Support unprocessed transcripts in neat features

GMOD · Dec 28, 2018 · 4f0576e · 4f0576e
1 parent 8236ade
commit 4f0576e
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Showing 3 changed files with 29 additions and 25 deletions.
diff --git a/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js b/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Gene.js
@@ -4,22 +4,28 @@ define([
     'dojo/_base/array',
     'JBrowse/View/FeatureGlyph/Gene',
     './Box',
-    './ProcessedTranscript'
+    './ProcessedTranscript',
+    './UnprocessedTranscript'
 ],
 function (
     declare,
     lang,
     array,
     Gene,
-    BoxGlyph,
-    ProcessedTranscriptGlyph
+    Box,
+    ProcessedTranscript,
+    UnprocessedTranscript,
+
 ) {
     return declare(Gene, {
         _boxGlyph: function () {
-            return this.__boxGlyph || (this.__boxGlyph = new BoxGlyph({ track: this.track, browser: this.browser, config: this.config }));
+            return this.__boxGlyph || (this.__boxGlyph = new Box({ track: this.track, browser: this.browser, config: this.config }));
         },
         _ptGlyph: function () {
-            return this.__ptGlyph || (this.__ptGlyph = new ProcessedTranscriptGlyph({ track: this.track, browser: this.browser, config: this.config }));
-        }
+            return this.__ptGlyph || (this.__ptGlyph = new ProcessedTranscript({ track: this.track, browser: this.browser, config: this.config }));
+        },
+        _ntGlyph: function() {
+            return this.__ntGlyph || ( this.__ntGlyph = new UnprocessedTranscript({ track: this.track, browser: this.browser, config: this.config }) );
+        },
     });
 });
diff --git a/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/ProcessedTranscript.js b/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/ProcessedTranscript.js
@@ -12,23 +12,5 @@ function (
     ProcessedTranscript,
     Segments
 ) {
-    return declare([ProcessedTranscript, Segments], {
-
-        _getFeatureHeight: function( viewInfo, feature ) {
-            var h = this.getStyle( feature, 'height');
-
-            if( viewInfo.displayMode == 'compact' )
-                h = Math.round( 0.45 * h );
-
-            if( this.getStyle( feature, 'strandArrow' ) ) {
-                var strand = feature.get('strand');
-                if( strand == 1 )
-                    h = Math.max( this._embeddedImages.plusArrow.height, h );
-                else if( strand == -1 )
-                    h = Math.max( this._embeddedImages.minusArrow.height, h );
-            }
-
-            return h;
-        }
-    });
+    return declare([ProcessedTranscript, Segments])
 });
diff --git a/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/UnprocessedTranscript.js b/plugins/NeatCanvasFeatures/js/View/FeatureGlyph/UnprocessedTranscript.js
@@ -0,0 +1,16 @@
+define([
+    'dojo/_base/declare',
+    'dojo/_base/array',
+    'dojox/color/Palette',
+    'JBrowse/View/FeatureGlyph/UnprocessedTranscript',
+    './Segments'
+],
+function (
+    declare,
+    array,
+    Palette,
+    UnprocessedTranscript,
+    Segments
+) {
+    return declare([Segments,UnprocessedTranscript])
+});