Extending Embedding and Customizing JBrowse

Revision as of 20:50, 7 March 2011 by MitchSkinner (Talk | contribs)

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Result of discussions at GMOD satellite meeting, March 2011

Potential upcoming changes to JSON format:


TODO/wishlist for JBrowse:

  • namespace CSS
  • putting track list into separate DOM element (e.g., Drupal "block")
  • "Browser" API: anything you can do manually
  • Hooks:
    • featureCreate: has access to: feature data, feature HTML element, can:
      • style the element, and
      • add callbacks to the element
    • featureEventHooks:
{ click: function(feature array, HTML element, getAttr, event)
 mouseover: function(...
 mouseout: ...
 [DOM event name]: [callback function]
current approach:
{ "start": 1,
  "end": 2,
  "strand": 3,
changing to: getAttr
    • access to region selections (e.g., for creation of lists of features)
    • function that: takes currently visible sequence, PSSM or set of regexes, returns: set of regions

"Browser" API extensions:

Browser.iterateFeaturesInTrack("gene", function(feature, elem, getAttr) {if (getAttr(feature, "id") == "foo") {elem.style.backgroundColor="red"}})

?Browser.filterTrackBy("gene", function(feature, elem, getAttr { return (getAttr(feature, "id") == "foo") });


  • all genes in a given pathway with expression > 2 s.d. above average
  • all genes tagged with a given GO term