@gmod/jbrowse

{ "tracks" : [ { "feature" : [ "remark" ], "autocomplete" : "all", "track" : "ExampleFeatures", "class" : "feature2", "category": "Miscellaneous", "key" : "HTMLFeatures - Example Features" }, { "feature" : [ "protein_coding_primary_transcript", "polypeptide" ], "track" : "NameTest", "class" : "feature2", "category": "Miscellaneous", "key" : "HTMLFeatures - Name test track has a really long track label" }, { "feature" : [ "SNP" ], "track" : "snps", "class" : "triangle hgred", "category": "Miscellaneous", "key" : "HTMLFeatures - SNPs" }, { "feature" : [ "polypeptide_domain" ], "track" : "Motifs", "class" : "feature3", "description" : 1, "key" : "HTMLFeatures - Example motifs", "category": "Miscellaneous", "style": { "label": "function(feature) { return feature.get('Name')+' (via JS callback)' }", "description": "function(feature) { return feature.get('Name')+': '+feature.get('Note'); }" } }, { "feature" : [ "match" ], "track" : "malformed_alignments", "class" : "feature4", "key" : "HTMLFeatures - Features with right-click menus", "shortDescription": "Features with customized right-click menus", "metadata": { "category": "Miscellaneous", "Description": "Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback." }, "hooks": { "modify": "function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()*5)];}" }, "menuTemplate" : [ { "label" : "Item with submenu", # hello this is a comment "children" : [ { "label" : "Check gene on databases", "children" : [ { "label" : "Query trin for {name}", "iconClass" : "dijitIconBookmark", "action": "newWindow", "url" : "http://wiki.trin.org.au/{name}-{start}-{end}" }, { "label" : "Query example.com for {name}", "iconClass" : "dijitIconSearch", "url" : "http://example.com/{name}-{start}-{end}" } ] }, { "label" : "2nd child of demo" }, { "label" : "3rd child: this is a track" } ] }, { "label" : "Open example.com in an iframe popup", "title" : "The magnificent example.com (feature {name})", "iconClass" : "dijitIconDatabase", "action": "iframeDialog", "url" : "http://www.example.com?featurename={name}" }, { "label" : "Open popup with XHR HTML snippet (btw this is feature {name})", "title": "function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }", "iconClass" : "dijitIconDatabase", "action": "xhrDialog", "url" : "sample_data/test_snippet.html?featurename={name}:{start}-{end}" }, { "label" : "Popup with content snippet from a function (feature {name})", "title": "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }", "iconClass" : "dijitIconDatabase", "action": "contentDialog", "content" : "function(track,feature,div) { return '<h2>'+feature.get('name')+'</h2><p>This is some test content!</p><p>This message brought to you by the number <span style=\"font-size: 300%\">'+Math.round(Math.random()*100)+'</span>.</p>';} " }, { "label" : "Popup with content snippet from string (feature {name})", "title": "{randomNumberTitle}", "iconClass" : "dijitIconDatabase", "action": "contentDialog", "content" : "<h2>{name}</h2><p>This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.</p>" }, { "label" : "{randomNumberLabel}", "iconClass" : "dijitIconDatabase", "action": "{exampleFeatureClick}" } ] }, { "feature" : [ "gene" ], "track" : "Genes", "class" : "feature5", "category": "Transcripts", "key" : "CanvasFeatures - Protein-coding genes", "metadata" : { "ncbi_submission_model" : "Generic", "insdc_first_public" : "2018-05-15T00:00:00Z", "Link: ENA study page" : "http://www.ebi.ac.uk/ena/", "library_total_amount_of_reads" : "3349981", "insdc_secondary_accession" : "SRS12345678", "insdc_center_name" : "INSDC Sample", "ncbi_submission_package" : "Generic.1.0", "sample_name" : "GSM12345678", "ENA first public" : "2018-05-16", "organism" : "Volvox", "study" : "SRP12345678 a study of volvox", "Link: RNASeq-er analysis results" : "ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/", "library_size_approx" : "1-5mln", "insdc_last_update" : "2018-05-15T01:18:23.110Z", "insdc_status" : "live", "developmental_stage" : "stage 6- 330 min", "tissue" : "embryo", "mapping_quality_approx" : "under 50%", "source_name" : "Volvox 6- 330 min", "mapping_fraction_of_uniquely_mapped_reads" : "0.429", "ENA last update" : "2018-05-16", "description_title" : "Volvox_mRNA_rep_2_6" }, "trackType": "NeatCanvasFeatures/View/Track/NeatFeatures", "unsafeMouseover": true, "onClick" : { "action" : "defaultDialog", "label" : "<div style='font:normal 12px Univers,Helvetica,Arial,sans-serif'><div style='font-weight:bold'>Custom tooltip</div><div style='color:blue;'>Feature name: {name}<br />Feature start: {start}<br />Feature end: {end}</div></div>", "title": "{type} {name}" }, "menuTemplate": [ { "label" : "View details", }, { "label" : "Zoom this gene", }, { "label" : "Highlight this gene", }, { "label" : "Popup with content snippet from string (feature {name})", "title": "{randomNumberTitle}", "iconClass" : "dijitIconDatabase", "action": "contentDialog", "content" : "<h2>{name}</h2>This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand." }], "fmtDetailValue_Name": "function(name,feature) { if(feature.get('type')=='gene') { return name + ' <a href=http://www.ncbi.nlm.nih.gov/gquery/?term='+name+'>[NCBI custom link]</a>'; } else { return name; } }", "fmtDetailField_Name": "function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }", "fmtDetailField_Load_id": "function(name,feature) { /* remove field from dialog box */ return null; }", "fmtMetaValue_Name": "function(name) { return name+' [Track with custom callbacks for About track popup]'; }", "fmtMetaField_Name": "function(name) { return 'Track Name'; }", "fmtMetaDescription_Name": "function(name) { return '[Custom description]'; }" }, { "feature" : [ "mRNA" ], "track" : "ReadingFrame", "trackType": "NeatHTMLFeatures/View/Track/NeatFeatures", "category" : "Transcripts", "class" : "cds", "phase": 1, "key" : "HTMLFeatures - mRNAs", "onClick": { "url": "http://www.ncbi.nlm.nih.gov/gquery/?term={name}", "label": "Search for {name} at NCBI\nFeature start {start}\nFeature end {end}", "title": "NCBI search box" } }, { "feature" : [ "CDS:bare_predicted", "mRNA:exonerate", "mRNA:predicted" ], "urlTemplate" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}", "track" : "CDS", "category" : "Transcripts", "class" : "cds", "key" : "CanvasFeatures - mixed mRNAs and CDSs", "trackType": "CanvasFeatures" }, { "track" : "Transcript", "description" : 1, "style": { "color": "#E32A3A", "description": "customdescription" }, "key" : "CanvasFeatures - transcripts", "trackType": "JBrowse/View/Track/CanvasFeatures", "feature" : [ "mRNA:exonerate" ], "category" : "Transcripts", "subfeatures" : true, "showNoteInAttributes": true, "onClick": "{exampleFeatureClick}" }, { "feature" : [ "BAC" ], "track" : "Clones", "class" : "exon", "description" : 1, "key" : "HTMLFeatures - Fingerprinted BACs", "category": "Miscellaneous" }, { "feature" : [ "EST_match:est" ], "track" : "EST", "class" : "est", "key" : "HTMLFeatures - ESTs", "category": "Miscellaneous" } ], "TRACK DEFAULTS" : { "autocomplete" : "all", "class" : "feature" }, "db_args" : { "-adaptor" : "memory", "-dir" : "docs/tutorial/data_files/volvox.gff3" }, "description" : "Volvox Example Database", "db_adaptor" : "Bio::DB::SeqFeature::Store" }