Add unprocessed transcript code

GMOD · Oct 26, 2018 · ec638ea · ec638ea
1 parent 6c6e555
commit ec638ea
Show file tree

Hide file tree

Showing 2 changed files with 38 additions and 1 deletion.
diff --git a/src/JBrowse/View/FeatureGlyph/Gene.js b/src/JBrowse/View/FeatureGlyph/Gene.js
@@ -3,13 +3,15 @@ define([
            'dojo/_base/lang',
            'dojo/_base/array',
            'JBrowse/View/FeatureGlyph/Box',
+           'JBrowse/View/FeatureGlyph/UnprocessedTranscript',
            'JBrowse/View/FeatureGlyph/ProcessedTranscript'
        ],
        function(
            declare,
            lang,
            array,
            BoxGlyph,
+           UnprocessedTranscript,
            ProcessedTranscriptGlyph
        ) {
 
@@ -20,6 +22,7 @@ _defaultConfig: function() {
         this.inherited(arguments),
         {
             transcriptType: 'mRNA',
+            noncodingType: ['ncRNA','transcript', 'lnc_RNA', 'lncRNA'],
             style: {
                 transcriptLabelFont: 'normal 10px Univers,Helvetica,Arial,sans-serif',
                 transcriptLabelColor: 'black',
@@ -33,6 +36,9 @@ _defaultConfig: function() {
 _boxGlyph: function() {
     return this.__boxGlyph || ( this.__boxGlyph = new BoxGlyph({ 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 }) );
+},
 _ptGlyph: function() {
     return this.__ptGlyph || ( this.__ptGlyph = new ProcessedTranscriptGlyph({ track: this.track, browser: this.browser, config: this.config }) );
 },
@@ -67,10 +73,11 @@ _getFeatureRectangle( viewArgs, feature ) {
         fRect.r = -Infinity;
 
         var transcriptType = this.getConfForFeature( 'transcriptType', feature );
+        var noncodingType = this.getConfForFeature( 'noncodingType', feature );
         for( var i = 0; i < subfeatures.length; i++ ) {
             var subRect = ( subfeatures[i].get('type') == transcriptType
                             ? this._ptGlyph()
-                            : this._boxGlyph()
+                            : (noncodingType.includes(subfeatures[i].get('type')) ?  this._ntGlyph() : this._boxGlyph())
                           )._getFeatureRectangle( subArgs, subfeatures[i] );
 
             padding = i == subfeatures.length-1 ? 0 : 1;

diff --git a/src/JBrowse/View/FeatureGlyph/UnprocessedTranscript.js b/src/JBrowse/View/FeatureGlyph/UnprocessedTranscript.js
@@ -0,0 +1,30 @@
+define([
+           'dojo/_base/declare',
+           'dojo/_base/Color',
+           'JBrowse/View/FeatureGlyph/Segments'
+       ],
+       function(
+           declare,
+           Color,
+           Segments
+       ) {
+
+return declare( Segments, {
+    _defaultConfig: function() {
+        return this._mergeConfigs(this.inherited(arguments), {
+            style: {
+                unprocessedTranscriptColor: 'red'
+            }
+        });
+    },
+    renderBox: function( context, viewInfo, feature, top, overallHeight, parentFeature, style ) {
+        style = style || lang.hitch( this, 'getStyle' );
+        return this.inherited(arguments, [context, viewInfo, feature, top, overallHeight, parentFeature, function(feat, attr) {
+            if(attr == 'color')
+                return style(parentFeature, 'unprocessedTranscriptColor')
+            return style(feat, attr)
+        }])
+    }
+
+});
+});