
)
[Sequence] => Array
(
[0] => 10
[1] => 13
)
[RequestHandler] => Array
(
[0] => 10
[1] => 14
)
)
[_loaded:protected] => Array
(
[Session] => SessionComponent Object
(
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[DataUtils] => DataUtilsComponent Object
(
[name] => DataUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FunctionalUtils
[2] => GeneFamilies
[3] => GenomeBrowser
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
)
[FunctionalAnnotationUtils] => FunctionalAnnotationUtilsComponent Object
(
[name] => FunctionalAnnotationUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => FunctionalUtils
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
[name] => GeneFamilies
[controller:GeneFamiliesComponent:private] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[Organism] => OrganismComponent Object
(
[name] => Organism
[controller:OrganismComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => GenomeBrowser
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
[settings] => Array
(
)
)
)
)
[Blast] => BlastComponent Object
(
[name] => Blast
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[WorkbenchUtils] => WorkbenchUtilsComponent Object
(
[name] => WorkbenchUtils
[controller:WorkbenchUtilsComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FormUtils
[2] => FunctionalUtils
[3] => GeneFamilies
[4] => WorkbenchSharedAccessRights
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FormUtils] => Array
(
[class] => FormUtils
[settings] => Array
(
)
)
[FunctionalUtils] => Array
(
[class] => FunctionalUtils
[settings] => Array
(
)
)
[GeneFamilies] => Array
(
[class] => GeneFamilies
[settings] => Array
(
)
)
[WorkbenchSharedAccessRights] => Array
(
[class] => WorkbenchSharedAccessRights
[settings] => Array
(
)
)
)
)
[PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
(
[name] => PhylogeneticModuleUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
[1] => FastaUtils
[2] => MsaUtils
[3] => PhylogeneticUtils
[4] => Sequence
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
[FastaUtils] => Array
(
[class] => FastaUtils
[settings] => Array
(
)
)
[MsaUtils] => Array
(
[class] => MsaUtils
[settings] => Array
(
)
)
[PhylogeneticUtils] => Array
(
[class] => PhylogeneticUtils
[settings] => Array
(
)
)
[Sequence] => Array
(
[class] => Sequence
[settings] => Array
(
)
)
)
)
[ExternalPrograms] => ExternalProgramsComponent Object
(
[name] => ExternalPrograms
[components] => Array
(
[0] => FastaUtils
)
[program_paths:ExternalProgramsComponent:private] => Array
(
[java] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => java/x86_64/21.0.2
)
[command] => java -Djava.awt.headless=true
)
[local_settings] => java -Djava.awt.headless=true
[db_connector] => mysql-connector-java-8.0.21.jar
)
[perl] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => perl
)
[command] => perl -w
)
[local_settings] => /usr/bin/perl
)
[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => bedops/x86_64/2.4.37
)
[command] =>
)
[local_settings] =>
)
[blastdbcmd] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
)
[command] => blastdbcmd
)
[local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
)
[blast] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
)
[command] =>
)
[local_settings] => /usr/local/blast/2.2.24/bin/
)
[muscle] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => muscle/x86_64/3.8.31
)
)
)
[mafft] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => mafft/x86_64/7.187
)
)
)
[phyml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => phyml/x86_64/20150219
)
)
)
[fasttree] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => fasttree/x86_64/2.1.7
)
)
)
[raxml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => raxml/x86_64/8.2.8
)
)
)
[iqtree] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => iqtree/x86_64/1.5.5
)
)
)
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[FastaUtils] => Array
(
[class] => FastaUtils
[settings] => Array
(
)
)
)
)
[FastaUtils] => FastaUtilsComponent Object
(
[name] => FastaUtils
[controller] => AnalysisController Object
*RECURSION*
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[components] => Array
(
)
[_componentMap:protected] => Array
(
)
)
[MsaUtils] => MsaUtilsComponent Object
*RECURSION*
[PhylogeneticUtils] => PhylogeneticUtilsComponent Object
(
[name] => PhylogeneticUtils
[controller] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => ExternalPrograms
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
)
)
[Sequence] => SequenceComponent Object
(
[name] => Sequence
[components] => Array
(
[0] => Blast
[1] => Coordinates
[2] => ExternalPrograms
)
[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[Blast] => Array
(
[class] => Blast
[settings] => Array
(
)
)
[Coordinates] => Array
(
[class] => Coordinates
[settings] => Array
(
)
)
[ExternalPrograms] => Array
(
[class] => ExternalPrograms
[settings] => Array
(
)
)
)
[controller] => AnalysisController Object
*RECURSION*
)
[RequestHandler] => RequestHandlerComponent Object
(
[ajaxLayout] => ajax
[enabled] => 1
[request] => CakeRequest Object
(
[params] => Array
(
[plugin] =>
[controller] => analysis
[action] => custom_tree_creation
[named] => Array
(
)
[pass] => Array
(
[0] => gene_id
[1] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
(
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[1] => 10
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[MsaUtils] => Array
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[1] => 11
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[PhylogeneticUtils] => Array
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[0] => 10
[1] => 12
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[Sequence] => Array
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[0] => 10
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[RequestHandler] => Array
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[_loaded:protected] => Array
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[settings] => Array
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[components] => Array
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[_componentMap:protected] => Array
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[DataUtils] => DataUtilsComponent Object
(
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[_componentMap:protected] => Array
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[FunctionalUtils] => Array
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[class] => FunctionalUtils
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[GeneFamilies] => Array
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[class] => GeneFamilies
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[GenomeBrowser] => Array
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*RECURSION*
[settings] => Array
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[components] => Array
(
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[_componentMap:protected] => Array
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[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
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(
)
)
)
)
[GeneFamilies] => GeneFamiliesComponent Object
(
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
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[components] => Array
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[_componentMap:protected] => Array
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[Organism] => OrganismComponent Object
(
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[controller:OrganismComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
[0] => GenomeBrowser
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
)
[_componentMap:protected] => Array
(
[GenomeBrowser] => Array
(
[class] => GenomeBrowser
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(
)
)
)
)
[Blast] => BlastComponent Object
(
[name] => Blast
[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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[WorkbenchUtils] => WorkbenchUtilsComponent Object
(
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[controller:WorkbenchUtilsComponent:private] => AnalysisController Object
*RECURSION*
[components] => Array
(
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[1] => FormUtils
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
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[_componentMap:protected] => Array
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[ExternalPrograms] => Array
(
[class] => ExternalPrograms
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[FormUtils] => Array
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[class] => FormUtils
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)
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[FunctionalUtils] => Array
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[class] => FunctionalUtils
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)
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[GeneFamilies] => Array
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[class] => GeneFamilies
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)
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[WorkbenchSharedAccessRights] => Array
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[class] => WorkbenchSharedAccessRights
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)
)
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[PhylogeneticModuleUtils] => PhylogeneticModuleUtilsComponent Object
(
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[components] => Array
(
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[_componentMap:protected] => Array
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[ExternalPrograms] => Array
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[class] => ExternalPrograms
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[FastaUtils] => Array
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[class] => FastaUtils
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)
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[MsaUtils] => Array
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[class] => MsaUtils
[settings] => Array
(
)
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[PhylogeneticUtils] => Array
(
[class] => PhylogeneticUtils
[settings] => Array
(
)
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[Sequence] => Array
(
[class] => Sequence
[settings] => Array
(
)
)
)
)
[ExternalPrograms] => ExternalProgramsComponent Object
(
[name] => ExternalPrograms
[components] => Array
(
[0] => FastaUtils
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[program_paths:ExternalProgramsComponent:private] => Array
(
[java] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[command] => java -Djava.awt.headless=true
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[local_settings] => java -Djava.awt.headless=true
[db_connector] => mysql-connector-java-8.0.21.jar
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[perl] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => perl
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[command] => perl -w
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[local_settings] => /usr/bin/perl
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[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
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[local_settings] =>
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[bedops] => Array
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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
)
[blast] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
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[command] =>
)
[local_settings] => /usr/local/blast/2.2.24/bin/
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[muscle] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => muscle/x86_64/3.8.31
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[mafft] => Array
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[cluster_settings] => Array
(
[modules] => Array
(
[0] => mafft/x86_64/7.187
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)
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[phyml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[0] => phyml/x86_64/20150219
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)
)
[fasttree] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => fasttree/x86_64/2.1.7
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)
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[raxml] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[0] => raxml/x86_64/8.2.8
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)
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[iqtree] => Array
(
[cluster_settings] => Array
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[modules] => Array
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[0] => iqtree/x86_64/1.5.5
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)
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[_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*
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[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] =>
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[data] => Array
(
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[query] => Array
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[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_detectors:protected] => Array
(
[get] => Array
(
[env] => REQUEST_METHOD
[value] => GET
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[patch] => Array
(
[env] => REQUEST_METHOD
[value] => PATCH
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[post] => Array
(
[env] => REQUEST_METHOD
[value] => POST
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[put] => Array
(
[env] => REQUEST_METHOD
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[delete] => Array
(
[env] => REQUEST_METHOD
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[head] => Array
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[env] => REQUEST_METHOD
[value] => HEAD
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[env] => REQUEST_METHOD
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[ssl] => Array
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[env] => HTTPS
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[ajax] => Array
(
[env] => HTTP_X_REQUESTED_WITH
[value] => XMLHttpRequest
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[flash] => Array
(
[env] => HTTP_USER_AGENT
[pattern] => /^(Shockwave|Adobe) Flash/
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[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
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[json] => Array
(
[accept] => Array
(
[0] => application/json
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[param] => ext
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[xml] => Array
(
[accept] => Array
(
[0] => application/xml
[1] => text/xml
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[param] => ext
[value] => xml
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[_input:protected] =>
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[response] => CakeResponse Object
(
[_statusCodes:protected] => Array
(
[100] => Continue
[101] => Switching Protocols
[200] => OK
[201] => Created
[202] => Accepted
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[204] => No Content
[205] => Reset Content
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[300] => Multiple Choices
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[302] => Found
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[305] => Use Proxy
[307] => Temporary Redirect
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[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] => */*
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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
(
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[1] => application/vnd.ms-excel
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[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
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[prt] => application/pro_eng
[ps] => application/postscript
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[set] => application/set
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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
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[xll] => application/vnd.ms-excel
[xlm] => application/vnd.ms-excel
[xls] => application/vnd.ms-excel
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[xlw] => application/vnd.ms-excel
[zip] => application/zip
[aif] => audio/x-aiff
[aifc] => audio/x-aiff
[aiff] => audio/x-aiff
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[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
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[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
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[xml] => Array
(
[0] => Array
(
[0] => RequestHandlerComponent Object
*RECURSION*
[1] => convertXml
)
)
)
[_viewClassMap:protected] => Array
(
[json] => Json
[xml] => Xml
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[_Collection:protected] => ComponentCollection Object
*RECURSION*
[settings] => Array
(
[checkHttpCache] => 1
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
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[isAjax] =>
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[data] => Array
(
)
[query] => Array
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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[command] => perl -w
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[local_settings] => /usr/bin/perl
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[bash] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
)
[command] =>
)
[local_settings] =>
)
[bedops] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[0] => bedops/x86_64/2.4.37
)
[command] =>
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[local_settings] =>
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[blastdbcmd] => Array
(
[cluster_settings] => Array
(
[modules] => Array
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[0] => blast
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[command] => blastdbcmd
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[local_settings] => /usr/local/blast/2.2.24/bin/blastdbcmd
)
[blast] => Array
(
[cluster_settings] => Array
(
[modules] => Array
(
[0] => blast
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[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] => arahy.Tifrunner.gnm1.ann1.87PAU8
)
[isAjax] =>
)
[data] => Array
(
)
[query] => Array
(
)
[url] => analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[base] => /plaza.dev/_dev_instances/feedback
[webroot] => /plaza.dev/_dev_instances/feedback/
[here] => /plaza.dev/_dev_instances/feedback/analysis/custom_tree_creation/gene_id/arahy.Tifrunner.gnm1.ann1.87PAU8
[_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
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[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
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[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
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[passParams] => 1
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)
)
[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
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[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Configuration Object
*RECURSION*
[1] => afterDelete
)
[passParams] =>
)
)
)
)
[_isGlobal:protected] =>
)
[_validator:protected] =>
)
[AnnotSource] => AnnotSource Object
(
[name] => AnnotSource
[useTable] => annot_sources
[primaryKey] => species
[displayField] => common_name
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
[table] => annot_sources
[_schema:protected] => Array
(
[source] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 255
[collate] => latin1_swedish_ci
[charset] => latin1
)
[url] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 250
[collate] => latin1_swedish_ci
[charset] => latin1
)
[species] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 21
[key] => primary
[collate] => latin1_swedish_ci
[charset] => latin1
)
[common_name] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 100
[key] => index
[collate] => latin1_swedish_ci
[charset] => latin1
)
[eco_type] => Array
(
[type] => string
[null] => 1
[default] =>
[length] => 100
[collate] => latin1_swedish_ci
[charset] => latin1
)
[description] => Array
(
[type] => text
[null] =>
[default] =>
[length] =>
[collate] => latin1_swedish_ci
[charset] => latin1
)
[paper] => Array
(
[type] => text
[null] => 1
[default] =>
[length] =>
[collate] => latin1_swedish_ci
[charset] => latin1
)
[pubmed_id] => Array
(
[type] => integer
[null] => 1
[default] =>
[length] =>
[unsigned] =>
)
[tax_id] => Array
(
[type] => integer
[null] =>
[default] => 0
[length] =>
[unsigned] =>
)
[mitochondrion] => Array
(
[type] => string
[null] => 1
[default] =>
[length] => 15
[collate] => latin1_swedish_ci
[charset] => latin1
)
[chloroplast] => Array
(
[type] => string
[null] => 1
[default] =>
[length] => 15
[collate] => latin1_swedish_ci
[charset] => latin1
)
[disclaimer] => Array
(
[type] => text
[null] => 1
[default] =>
[length] =>
[collate] => latin1_swedish_ci
[charset] => latin1
)
)
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
[alias] => AnnotSource
[tableToModel] => Array
(
[annot_sources] => AnnotSource
)
[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
(
)
[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[whitelist] => Array
(
)
[cacheSources] => 1
[findQueryType] =>
[recursive] => 1
[order] =>
[virtualFields] => Array
(
)
[_associationKeys:protected] => Array
(
[belongsTo] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => counterCache
)
[hasOne] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => dependent
)
[hasMany] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => limit
[6] => offset
[7] => dependent
[8] => exclusive
[9] => finderQuery
[10] => counterQuery
)
[hasAndBelongsToMany] => Array
(
[0] => className
[1] => joinTable
[2] => with
[3] => foreignKey
[4] => associationForeignKey
[5] => conditions
[6] => fields
[7] => order
[8] => limit
[9] => offset
[10] => unique
[11] => finderQuery
)
)
[_associations:protected] => Array
(
[0] => belongsTo
[1] => hasOne
[2] => hasMany
[3] => hasAndBelongsToMany
)
[__backAssociation] => Array
(
)
[__backInnerAssociation] => Array
(
)
[__backOriginalAssociation] => Array
(
)
[__backContainableAssociation] => Array
(
)
[__safeUpdateMode] =>
[useConsistentAfterFind] => 1
[_insertID:protected] =>
[_sourceConfigured:protected] => 1
[findMethods] => Array
(
[all] => 1
[first] => 1
[count] => 1
[neighbors] => 1
[list] => 1
[threaded] => 1
)
[_eventManager:protected] => CakeEventManager Object
(
[_listeners:protected] => Array
(
[Model.beforeFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => beforeFind
)
[passParams] => 1
)
)
)
[Model.afterFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => afterFind
)
[passParams] => 1
)
)
)
[Model.beforeValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => beforeValidate
)
[passParams] => 1
)
)
)
[Model.afterValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => afterValidate
)
[passParams] =>
)
)
)
[Model.beforeSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => beforeSave
)
[passParams] => 1
)
)
)
[Model.afterSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => afterSave
)
[passParams] => 1
)
)
)
[Model.beforeDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => beforeDelete
)
[passParams] => 1
)
)
)
[Model.afterDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => AnnotSource
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
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[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => AnnotSource Object
*RECURSION*
[1] => afterDelete
)
[passParams] =>
)
)
)
)
[_isGlobal:protected] =>
)
[_validator:protected] =>
)
[GeneFamilyTypes] => GeneFamilyTypes Object
(
[name] => GeneFamilyTypes
[useTable] => gene_family_types
[primaryKey] => id
[displayField] => name
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
[table] => gene_family_types
[_schema:protected] => Array
(
[id] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 10
[key] => primary
[collate] => latin1_swedish_ci
[comment] => unique identifier for this gene family type. foreign key to other GF tables
[charset] => latin1
)
[name] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 50
[collate] => latin1_swedish_ci
[comment] => description of gene family type
[charset] => latin1
)
[prefix] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 10
[collate] => latin1_swedish_ci
[comment] => prefix used for building the gf type. for compatibility reasons. shouldn't be used.
[charset] => latin1
)
[gene_type] => Array
(
[type] => enum('coding','rna','pseudo','te')
[null] =>
[default] => coding
[length] => 6
[collate] => latin1_swedish_ci
[comment] => should match type from table annotation
[charset] => latin1
)
[method] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 500
[collate] => latin1_swedish_ci
[comment] => JSON style information of the building method+parameters used
[charset] => latin1
)
[ancestry] => Array
(
[type] => enum('homology','orthology','homeology','other')
[null] =>
[default] => homology
[length] => 9
[key] => index
[collate] => latin1_swedish_ci
[comment] => type of gene family content
[charset] => latin1
)
[parent_id] => Array
(
[type] => string
[null] => 1
[default] =>
[length] => 10
[collate] => latin1_swedish_ci
[comment] => link to the parent id if appropriate
[charset] => latin1
)
)
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
[alias] => GeneFamilyTypes
[tableToModel] => Array
(
[gene_family_types] => GeneFamilyTypes
)
[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
(
)
[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[whitelist] => Array
(
)
[cacheSources] => 1
[findQueryType] =>
[recursive] => 1
[order] =>
[virtualFields] => Array
(
)
[_associationKeys:protected] => Array
(
[belongsTo] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => counterCache
)
[hasOne] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => dependent
)
[hasMany] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => limit
[6] => offset
[7] => dependent
[8] => exclusive
[9] => finderQuery
[10] => counterQuery
)
[hasAndBelongsToMany] => Array
(
[0] => className
[1] => joinTable
[2] => with
[3] => foreignKey
[4] => associationForeignKey
[5] => conditions
[6] => fields
[7] => order
[8] => limit
[9] => offset
[10] => unique
[11] => finderQuery
)
)
[_associations:protected] => Array
(
[0] => belongsTo
[1] => hasOne
[2] => hasMany
[3] => hasAndBelongsToMany
)
[__backAssociation] => Array
(
)
[__backInnerAssociation] => Array
(
)
[__backOriginalAssociation] => Array
(
)
[__backContainableAssociation] => Array
(
)
[__safeUpdateMode] =>
[useConsistentAfterFind] => 1
[_insertID:protected] =>
[_sourceConfigured:protected] => 1
[findMethods] => Array
(
[all] => 1
[first] => 1
[count] => 1
[neighbors] => 1
[list] => 1
[threaded] => 1
)
[_eventManager:protected] => CakeEventManager Object
(
[_listeners:protected] => Array
(
[Model.beforeFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => beforeFind
)
[passParams] => 1
)
)
)
[Model.afterFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => afterFind
)
[passParams] => 1
)
)
)
[Model.beforeValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => beforeValidate
)
[passParams] => 1
)
)
)
[Model.afterValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => afterValidate
)
[passParams] =>
)
)
)
[Model.beforeSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => beforeSave
)
[passParams] => 1
)
)
)
[Model.afterSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => afterSave
)
[passParams] => 1
)
)
)
[Model.beforeDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => beforeDelete
)
[passParams] => 1
)
)
)
[Model.afterDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GeneFamilyTypes
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GeneFamilyTypes Object
*RECURSION*
[1] => afterDelete
)
[passParams] =>
)
)
)
)
[_isGlobal:protected] =>
)
[_validator:protected] =>
)
[Similarities] => Similarities Object
(
[name] => Similarities
[useTable] => similarities
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
[table] => similarities
[primaryKey] => id
[_schema:protected] => Array
(
[species] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 21
[key] => index
[collate] => latin1_swedish_ci
[charset] => latin1
)
[query] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 50
[key] => primary
[collate] => latin1_swedish_ci
[charset] => latin1
)
[hits] => Array
(
[type] => binary
[null] =>
[default] =>
[length] =>
)
)
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
[alias] => Similarities
[tableToModel] => Array
(
[similarities] => Similarities
)
[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
(
)
[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[whitelist] => Array
(
)
[cacheSources] => 1
[findQueryType] =>
[recursive] => 1
[order] =>
[virtualFields] => Array
(
)
[_associationKeys:protected] => Array
(
[belongsTo] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => counterCache
)
[hasOne] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => dependent
)
[hasMany] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => limit
[6] => offset
[7] => dependent
[8] => exclusive
[9] => finderQuery
[10] => counterQuery
)
[hasAndBelongsToMany] => Array
(
[0] => className
[1] => joinTable
[2] => with
[3] => foreignKey
[4] => associationForeignKey
[5] => conditions
[6] => fields
[7] => order
[8] => limit
[9] => offset
[10] => unique
[11] => finderQuery
)
)
[_associations:protected] => Array
(
[0] => belongsTo
[1] => hasOne
[2] => hasMany
[3] => hasAndBelongsToMany
)
[__backAssociation] => Array
(
)
[__backInnerAssociation] => Array
(
)
[__backOriginalAssociation] => Array
(
)
[__backContainableAssociation] => Array
(
)
[__safeUpdateMode] =>
[useConsistentAfterFind] => 1
[_insertID:protected] =>
[_sourceConfigured:protected] => 1
[findMethods] => Array
(
[all] => 1
[first] => 1
[count] => 1
[neighbors] => 1
[list] => 1
[threaded] => 1
)
[_eventManager:protected] => CakeEventManager Object
(
[_listeners:protected] => Array
(
[Model.beforeFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => beforeFind
)
[passParams] => 1
)
)
)
[Model.afterFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => afterFind
)
[passParams] => 1
)
)
)
[Model.beforeValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => beforeValidate
)
[passParams] => 1
)
)
)
[Model.afterValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => afterValidate
)
[passParams] =>
)
)
)
[Model.beforeSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => beforeSave
)
[passParams] => 1
)
)
)
[Model.afterSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => afterSave
)
[passParams] => 1
)
)
)
[Model.beforeDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => beforeDelete
)
[passParams] => 1
)
)
)
[Model.afterDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => Similarities
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => Similarities Object
*RECURSION*
[1] => afterDelete
)
[passParams] =>
)
)
)
)
[_isGlobal:protected] =>
)
[_validator:protected] =>
)
[GfDatum] => GfDatum Object
(
[name] => GfDatum
[useTable] => gf_data
[belongsTo] => Array
(
[Annotation] => Array
(
[className] => Annotation
[foreignKey] => gene_id
[conditions] =>
[fields] =>
[order] =>
[counterCache] =>
)
[Genefamily] => Array
(
[className] => GeneFamily
[foreignKey] => gf_id
[conditions] =>
[fields] =>
[order] =>
[counterCache] =>
)
)
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
[table] => gf_data
[primaryKey] => id
[_schema:protected] => Array
(
[gf_id] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 50
[key] => primary
[collate] => latin1_swedish_ci
[charset] => latin1
)
[gf_type] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 10
[key] => index
[collate] => latin1_swedish_ci
[comment] => links to gene_family_types id
[charset] => latin1
)
[species] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 21
[key] => index
[collate] => latin1_swedish_ci
[charset] => latin1
)
[gene_id] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 50
[key] => primary
[collate] => latin1_swedish_ci
[charset] => latin1
)
[synteny_data] => Array
(
[type] => text
[null] => 1
[default] =>
[length] =>
[collate] => latin1_swedish_ci
[charset] => latin1
)
[cluster_data] => Array
(
[type] => float
[null] => 1
[default] =>
[length] =>
[unsigned] =>
)
[outlier] => Array
(
[type] => smallinteger
[null] =>
[default] => 0
[length] =>
[unsigned] =>
)
)
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[tablePrefix] =>
[plugin] =>
[alias] => GfDatum
[tableToModel] => Array
(
[gf_data] => GfDatum
)
[cacheQueries] =>
[hasOne] => Array
(
)
[hasMany] => Array
(
)
[hasAndBelongsToMany] => Array
(
)
[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[whitelist] => Array
(
)
[cacheSources] => 1
[findQueryType] =>
[recursive] => 1
[order] =>
[virtualFields] => Array
(
)
[_associationKeys:protected] => Array
(
[belongsTo] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => counterCache
)
[hasOne] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => dependent
)
[hasMany] => Array
(
[0] => className
[1] => foreignKey
[2] => conditions
[3] => fields
[4] => order
[5] => limit
[6] => offset
[7] => dependent
[8] => exclusive
[9] => finderQuery
[10] => counterQuery
)
[hasAndBelongsToMany] => Array
(
[0] => className
[1] => joinTable
[2] => with
[3] => foreignKey
[4] => associationForeignKey
[5] => conditions
[6] => fields
[7] => order
[8] => limit
[9] => offset
[10] => unique
[11] => finderQuery
)
)
[_associations:protected] => Array
(
[0] => belongsTo
[1] => hasOne
[2] => hasMany
[3] => hasAndBelongsToMany
)
[__backAssociation] => Array
(
)
[__backInnerAssociation] => Array
(
)
[__backOriginalAssociation] => Array
(
)
[__backContainableAssociation] => Array
(
)
[__safeUpdateMode] =>
[useConsistentAfterFind] => 1
[_insertID:protected] =>
[_sourceConfigured:protected] => 1
[findMethods] => Array
(
[all] => 1
[first] => 1
[count] => 1
[neighbors] => 1
[list] => 1
[threaded] => 1
)
[_eventManager:protected] => CakeEventManager Object
(
[_listeners:protected] => Array
(
[Model.beforeFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => beforeFind
)
[passParams] => 1
)
)
)
[Model.afterFind] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => afterFind
)
[passParams] => 1
)
)
)
[Model.beforeValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => beforeValidate
)
[passParams] => 1
)
)
)
[Model.afterValidate] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => afterValidate
)
[passParams] =>
)
)
)
[Model.beforeSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => beforeSave
)
[passParams] => 1
)
)
)
[Model.afterSave] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => afterSave
)
[passParams] => 1
)
)
)
[Model.beforeDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => beforeDelete
)
[passParams] => 1
)
)
)
[Model.afterDelete] => Array
(
[10] => Array
(
[0] => Array
(
[callable] => Array
(
[0] => BehaviorCollection Object
(
[modelName] => GfDatum
[_methods:protected] => Array
(
)
[_mappedMethods:protected] => Array
(
)
[_enabled:protected] => Array
(
)
[_loaded:protected] => Array
(
)
[defaultPriority] => 10
)
[1] => trigger
)
[passParams] =>
)
[1] => Array
(
[callable] => Array
(
[0] => GfDatum Object
*RECURSION*
[1] => afterDelete
)
[passParams] =>
)
)
)
)
[_isGlobal:protected] =>
)
[_validator:protected] =>
)
[AdExperiments] => AdExperiments Object
(
[name] => AdExperiments
[useTable] => ad_experiments
[primaryKey] => exp_id
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] => db_plaza_public_dicots_05
[table] => ad_experiments
[_schema:protected] => Array
(
[exp_id] => Array
(
[type] => smallinteger
[null] =>
[default] => 0
[length] =>
[unsigned] => 1
[key] => primary
)
[description] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 255
[collate] => latin1_swedish_ci
[charset] => latin1
)
[description_advanced] => Array
(
[type] => text
[null] => 1
[default] =>
[length] =>
[collate] => latin1_swedish_ci
[charset] => latin1
)
[organisms] => Array
(
[type] => string
[null] =>
[default] =>
[length] => 512
[collate] => latin1_swedish_ci
[charset] => latin1
)
[to_show] => Array
(
[type] => enum('true','false')
[null] =>
[default] => false
[length] => 5
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[1] => trigger
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[passParams] =>
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[1] => Array
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[passParams] =>
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[1] => Array
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[callable] => Array
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[_enabled:protected] => Array
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[_loaded:protected] => Array
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[1] => Array
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[callable] => Array
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[Model.afterValidate] => Array
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[0] => Array
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[1] => afterDelete
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[null] =>
[default] =>
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[_mappedMethods:protected] => Array
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[_loaded:protected] => Array
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[cacheSources] => 1
[findQueryType] =>
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[order] =>
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[0] => className
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[2] => with
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[_associations:protected] => Array
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[0] => belongsTo
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[__safeUpdateMode] =>
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[first] => 1
[count] => 1
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[_eventManager:protected] => CakeEventManager Object
(
[_listeners:protected] => Array
(
[Model.beforeFind] => Array
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[callable] => Array
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[0] => BehaviorCollection Object
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[Model.beforeValidate] => Array
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[0] => Array
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[defaultPriority] => 10
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[_loaded:protected] => Array
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[defaultPriority] => 10
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[1] => trigger
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[_validator:protected] =>
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[Msa] => Msa Object
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[name] => Msa
[useTable] => msa
[primaryKey] => msa_id
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] =>
[table] => msa
[_schema:protected] =>
[validate] => Array
(
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[validationErrors] => Array
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[validationDomain] =>
[plugin] =>
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[tableToModel] => Array
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[msa] => Msa
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[hasOne] => Array
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[Behaviors] => BehaviorCollection Object
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[0] => className
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[_eventManager:protected] =>
[_validator:protected] =>
)
[Trees] => Trees Object
(
[name] => Trees
[useTable] => trees
[useDbConfig] => default
[id] =>
[data] => Array
(
)
[schemaName] =>
[table] => trees
[primaryKey] => id
[_schema:protected] =>
[validate] => Array
(
)
[validationErrors] => Array
(
)
[validationDomain] =>
[plugin] =>
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[tableToModel] => Array
(
[trees] => Trees
)
[cacheQueries] =>
[belongsTo] => Array
(
)
[hasOne] => Array
(
)
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[hasAndBelongsToMany] => Array
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[actsAs] =>
[Behaviors] => BehaviorCollection Object
(
[modelName] => Trees
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(
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[_mappedMethods:protected] => Array
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[_enabled:protected] => Array
(
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[_loaded:protected] => Array
(
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[defaultPriority] => 10
)
[whitelist] => Array
(
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[cacheSources] => 1
[findQueryType] =>
[recursive] => 1
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(
[0] => className
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[0] => className
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[11] => finderQuery
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[_associations:protected] => Array
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[0] => belongsTo
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)
[__backContainableAssociation] => Array
(
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[__safeUpdateMode] =>
[useConsistentAfterFind] => 1
[_insertID:protected] =>
[_sourceConfigured:protected] =>
[findMethods] => Array
(
[all] => 1
[first] => 1
[count] => 1
[neighbors] => 1
[list] => 1
[threaded] => 1
)
[_eventManager:protected] =>
[_validator:protected] =>
)
)
controller Notice (8) : Trying to get property 'Configuration' of non-object [APP/Controller/Component/GenomeBrowserComponent.php , line 105 ]Code Context
//Construct url for synteny-scores
$species_tree = $this -> controller -> Configuration -> getBasicSpeciesTree ();
$species = 'arhy'
$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/arhy/'
$genome_file_name = 'arhy.fasta.gz'
$annotation_file_name = 'annotation.all_transcripts.all_features.arhy.gff3.gz'
$genome_file_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/Genomes/arhy.fasta.gz'
$annotation_file_url = 'https://ftp.psb.ugent.be/pub/plaza/plaza_public_dicots_05/GFF/arhy/annotation.all_transcripts.all_features.arhy.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' ))));