misc minor fixes

src/JBrowse/Store/SeqFeature/Boolean.js

@@ -136,12 +136,12 @@ getFeatures: function( query, featCallback, doneCallback, errorCallback ) {
             // reduce the display, mask, and invMask objects into arrays
             var masks = [];
             for ( var feats in featureArrays.mask ) {
-                masks = thisB.orSpan( masks, thisB.toSpan( featureArrays.mask[feats] ) );
+                masks = thisB.orSpan( masks, thisB.toSpan( featureArrays.mask[feats], query ) );
             }
             masks = thisB.notSpan( masks, query );
             var invMasks = [];
             for ( var feats in featureArrays.invMask ) {
-                invMasks = thisB.orSpan( invMasks, thisB.toSpan( featureArrays.invMask[feats] ) );
+                invMasks = thisB.orSpan( invMasks, thisB.toSpan( featureArrays.invMask[feats], query ) );
             }
             var features = [];
             for ( var feats in featureArrays.display ) {
@@ -183,12 +183,12 @@ makeSpan: function( args ) {
     // given a list of pseudo-features, outputs a list of non-overlapping spans
     var features = args.features || [];
     var spans = args.spans || [];
-    if ( features.length == 0 ) { return spans; }
+    if ( features.length == 0 ) { return spans.sort(function(a,b){return a.start-b.start}); }
     // if the span is empty, the function does nothing
     if( spans.length == 0 ) {
         spans.push({ start: features[0].start, end: features[0].end });
         features.splice(0,1);
-        if ( features.length == 0 ) { return spans; }
+        if ( features.length == 0 ) { return spans.sort(function(a,b){return a.start-b.start}); }
     }
     for (var span in spans) {
     if (spans.hasOwnProperty(span)) {
@@ -213,12 +213,13 @@ inSpan: function( feature, span ) {
 
 },
 
-toSpan: function( features ) {
+toSpan: function( features, query ) {
     // given a set of features, makes a set of span objects with the same start and end points (a.k.a. pseudo-features)
     var spans = [];
     for (var feature in features) {
     if (features.hasOwnProperty(feature)) {
-        spans.push( { start: features[feature].get('start'), end: features[feature].get('end') } );
+        spans.push( { start: Math.max( features[feature].get('start'), query.start ), 
+                      end:   Math.min( features[feature].get('end'),   query.end   ) } );
     }}
     return spans;
 },
@@ -273,6 +274,10 @@ notSpan: function( spans, query ) {
         invSpan[i] = { start: span.end };
     }}
     invSpan[i].end = query.end;
+    if (invSpan[i].end <= invSpan[i].start) {
+        invSpan.splice(i,1); }
+    if (invSpan[0].end <= invSpan[0].start) {
+        invSpan.splice(0,1); }
     return invSpan;
 },
 

src/JBrowse/View/Track/SNPCoverage.js

@@ -284,22 +284,22 @@ return declare( [Wiggle, MismatchesMixin],
                 }
             });
         }, this );
-        return context;
     },
 
     // Overwrites the method from WiggleBase
     _draw: function( scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale, pixels, spans ) {
         // Note: pixels currently has no meaning, as the function that generates it is not yet defined for this track
         this._preDraw(      scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale );
-        var context = this._drawFeatures( scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale, spans );
+        this._drawFeatures( scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale );
         if ( spans ) {
-            this._maskBySpans( scale, leftBase, canvas, context, spans );
+            this._maskBySpans( scale, leftBase, canvas, spans );
         }
         this._postDraw(     scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale );
     },
 
     /* If it's a boolean track, mask accordingly */
-    _maskBySpans: function( scale, leftBase, canvas, context, spans ) {
+    _maskBySpans: function( scale, leftBase, canvas, spans ) {
+        var context = canvas.getContext('2d');
         var canvasHeight = canvas.height;
         var booleanAlpha = this.config.style.masked_transparancy || 45;
         this.config.style.masked_transparancy = booleanAlpha;
@@ -311,7 +311,7 @@ return declare( [Wiggle, MismatchesMixin],
             var img = context.getImageData(l, 0, w, canvasHeight);
             var pixels = img.data;
             for ( var i = 0, n = pixels.length; i < n; i += 4 ) {
-                /* Note: the default calnvas values are transparent black,
+                /* Note: the default canvas values are transparent black,
                  * so we don't want to change the opacity of transparent pixels */
                 if ( pixels[i+3] != 0 ) { pixels[i+3] = booleanAlpha;}
             }

src/JBrowse/View/Track/Wiggle/Density.js

@@ -65,9 +65,9 @@ return declare( WiggleBase,
         if (spans.hasOwnProperty(index)) {
             var w = Math.ceil(( spans[index].end   - spans[index].start ) * scale );
             var l = Math.round(( spans[index].start - leftBase ) * scale );
-            context.fillRect( l, 0, w-1, canvasHeight );
-            context.clearRect( l, 0, w-1, canvasHeight/3);
-            context.clearRect( l, (2/3)*canvasHeight, w-1, canvasHeight/3);
+            context.fillRect( l, 0, w, canvasHeight );
+            context.clearRect( l, 0, w, canvasHeight/3);
+            context.clearRect( l, (2/3)*canvasHeight, w, canvasHeight/3);
         }}
         dojo.forEach( pixels, function(p,i) {
             if (!p) {