add a "Highlight feature" to the default HTMLFeatures right-click men…

…u, references #76
GMOD · Feb 26, 2013 · 5300c29 · 5300c29
1 parent d200087
commit 5300c29
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Showing 3 changed files with 38 additions and 9 deletions.
diff --git a/src/JBrowse/Browser.js b/src/JBrowse/Browser.js
@@ -453,6 +453,7 @@ Browser.prototype.initView = function() {
             // make the menu item for clearing the current highlight
             this._highlightClearButton = new dijitMenuItem(
                 {
+                    label: 'Clear highlight',
                     onClick: dojo.hitch( this, function() {
                                              var h = this.getHighlight();
                                              if( h ) {
@@ -2179,7 +2180,7 @@ Browser.prototype.setHighlight = function( newHighlight ) {
 Browser.prototype._updateHighlightClearButton = function() {
     if( this._highlightClearButton ) {
         this._highlightClearButton.set( 'disabled', !!! this._highlight );
-        this._highlightClearButton.set( 'label', 'Clear highlight' + ( this._highlight ? ' ' + this._highlight : '' ));
+        this._highlightClearButton.set( 'label', 'Clear highlight' + ( this._highlight ? ' - ' + this._highlight : '' ));
     }
 };
 
@@ -2191,6 +2192,15 @@ Browser.prototype.clearHighlight = function() {
     }
 };
 
+Browser.prototype.setHighlightAndRedraw = function( location ) {
+    var oldHighlight = this.getHighlight();
+    if( oldHighlight )
+        this.view.hideRegion( oldHighlight );
+    this.view.hideRegion( location );
+    this.setHighlight( location );
+    this.view.showVisibleBlocks( false );
+};
+
 /**
  * Clears the old highlight if necessary, sets the given new
  * highlight, and updates the display to show the highlighted location.

diff --git a/src/JBrowse/Model/Location.js b/src/JBrowse/Model/Location.js
@@ -1,7 +1,9 @@
 define([
+           'dojo/_base/array',
            'JBrowse/Util'
        ],
        function(
+           array,
            Util
        ) {
 
@@ -15,18 +17,26 @@ return Util.fastDeclare(
 
             if( args.location )
                 this._populate( args.location );
+            if( args.feature ) {
+                var f = args.feature;
+                this._populate({ start: f.get('start'),
+                                 end: f.get('end'),
+                                 ref: f.get('seq_id'),
+                                 strand: f.get('strand'),
+                                 objectName: f.get('Name') || f.get('ID')
+                               });
+            }
 
             this._populate( args );
 
         }
     },
     _populate: function( args ) {
-        this.ref = args.ref;
-        this.start = args.start;
-        this.end = args.end;
-        this.strand = args.strand;
-        this.tracks = args.tracks;
-        this.objectName = args.objectName;
+        array.forEach( 'ref,start,end,strand,tracks,objectName'.split(','),
+                       function( p ) {
+                           if( p in args )
+                               this[p] = args[p];
+                       }, this);
     },
 
     toString: function() {

diff --git a/src/JBrowse/View/Track/HTMLFeatures.js b/src/JBrowse/View/Track/HTMLFeatures.js
@@ -15,7 +15,8 @@ define( [
             'JBrowse/View/Track/ExportMixin',
             'JBrowse/View/Track/FeatureDetailMixin',
             'JBrowse/Util',
-            'JBrowse/View/GranularRectLayout'
+            'JBrowse/View/GranularRectLayout',
+            'JBrowse/Model/Location'
         ],
       function( declare,
                 lang,
@@ -33,7 +34,8 @@ define( [
                 ExportMixin,
                 FeatureDetailMixin,
                 Util,
-                Layout
+                Layout,
+                Location
               ) {
 
 var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetailMixin ], {
@@ -114,6 +116,13 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
                   action: 'contentDialog',
                   iconClass: 'dijitIconTask',
                   content: dojo.hitch( this, 'defaultFeatureDetail' )
+                },
+                { label: 'Highlight feature',
+                  action: function( feature ) {
+                     var loc = new Location({ feature: this.feature, tracks: [this.track] });
+                     this.track.browser.setHighlightAndRedraw(loc);
+                  },
+                  iconClass: 'dijitIconFilter'
                 }
             ]
         };