Change PairUtils name

GMOD · Nov 18, 2018 · 4c45607 · 4c45607
1 parent b4ed334
commit 4c45607
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Showing 5 changed files with 27 additions and 17 deletions.
diff --git a/src/JBrowse/View/FeatureGlyph/Alignment.js b/src/JBrowse/View/FeatureGlyph/Alignment.js
@@ -2,14 +2,14 @@ define([
            'dojo/_base/declare',
            'dojo/_base/array',
            'JBrowse/View/FeatureGlyph/Box',
-           'JBrowse/View/FeatureGlyph/PairUtils',
+           'JBrowse/View/FeatureGlyph/AlignmentColoring',
            'JBrowse/Store/SeqFeature/_MismatchesMixin'
        ],
        function(
            declare,
            array,
            BoxGlyph,
-           PairUtils,
+           AlignmentColoring,
            MismatchesMixin
        ) {
 
@@ -32,7 +32,7 @@ return declare( [BoxGlyph,MismatchesMixin], {
             {
                 //maxFeatureScreenDensity: 400
                 style: {
-                    color: PairUtils.colorAlignment,
+                    color: AlignmentColoring.colorAlignment,
                     color_fwd_strand_not_proper: '#ECC8C8',
                     color_rev_strand_not_proper: '#BEBED8',
                     color_fwd_strand: '#EC8B8B',

diff --git a/src/JBrowse/View/FeatureGlyph/PairUtils.js → ...se/View/FeatureGlyph/AlignmentColoring.js b/src/JBrowse/View/FeatureGlyph/PairUtils.js → ...se/View/FeatureGlyph/AlignmentColoring.js
@@ -3,14 +3,14 @@ define( [
 ],
 function(Util) {
 
-var PairUtils = {
+var AlignmentColoring = {
     colorAlignment(feature, score, glyph, track) {
         var strand = feature.get('strand');
         if (Math.abs(strand) != 1 && strand != '+' && strand != '-') {
             return track.colorForBase('reference');
         }
         else if (track.config.colorByOrientation) {
-            return PairUtils.colorByOrientation(feature, score, glyph, track)
+            return AlignmentColoring.colorByOrientation(feature, score, glyph, track)
         }
         else if (track.config.useXS) {
             var xs = feature.get('xs')
@@ -92,21 +92,21 @@ var PairUtils = {
 
     colorArcs(feature, score, glyph, track) {
         if (track.config.colorByOrientation) {
-            return PairUtils.colorByOrientation(feature, score, glyph, track)
+            return AlignmentColoring.colorByOrientation(feature, score, glyph, track)
         } else {
-            return PairUtils.colorByInsertDistance(feature, score, glyph, track)
+            return AlignmentColoring.colorByInsertDistance(feature, score, glyph, track)
         }
     },
 
     colorConnector(feature, score, glyph, track) {
         if (track.config.colorByOrientation) {
-            return PairUtils.colorByOrientation(feature, score, glyph, track)
+            return AlignmentColoring.colorByOrientation(feature, score, glyph, track)
         } else {
             return 'black'
         }
     }
 };
 
-return PairUtils;
+return AlignmentColoring;
 
 });
diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -3,14 +3,14 @@ define([
     'dojo/_base/array',
     'dojo/_base/lang',
     'JBrowse/View/FeatureGlyph/Alignment',
-    'JBrowse/View/FeatureGlyph/PairUtils'
+    'JBrowse/View/FeatureGlyph/AlignmentColoring'
 ],
 function(
     declare,
     array,
     lang,
     Alignment,
-    PairUtils
+    AlignmentColoring
 ) {
 
 
@@ -65,7 +65,7 @@ _defaultConfig() {
         readCloudLog: true,
         readCloudStretch: 20,
         style: {
-            connectorColor: PairUtils.colorConnector,
+            connectorColor: AlignmentColoring.colorConnector,
             connectorThickness: 1,
         }
     });

diff --git a/src/JBrowse/View/FeatureGlyph/PairedArc.js b/src/JBrowse/View/FeatureGlyph/PairedArc.js
@@ -3,21 +3,21 @@ define([
     'dojo/_base/array',
     'dojo/_base/lang',
     'JBrowse/View/FeatureGlyph/Box',
-    'JBrowse/View/FeatureGlyph/PairUtils'
+    'JBrowse/View/FeatureGlyph/AlignmentColoring'
 ],
 function(
     declare,
     array,
     lang,
     FeatureGlyph,
-    PairUtils
+    AlignmentColoring
 ) {
     return declare(FeatureGlyph, {
 
         _defaultConfig: function() {
             return this._mergeConfigs(lang.clone(this.inherited(arguments)), {
                 style: {
-                    color: PairUtils.colorArcs,
+                    color: AlignmentColoring.colorArcs,
                     color_pair_lr: 'grey',
                     color_pair_rr: 'navy',
                     color_pair_rl: 'teal',

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -33,11 +33,11 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 hideUnmapped: true,
                 hideUnsplicedReads: false,
                 hideMissingMatepairs: false,
-                hideForwardStrant: false,
+                hideForwardStrand: false,
                 hideReverseStrand: false,
                 useXS: false,
+                useTS: false,
                 useReverseTemplate: false,
-                useXSOption: true,
                 useReverseTemplateOption: true,
                 viewAsPairs: false,
                 readCloud: false,
@@ -135,6 +135,16 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
             }
         });
+
+        c.children.push({
+            label: 'Color by TS tag (RNA-seq strandedness)',
+            type: 'dijit/CheckedMenuItem',
+            checked: this.config.useTS,
+            onClick: function(event) {
+                thisB.config.useTS = this.get('checked');
+                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+            }
+        });
         c.children.push({
             label: 'Color mate pair as flipped (RNA-seq strandedness)',
             type: 'dijit/CheckedMenuItem',