add warning when users open bam or bigwig files with no data for the …

…current reference sequence, closes #178

release-notes.txt

@@ -39,6 +39,10 @@
    main browser window, and a description to be shown in a pop-up
    dialog when the title is clicked (issue #206).
 
+ * Where possible (i.e. supported by the data store), JBrowse will now
+   pop up a warning if a local data file is opened that contains no
+   data for the current reference sequence (issue #178).
+
 1.8.1     2013-02-12 12:56:24 EST5EDT
 
  * Added support for `cigarAttribute` and `mdAttributes` configuration

src/JBrowse/GenomeView.js

@@ -9,7 +9,8 @@ define([
            'JBrowse/View/Track/GridLines',
            'JBrowse/BehaviorManager',
            'JBrowse/View/Animation/Zoomer',
-           'JBrowse/View/Animation/Slider'
+           'JBrowse/View/Animation/Slider',
+           'JBrowse/View/InfoDialog'
        ], function(
            declare,
            array,
@@ -21,7 +22,8 @@ define([
            GridLinesTrack,
            BehaviorManager,
            Zoomer,
-           Slider
+           Slider,
+           InfoDialog
        ) {
 
 var dojof = Util.dojof;
@@ -1983,6 +1985,7 @@ GenomeView.prototype._getTracks = function( /**Array[String]*/ trackNames ) {
  *                        rendering of this track
  */
 GenomeView.prototype.renderTrack = function( /**Object*/ trackConfig ) {
+    var thisB = this;
 
     if( !trackConfig )
         return null;
@@ -2025,6 +2028,29 @@ GenomeView.prototype.renderTrack = function( /**Object*/ trackConfig ) {
         if( typeof store.setTrack == 'function' )
             store.setTrack( track );
 
+        // if we can, check that the current reference sequence is
+        // contained in the store
+        if( store.getRefSeqs ) {
+            var foundRef, curRefName = this.ref.name;
+            store.getRefSeqs(
+                function( ref ) {
+                    foundRef = foundRef || ref.name == curRefName;
+                },
+                function() {
+                    if( ! foundRef )
+                        new InfoDialog({
+                            title: 'Reference warning',
+                            content: 'WARNING: The data for track "'
+                              +(trackConfig.key||trackConfig.label)
+                              +'" contains no data for the current'
+                              +' reference sequence ('
+                              +thisB.ref.name
+                              +').'
+                        }).show();
+                }
+            );
+        }
+
         trackDiv.track = track;
 
         var heightUpdate = dojo.hitch( this, 'trackHeightUpdate', trackName );

src/JBrowse/Store/SeqFeature/BAM.js

@@ -72,6 +72,18 @@ var BAMStore = declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesM
         });
     },
 
+    /**
+     * Fetch the list of reference sequences represented in the store.
+     */
+    getRefSeqs: function( seqCallback, finishCallback, errorCallback ) {
+        var thisB = this;
+        this._deferred.stats.then( function() {
+            array.forEach( thisB.bam.indexToChr || [], function( rec ) {
+                seqCallback({ name: rec.name, length: rec.length, start: 0, end: rec.length });
+            });
+            finishCallback();
+        }, errorCallback );
+    },
 
     /**
      * Fetch a region of the current reference sequence and use it to

src/JBrowse/Store/SeqFeature/BigWig.js

@@ -159,8 +159,8 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
      */
     _readChromTree: function(callback) {
         var thisB = this;
-        this.chromsToIDs = {};
-        this.idsToChroms = {};
+        this.refsByNumber = {};
+        this.refsByName = {};
 
         var udo = this.unzoomedDataOffset;
         while ((udo % 4) != 0) {
@@ -207,16 +207,18 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
                                            key += String.fromCharCode(charCode);
                                        }
                                    }
-                                   var chromId = readInt( ba, offset );
-                                   var chromSize = readInt( ba, offset+4 );
+                                   var refId = readInt( ba, offset );
+                                   var refSize = readInt( ba, offset+4 );
                                    offset += 8;
 
-                                   //dlog(key + ':' + chromId + ',' + chromSize);
-                                   thisB.chromsToIDs[key] = chromId;
+                                   var refRec = { name: key, id: refId, length: refSize };
+
+                                   //dlog(key + ':' + refId + ',' + refSize);
+                                   thisB.refsByName[key] = refRec;
                                    if (key.indexOf('chr') == 0) {
-                                       thisB.chromsToIDs[key.substr(3)] = chromId;
+                                       thisB.refsByName[key.substr(3)] = refRec;
                                    }
-                                   thisB.idsToChroms[chromId] = key;
+                                   thisB.refsByNumber[refId] = refRec;
                                } else {
                                    // parse index node
                                    offset += keySize;
@@ -233,6 +235,18 @@ return declare([ SeqFeatureStore, DeferredFeaturesMixin, DeferredStatsMixin ],
             });
     },
 
+    getRefSeqs: function( seqCallback, finishCallback, errorCallback ) {
+        var thisB = this;
+        this._deferred.features.then(function() {
+            var refs =  thisB.refsByName;
+            for( var name in refs ) {
+                if( refs.hasOwnProperty(name) )
+                    seqCallback( refs[name] );
+            }
+            finishCallback();
+        }, errorCallback );
+    },
+
     _getFeatures: function( query, featureCallback, endCallback, errorCallback ) {
 
         var chrName = query.ref;

src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js

@@ -158,7 +158,7 @@ var RequestWorker = declare( null,
         }
 
         var f = new Feature();
-        f.segment = this.window.bwg.idsToChroms[this.chr];
+        f.segment = (this.window.bwg.refsByNumber[this.chr]||{}).name;
         f.min = fmin;
         f.max = fmax;
         f.type = 'remark';

src/JBrowse/Store/SeqFeature/BigWig/Window.js

@@ -31,15 +31,15 @@ return declare( null,
 
     readWigData: function(chrName, min, max, callback) {
         // console.log( 'reading wig data from '+chrName+':'+min+'..'+max);
-        var chr = this.bwg.chromsToIDs[chrName];
-        if (chr === undefined) {
+        var chr = this.bwg.refsByName[chrName];
+        if ( ! chr ) {
             // Not an error because some .bwgs won't have data for all chromosomes.
 
             // dlog("Couldn't find chr " + chrName);
-            // dlog('Chroms=' + miniJSONify(this.bwg.chromsToIDs));
+            // dlog('Chroms=' + miniJSONify(this.bwg.refsByName));
             callback([]);
         } else {
-            this.readWigDataById(chr, min, max, callback);
+            this.readWigDataById( chr.id, min, max, callback);
         }
     },