Partial fix for WebApollo issue #13, where annotation editing causes …

…unexpected layout change (when there are overlapping annotations), making it appear like edits were actually done on a different annotation.

WebApollo/js/Store/SeqFeature/ScratchPad.js

@@ -8,14 +8,36 @@ return declare( SeqFeatureStore,
 {
     constructor: function( args ) {
         this.features = {};
+	this.sorted_feats = [];
         this._calculateStats();
     },
 
     insert: function( feature ) {
         this.features[ feature.id() ] = feature;
+//	this._sort();
         this._calculateStats();
     },
 
+    replace: function( feature ) {
+	this.features[ feature.id() ] = feature;
+//	this._sort();
+        this._calculateStats();
+    }, 
+
+/*    _sort: function()  {
+	sorted_feats.sort(function(a, b) {
+	    var astart = a.get('start');
+	    var bstart = b.get('start');
+            if (astart != bstart)  {
+		return astart - bstart;
+	    }
+            else {
+		return b.get('end') - a.get('end');
+	    }
+	} );
+    }, 
+*/
+
 /*
     delete: function( feature ) {
 	this.deleteFeatureById[ feature.id() ];
@@ -26,6 +48,7 @@ return declare( SeqFeatureStore,
 	delete  this.features[ id ];
         this._calculateStats();
     },
+
 
     /* if feature with given id is present in store, return it.  Otherwise return null */
     getFeatureById: function( id )  {

WebApollo/js/View/Track/AnnotTrack.js

@@ -356,9 +356,14 @@ var AnnotTrack = declare( DraggableFeatureTrack,
      *  received notification from server ChangeNotificationListener that annotations were updated
      *  currently handled as if receiving DELETE followed by ADD command
      */
-    annotationsUpdatedNotification: function(annots)  {
-	this.annotationsDeletedNotification(annots);
-	this.annotationsAddedNotification(annots);
+    annotationsUpdatedNotification: function(responseFeatures)  {
+	// this.annotationsDeletedNotification(annots);
+	// this.annotationsAddedNotification(annots);
+        for (var i = 0; i < responseFeatures.length; ++i) {
+            var feat = JSONUtils.createJBrowseFeature( responseFeatures[i] );
+            // var id = responseFeatures[i].uniquename;
+            this.store.replace(feat);
+        }
     },
 
     /**