Add read cloud function to paired reads track

GMOD · Oct 31, 2018 · 007718e · 007718e
1 parent 5561cf5
commit 007718e
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Showing 2 changed files with 44 additions and 8 deletions.
diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -45,7 +45,7 @@ renderConnector( context, fRect ) {
     }
 },
 
-_defaultConfig: function() {
+_defaultConfig() {
     return this._mergeConfigs(
         dojo.clone( this.inherited(arguments) ),
         {
@@ -128,6 +128,27 @@ _defaultConfig: function() {
             }
         }
     );
+},
+layoutFeature(viewArgs, layout, feature) {
+    var rect = this.inherited(arguments);
+    if (!rect) {
+        return rect;
+    }
+    if(this.config.readCloud) {
+        if(feature.pairedFeature()) {
+            var tlen = feature.f1.get('template_length')
+            var t = Math.abs(tlen)
+
+            // need to set the top of the inner rect
+            rect.rect.t = t / (this.config.scaleFactor||1);
+            rect.t = t / (this.config.scaleFactor||1);
+        } else {
+            rect.t = 0
+            rect.rect.t = 0
+        }
+    }
+
+    return rect;
 }
 
 });

diff --git a/src/JBrowse/View/Track/PairedReads.js b/src/JBrowse/View/Track/PairedReads.js
@@ -12,14 +12,29 @@ define( [
         ) {
 
 return declare(CanvasFeatures, {
-	_defaultConfig: function() {
-		return Util.deepUpdate(lang.clone(this.inherited(arguments)), {
-			glyph: 'JBrowse/View/FeatureGlyph/PairedAlignment',
-			maxFeatureScreenDensity: 60,
-			style: {
+    _defaultConfig: function() {
+        return Util.deepUpdate(lang.clone(this.inherited(arguments)), {
+            glyph: 'JBrowse/View/FeatureGlyph/PairedAlignment',
+            maxFeatureScreenDensity: 60,
+            readCloud: false,
+            style: {
                 showLabels: false
             }
-		});
-	}
+        });
+    },
+    // override getLayout to access addRect method
+    _getLayout: function() {
+        var layout = this.inherited(arguments);
+        if(this.config.readCloud) {
+            layout = declare.safeMixin(layout, {
+                addRect: function() {
+                    this.pTotalHeight = this.maxHeight;
+                    return 0;
+                }
+            });
+        }
+        return layout;
+    }
+
 });
 });