tweak track creation API to instantiate the store inside GenomeView, …

…and make the track constructor just take an object for its args
GMOD · Jun 29, 2012 · c3bf63e · c3bf63e
1 parent 6e53854
commit c3bf63e
Show file tree

Hide file tree

Showing 2 changed files with 48 additions and 40 deletions.
diff --git a/src/JBrowse/GenomeView.js b/src/JBrowse/GenomeView.js
@@ -1527,19 +1527,40 @@ GenomeView.prototype.renderTrack = function( /**Object*/ trackConfig ) {
     });
     trackDiv.trackName = trackName;
 
-    require( [trackClass], dojo.hitch(this,function(trackClass) {
+    // figure out what data store class to use with the track,
+    // applying some defaults if it is not explicit in the
+    // configuration
+    var storeClass =
+        trackConfig.storeClass               ? trackConfig.storeClass :
+        /\/HTMLFeatures$/.test( trackClass ) ? 'JBrowse/Store/SeqFeature/NCList'+( trackConfig.backendVersion == 0 ? '_v0' : '' ) :
+        /\/FixedImage/.test( trackClass )    ? 'JBrowse/Store/TiledImage/Fixed' +( trackConfig.backendVersion == 0 ? '_v0' : '' )  :
+        /\/Sequence$/.test( trackClass )     ? 'JBrowse/Store/Sequence/StaticChunked' :
+                                                null;
+    if( ! storeClass ) {
+        console.error( "Unable to find an appropriate data store to use with a "
+                       + trackClass + " track, please explicitly specify a "
+                       + "storeClass in the configuration." );
+        return trackDiv;
+    }
 
-        var track = new trackClass(
-            trackConfig,
-            this.ref,
-            {
+    require( [ trackClass, storeClass ], dojo.hitch(this,function( trackClass, storeClass ) {
+
+        var store = new storeClass({
+            urlTemplate: trackConfig.urlTemplate,
+            baseUrl: trackConfig.baseUrl,
+            refSeq: this.ref
+        });
+
+        var track = new trackClass({
+                refSeq: this.ref,
+                config: trackConfig,
                 changeCallback: dojo.hitch( this, 'showVisibleBlocks', true ),
                 trackPadding: this.trackPadding,
                 charWidth: this.charWidth,
-                seqHeight: this.seqHeight
+                seqHeight: this.seqHeight,
+                store: store
             });
 
-
         // tell the track to get its data, since we're going to display it.
         track.load();
 

diff --git a/src/JBrowse/View/Track/HTMLFeatures.js b/src/JBrowse/View/Track/HTMLFeatures.js
@@ -12,51 +12,38 @@ var HTMLFeatures = declare( BlockBased,
      * A track that draws discrete features using `div` elements.
      * @constructs
      * @extends JBrowse.View.Track.BlockBased
+     * @param args.config {Object} track configuration. Must include key, label
+     * @param args.refSeq {Object} reference sequence object with name, start,
+     *   and end members.
+     * @param args.changeCallback {Function} optional callback for
+     *   when the track's data is loaded and ready
+     * @param args.trackPadding {Number} distance in px between tracks
      */
-    constructor: function( config, refSeq, browserParams ) {
-        //config: object with:
-        //            key:   display text track name
-        //            label: internal track name (no spaces, odd characters)
-        //            baseUrl: base URL to use for resolving relative URLs
-        //                     contained in the track's configuration
-        //            config: configuration info for this track
-        //refSeq: object with:
-        //         name:  refseq name
-        //         start: refseq start
-        //         end:   refseq end
-        //browserParams: object with:
-        //                changeCallback: function to call once JSON is loaded
-        //                trackPadding: distance in px between tracks
-        //                baseUrl: base URL for the URL in config
-
+    constructor: function( args ) {
+        var config = args.config;
         BlockBased.call( this, config.label, config.key,
-                         false, browserParams.changeCallback);
+                         false, args.changeCallback);
         this.fields = {};
         this.refSeq = refSeq;
 
-        // TODO: this featureStore object should eventuallly be
+        //number of histogram bins per block
+        this.numBins = 25;
+        this.histLabel = false;
+        this.padding = 5;
+        this.trackPadding = args.trackPadding;
+
+        this.config = config;
+
+
+        // this featureStore object should eventually be
         // instantiated by Browser and passed into this constructor, not
         // constructed here.
-        var storeclass = config.backendVersion == 0 ? SeqFeatureStore.NCList_v0 : SeqFeatureStore.NCList;
-        this.featureStore = new storeclass({
-                                               urlTemplate: config.urlTemplate,
-                                               baseUrl: config.baseUrl,
-                                               refSeq: refSeq,
-                                               track: this
-                                           });
+        this.featureStore = args.store;
 
         // connect the store and track loadSuccess and loadFailed events
         // to eachother
         dojo.connect( this.featureStore, 'loadSuccess', this, 'loadSuccess' );
         dojo.connect( this.featureStore, 'loadFail',    this, 'loadFail' );
-
-        //number of histogram bins per block
-        this.numBins = 25;
-        this.histLabel = false;
-        this.padding = 5;
-        this.trackPadding = browserParams.trackPadding;
-
-        this.config = config;
     },
 
     /**