genoverse 3.2.0

package/js/Track/Controller/Sequence.js

@@ -0,0 +1,17 @@
+Genoverse.Track.Controller.Sequence = Genoverse.Track.Controller.extend({
+  getClickedFeatures: function (x, y) {
+    var feature = this.base(x, y)[0];
+
+    return feature ? this.makeSeqFeatureMenu(feature, Math.floor(x / this.scale)) : false;
+  },
+
+  makeSeqFeatureMenu: function (feature, pos) {
+    feature.featureMenus      = feature.featureMenus      || {};
+    feature.featureMenus[pos] = feature.featureMenus[pos] || {
+      title    : feature.sequence.charAt(pos - feature.start),
+      Location : feature.chr + ':' + pos
+    };
+
+    return feature.featureMenus[pos].title ? feature.featureMenus[pos] : undefined;
+  }
+});

package/js/Track/Controller/Stranded.js

@@ -0,0 +1,73 @@
+Genoverse.Track.Controller.Stranded = Genoverse.Track.Controller.extend({
+  constructor: function (properties) {
+    this.base(properties);
+
+    if (typeof this._makeImage === 'function') {
+      return;
+    }
+
+    var strand        = this.prop('strand');
+    var featureStrand = this.prop('featureStrand');
+
+    if (strand === -1) {
+      this._makeImage = this.track.makeReverseImage ? $.proxy(this.track.makeReverseImage, this) : this.makeImage;
+      this.makeImage  = $.noop;
+    } else {
+      strand = this.prop('strand', 1);
+
+      this._makeImage = this.makeImage;
+      this.makeImage  = this.makeForwardImage;
+
+      var track = this.track;
+
+      setTimeout(function () {
+        track.reverseTrack = track.browser.addTrack(track.constructor.extend({
+          id           : track.id ? track.id + 'Reverse' : undefined,
+          strand       : -1,
+          url          : false,
+          order        : typeof track.orderReverse === 'number' ? track.orderReverse : track.order,
+          forwardTrack : track
+        }));
+
+        $.each(track.controller._deferredReverseTrackImages, function (i, args) { track.controller._makeReverseTrackImage.apply(track.controller, args); });
+        delete track.controller._deferredReverseTrackImages;
+      }, 1);
+    }
+
+    if (!featureStrand) {
+      this.prop('featureStrand', strand);
+    }
+  },
+
+  makeForwardImage: function (params) {
+    this._makeReverseTrackImage(params, this._makeImage(params));
+  },
+
+  _makeReverseTrackImage: function (params, deferred) {
+    var reverseTrack = this.prop('reverseTrack');
+
+    if (!reverseTrack) {
+      this._deferredReverseTrackImages = (this._deferredReverseTrackImages || []).concat([[ params, deferred ]]);
+      return;
+    }
+
+    if (deferred && typeof deferred.done === 'function') {
+      deferred.done(function () {
+        reverseTrack.controller._makeImage(params, deferred);
+      });
+    } else {
+      reverseTrack.controller._makeImage(params, deferred);
+    }
+  },
+
+  destroy: function () {
+    if (this.removing) {
+      return;
+    }
+
+    this.removing = true;
+
+    this.browser.removeTrack(this.prop('forwardTrack') || this.prop('reverseTrack'));
+    this.base();
+  }
+});