WIP, but the region highlighting needs a more sophisticated event fra…

…mework in jbrowse to start working
GMOD · Mar 8, 2012 · 32f8c80 · 32f8c80
1 parent 236dd1c
commit 32f8c80
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/index.html b/index.html
@@ -54,6 +54,7 @@
                                    defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                    queryParams: queryParams,
                                    location: queryParams.loc,
+                                   highlight: queryParams.highlight,
                                    tracks: queryParams.tracks,
 				   show_nav: queryParams.nav,
 				   show_tracklist: queryParams.tracklist,

diff --git a/js/Browser.js b/js/Browser.js
@@ -88,12 +88,14 @@ Browser.prototype.initialize = function() {
         this.origTracklist = this.params.defaultTracks;
     }
 
+    // load our ref seqs
     var brwsr = this;
     Util.maybeLoad(this.params.refSeqs.url, this.params.refSeqs,
                    function(o) {
                        brwsr.addRefseqs(o);
                    });
 
+    // load our tracks
     for (var i = 0; i < this.params.tracklists.length; i++) {
         (function(tracklist) {
              Util.maybeLoad(tracklist.url,
@@ -106,6 +108,11 @@ Browser.prototype.initialize = function() {
                             });
          })(this.params.tracklists[i]);
     }
+
+    // set a highlighted region, if any was passed
+    if( this.params.highlight ) {
+        this.highlightRegion( this.params.highlight );
+    }
 };
 
 /**
@@ -496,7 +503,7 @@ Browser.prototype.highlightRegion = function(loc) {
 
     // Capture location for highlighting DNA sequence.
     // Tracks are initialized by one of the deferred functions!
-    loc = Util.parseLocString(loc);
+    loc = Util.parseLocString(loc );
     if( !loc || !loc.ref || loc.start === undefined || loc.start === undefined )
         return;
 

diff --git a/js/SequenceTrack.js b/js/SequenceTrack.js
@@ -25,7 +25,6 @@ function SequenceTrack(trackMeta, refSeq, browserParams) {
     this.url = Util.resolveUrl(trackMeta.sourceUrl,
                                Util.fillTemplate(trackMeta.config.urlTemplate,
                                                  {'refseq': refSeq.name}) );
-    this.hilightLoc = {ref: null, start:-1, end:-1};
 
 }
 
@@ -114,7 +113,7 @@ SequenceTrack.prototype.complement = (function() {
 
 SequenceTrack.prototype.highlightSeq = function ( start, end, seq ) {
     var container  = document.createElement("div"),
-        hloc = this.hilightLoc;
+        hloc       = this.hilightLoc;
 
     if( hloc && hloc.ref == this.refSeq.name && hloc.start < end && hloc.end > start ) {
         // start, end coords are interbase (half-open intervals)