{
   "dataset_id" : "volvox",
   "formatVersion" : 1,
   "include" : [
      "../../raw/volvox/functions.conf"
   ],
   "names" : {
      "type" : "Hash",
      "url" : "names/"
   },
   "plugins" : [
      "HideTrackLabels",
      "NeatCanvasFeatures",
      "NeatHTMLFeatures"
   ],
   "tracks" : [
      {
         "category" : "Reference sequence",
         "chunkSize" : 20000,
         "key" : "Reference sequence",
         "label" : "DNA",
         "seqType" : "dna",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "type" : "SequenceTrack",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "feature" : [
            "remark"
         ],
         "key" : "HTMLFeatures - Example Features",
         "label" : "ExampleFeatures",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature2"
         },
         "track" : "ExampleFeatures",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/ExampleFeatures/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "feature" : [
            "protein_coding_primary_transcript",
            "polypeptide"
         ],
         "key" : "HTMLFeatures - Name test track has a really long track label",
         "label" : "NameTest",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature2"
         },
         "track" : "NameTest",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/NameTest/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "feature" : [
            "SNP"
         ],
         "key" : "HTMLFeatures - SNPs",
         "label" : "snps",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "triangle hgred"
         },
         "track" : "snps",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/snps/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "description" : 1,
         "feature" : [
            "polypeptide_domain"
         ],
         "key" : "HTMLFeatures - Example motifs",
         "label" : "Motifs",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature3",
            "description" : "function(feature) { return feature.get('Name')+': '+feature.get('Note'); }",
            "label" : "function(feature) { return feature.get('Name')+' (via JS callback)' }"
         },
         "track" : "Motifs",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/Motifs/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "compress" : 0,
         "feature" : [
            "match"
         ],
         "hooks" : {
            "modify" : "function( track, feature, div ) { div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()*5)];}"
         },
         "key" : "HTMLFeatures - Features with right-click menus",
         "label" : "malformed_alignments",
         "menuTemplate" : [
            {
               "children" : [
                  {
                     "children" : [
                        {
                           "action" : "newWindow",
                           "iconClass" : "dijitIconBookmark",
                           "label" : "Query trin for {name}",
                           "url" : "http://wiki.trin.org.au/{name}-{start}-{end}"
                        },
                        {
                           "iconClass" : "dijitIconSearch",
                           "label" : "Query example.com for {name}",
                           "url" : "http://example.com/{name}-{start}-{end}"
                        }
                     ],
                     "label" : "Check gene on databases"
                  },
                  {
                     "label" : "2nd child of demo"
                  },
                  {
                     "label" : "3rd child: this is a track"
                  }
               ],
               "label" : "Item with submenu"
            },
            {
               "action" : "iframeDialog",
               "iconClass" : "dijitIconDatabase",
               "label" : "Open example.com in an iframe popup",
               "title" : "The magnificent example.com (feature {name})",
               "url" : "http://www.example.com?featurename={name}"
            },
            {
               "action" : "xhrDialog",
               "iconClass" : "dijitIconDatabase",
               "label" : "Open popup with XHR HTML snippet (btw this is feature {name})",
               "title" : "function(track,feature,div) { return 'Random XHR HTML '+Math.random()+' title!'; }",
               "url" : "sample_data/test_snippet.html?featurename={name}:{start}-{end}"
            },
            {
               "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>';} ",
               "iconClass" : "dijitIconDatabase",
               "label" : "Popup with content snippet from a function (feature {name})",
               "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }"
            },
            {
               "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>",
               "iconClass" : "dijitIconDatabase",
               "label" : "Popup with content snippet from string (feature {name})",
               "title" : "{randomNumberTitle}"
            },
            {
               "action" : "{exampleFeatureClick}",
               "iconClass" : "dijitIconDatabase",
               "label" : "{randomNumberLabel}"
            }
         ],
         "metadata" : {
            "Description" : "Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.",
            "category" : "Miscellaneous"
         },
         "shortDescription" : "Features with customized right-click menus",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature4"
         },
         "track" : "malformed_alignments",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/malformed_alignments/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Transcripts",
         "compress" : 0,
         "feature" : [
            "gene"
         ],
         "fmtDetailField_Load_id" : "function(name,feature) { /* remove field from dialog box */ return null; }",
         "fmtDetailField_Name" : "function(name,feature) { if(feature.get('type')=='gene') { return 'Gene Name'; } else { return name; } }",
         "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; } }",
         "fmtMetaDescription_Name" : "function(name) { return '[Custom description]'; }",
         "fmtMetaField_Name" : "function(name) { return 'Track Name'; }",
         "fmtMetaValue_Name" : "function(name) { return name+' [Track with custom callbacks for About track popup]'; }",
         "key" : "CanvasFeatures - Protein-coding genes",
         "label" : "Genes",
         "menuTemplate" : [
            {
               "label" : "View details"
            },
            {
               "label" : "Zoom this gene"
            },
            {
               "label" : "Highlight this gene"
            },
            {
               "action" : "contentDialog",
               "content" : "<h2>{name}</h2>This is some test content about {type} {name}, which goes from {start} to {end} on the {strand} strand.",
               "iconClass" : "dijitIconDatabase",
               "label" : "Popup with content snippet from string (feature {name})",
               "title" : "{randomNumberTitle}"
            }
         ],
         "metadata" : {
            "ENA first public" : "2018-05-16",
            "ENA last update" : "2018-05-16",
            "Link: ENA study page" : "http://www.ebi.ac.uk/ena/",
            "Link: RNASeq-er analysis results" : "ftp://ftp.ebi.ac.uk/pub/databases/arrayexpress/",
            "description_title" : "Volvox_mRNA_rep_2_6",
            "developmental_stage" : "stage 6- 330 min",
            "insdc_center_name" : "INSDC Sample",
            "insdc_first_public" : "2018-05-15T00:00:00Z",
            "insdc_last_update" : "2018-05-15T01:18:23.110Z",
            "insdc_secondary_accession" : "SRS12345678",
            "insdc_status" : "live",
            "library_size_approx" : "1-5mln",
            "library_total_amount_of_reads" : "3349981",
            "mapping_fraction_of_uniquely_mapped_reads" : "0.429",
            "mapping_quality_approx" : "under 50%",
            "ncbi_submission_model" : "Generic",
            "ncbi_submission_package" : "Generic.1.0",
            "organism" : "Volvox",
            "sample_name" : "GSM12345678",
            "source_name" : "Volvox 6- 330 min",
            "study" : "SRP12345678 a study of volvox",
            "tissue" : "embryo"
         },
         "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}"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature5"
         },
         "track" : "Genes",
         "trackType" : "NeatCanvasFeatures/View/Track/NeatFeatures",
         "type" : "NeatCanvasFeatures/View/Track/NeatFeatures",
         "unsafeMouseover" : true,
         "urlTemplate" : "tracks/Genes/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Transcripts",
         "compress" : 0,
         "feature" : [
            "mRNA"
         ],
         "key" : "HTMLFeatures - mRNAs",
         "label" : "ReadingFrame",
         "onClick" : {
            "label" : "Search for {name} at NCBI\nFeature start {start}\nFeature end {end}",
            "title" : "NCBI search box",
            "url" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}"
         },
         "phase" : 1,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "cds"
         },
         "track" : "ReadingFrame",
         "trackType" : "NeatHTMLFeatures/View/Track/NeatFeatures",
         "type" : "NeatHTMLFeatures/View/Track/NeatFeatures",
         "urlTemplate" : "tracks/ReadingFrame/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Transcripts",
         "compress" : 0,
         "feature" : [
            "CDS:bare_predicted",
            "mRNA:exonerate",
            "mRNA:predicted"
         ],
         "key" : "CanvasFeatures - mixed mRNAs and CDSs",
         "label" : "CDS",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "cds",
            "linkTemplate" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}-{start}-{end}"
         },
         "track" : "CDS",
         "trackType" : "CanvasFeatures",
         "type" : "CanvasFeatures",
         "urlTemplate" : "tracks/CDS/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Transcripts",
         "compress" : 0,
         "description" : 1,
         "feature" : [
            "mRNA:exonerate"
         ],
         "key" : "CanvasFeatures - transcripts",
         "label" : "Transcript",
         "onClick" : "{exampleFeatureClick}",
         "showNoteInAttributes" : true,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature",
            "color" : "#E32A3A",
            "description" : "customdescription"
         },
         "subfeatures" : true,
         "track" : "Transcript",
         "trackType" : "JBrowse/View/Track/CanvasFeatures",
         "type" : "JBrowse/View/Track/CanvasFeatures",
         "urlTemplate" : "tracks/Transcript/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "description" : 1,
         "feature" : [
            "BAC"
         ],
         "key" : "HTMLFeatures - Fingerprinted BACs",
         "label" : "Clones",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "exon"
         },
         "track" : "Clones",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/Clones/{refseq}/trackData.json"
      },
      {
         "autocomplete" : "all",
         "category" : "Miscellaneous",
         "compress" : 0,
         "feature" : [
            "EST_match:est"
         ],
         "key" : "HTMLFeatures - ESTs",
         "label" : "EST",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "est"
         },
         "track" : "EST",
         "type" : "FeatureTrack",
         "urlTemplate" : "tracks/EST/{refseq}/trackData.json"
      },
      {
         "category" : "Miscellaneous",
         "compress" : 0,
         "displayMode" : "collapsed",
         "enableCollapsedMouseover" : true,
         "key" : "ChromHMM",
         "label" : "ChromHMM",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature",
            "color" : "{chromHMM}",
            "strandArrow" : false
         },
         "trackType" : "CanvasFeatures",
         "type" : "CanvasFeatures",
         "urlTemplate" : "tracks/ChromHMM/{refseq}/trackData.json"
      }
   ]
}
