annot.json

{
    "plugins" : [
      {
         "location" : "./plugins/WebApollo",
         "name" : "WebApollo"
      },
      {
         "location" : "./plugins/GCContent",
         "name" : "GCContent"
      },
      //{
      //   "location" : "./plugins/CACAO",
      //   "name" : "CACAO"
      //}
   ],
    "share_link" : 0,
    "tracks" : [
    {
         "autocomplete" : "none",
         "style" : {
            "className" : "annot",
            "renderClassName" : "annot-render",
            "subfeatureClasses" : {
               "non_canonical_three_prime_splice_site" : "noncanonical-splice-site",
               "wholeCDS" : null,
               "exon" : "container-100pct",
               "CDS" : "annot-CDS",
               "non_canonical_five_prime_splice_site" : "noncanonical-splice-site",
               "UTR" : "annot-UTR"
            },
            "arrowheadClass" : "annot-arrowhead",
            "alternateClasses" : {
               "terminator" : {
                  "renderClassName" : "black-80pct annot-apollo",
                  "className" : "black-80pct"
               },
               "transposable_element" : {
                  "renderClassName" : "blue-ibeam-render annot-apollo",
                  "className" : "blue-ibeam"
               },
               "pseudogene" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "light-purple-80pct"
               },
               "snRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               },
               "rRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               },
               "snoRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               },
               "repeat_region" : {
                  "className" : "magenta-80pct"
               },
               "ncRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               },
               "miRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               },
               "tRNA" : {
                  "renderClassName" : "gray-center-30pct annot-apollo",
                  "className" : "brightgreen-80pct"
               }
            },
            "uniqueIdField" : "id",
            "centerSubFeature" : {
               "non_canonical_three_prime_splice_site" : false,
               "non_canonical_five_prime_splice_site" : false
            }
         },
         "key" : "User-created Annotations",
         "storeClass" : "WebApollo/Store/SeqFeature/ScratchPad",
         "maxHeight" : 600,
         "phase" : 0,
         "compress" : 0,
         "label" : "Annotations",
         "type" : "WebApollo/View/Track/AnnotTrack",
         "subfeatures" : 1
      },
      {
        "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
        "type": "GCContent/View/Track/GCContentXY",
        "label": "GC Skew",
        "urlTemplate" : "../../../data/seq/{refseq_dirpath}/{refseq}-",
        "gcMode": "skew",
        "min_score": -1,
        "bicolor_pivot": 0
      },
      //{
      //  "storeClass": "CACAO/Store/SeqFeature/REST",
      //  "type": "CACAO/View/Track/CanvasFeatures",
      //  "label": "CACAO",
      //  "key": "CPT GO Annotations",
      //  "baseUrl": "https://cpt.tamu.edu/cacao-backend/jbrowse/",
      //}
    ],
   "favicon" : "./plugins/WebApollo/img/webapollo_favicon.ico",
   "alwaysOnTracks" : "DNA,Annotations",
   "classicMenu" : 1,
   "formatVersion" : 1
}