Add toggle to SNPCoverage

GMOD · Oct 24, 2018 · 7ccdf15 · 7ccdf15
1 parent 78b84ad
commit 7ccdf15
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Showing 4 changed files with 49 additions and 2 deletions.
diff --git a/src/JBrowse/View/FeatureGlyph.js b/src/JBrowse/View/FeatureGlyph.js
@@ -69,11 +69,35 @@ return declare( Component, {
     },
 
     mouseoverFeature: function( context, fRect ) {
+        var feature = fRect.f;
         this.renderFeature( context, fRect );
 
         // highlight the feature rectangle if we're moused over
         context.fillStyle = this.getStyle( fRect.f, 'mouseovercolor' );
+
         context.fillRect( fRect.rect.l, fRect.t, fRect.rect.w, fRect.rect.h );
+        if(this.config.style.strandInlay) {
+            var arrowWidth = 3;
+            var top = fRect.t;
+            var height = fRect.rect.h;
+            var left = fRect.rect.l;
+            var width = fRect.rect.w;
+            if(feature.get('strand') === 1) {
+                context.beginPath();
+                context.moveTo(left+width, top)
+                context.lineTo(left+width+arrowWidth, top+height/2)
+                context.lineTo(left+width, top+height)
+                context.closePath()
+                context.fill()
+            } else if(feature.get('strand') === -1) {
+                context.beginPath();
+                context.moveTo(left, top)
+                context.lineTo(left-arrowWidth, top+height/2)
+                context.lineTo(left, top+height)
+                context.closePath()
+                context.fill()
+            }
+        }
     },
 
     /**

diff --git a/src/JBrowse/View/FeatureGlyph/Box.js b/src/JBrowse/View/FeatureGlyph/Box.js
@@ -218,7 +218,7 @@ return declare([ FeatureGlyph, FeatureLabelMixin], {
             context.fillStyle = bgcolor;
             context.fillRect( left, top, Math.max(1,width), height );
             if(this.config.style.strandInlay && width > 1) {
-                var arrowWidth = 8
+                var arrowWidth = 3
                 if(feature.get('strand') === 1) {
                     context.beginPath();
                     context.moveTo(left+width, top)

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -87,6 +87,15 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
         }
 
 
+        displayOptions.push({
+            label: 'View coverage',
+            type: 'dijit/RadioMenuItem',
+            group: 'g2',
+            onClick: function(event) {
+                thisB.config.type = 'JBrowse/View/Track/SNPCoverage'
+                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+            }
+        });
         displayOptions.push({
             label: 'View normal',
             type: 'dijit/RadioMenuItem',

diff --git a/src/JBrowse/View/Track/SNPCoverage.js b/src/JBrowse/View/Track/SNPCoverage.js
@@ -281,7 +281,21 @@ return declare( [WiggleXY, AlignmentsMixin],
     },
 
     _trackMenuOptions: function() {
-        return all([ this.inherited(arguments), this._alignmentsFilterTrackMenuOptions() ])
+        var thisB = this;
+        var displayOptions = [];
+
+
+        displayOptions.push({
+            label: 'View alignments',
+            type: 'dijit/RadioMenuItem',
+            group: 'g2',
+            onClick: function(event) {
+                thisB.config.type = 'JBrowse/View/Track/Alignments2'
+                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+            }
+        });
+
+        return all([ this.inherited(arguments), this._alignmentsFilterTrackMenuOptions(), displayOptions ])
             .then( function( options ) {
                        var o = options.shift();
                        options.unshift({ type: 'dijit/MenuSeparator' } );