Make read cloud specific options into separate track menu

GMOD · Nov 27, 2018 · 718465c · 718465c
1 parent 72f66e4
commit 718465c
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Showing 3 changed files with 53 additions and 26 deletions.
diff --git a/src/JBrowse/View/Dialog/SetTrackHeight.js b/src/JBrowse/View/Dialog/SetTrackHeight.js
@@ -2,7 +2,7 @@ define([
            'dojo/_base/declare',
            'dojo/dom-construct',
            'dijit/focus',
-            'dijit/form/NumberSpinner',
+           'dijit/form/NumberSpinner',
            'JBrowse/View/Dialog/WithActionBar',
            'dojo/on',
            'dijit/form/Button',
@@ -14,7 +14,7 @@ define([
 return declare( ActionBarDialog, {
     /**
      * Dijit Dialog subclass that pops up prompt for the user to
-     * manually set a new highlight.
+     * manually set a new track height.
      * @lends JBrowse.View.InfoDialog
      */
     title: 'Set new track height',
@@ -24,7 +24,8 @@ return declare( ActionBarDialog, {
         this.browser = args.browser;
         this.setCallback    = args.setCallback || function() {};
         this.cancelCallback = args.cancelCallback || function() {};
-        this.heightConstraints = { min: 10, max: 750 };
+        this.heightConstraints = { min: 10, max: args.maxHeight||750 };
+        this.msg = args.msg
     },
 
     _fillActionBar: function( actionBar ) {
@@ -60,7 +61,7 @@ return declare( ActionBarDialog, {
         this.set('content', [
                      dom.create('label', { "for": 'newhighlight_locstring', innerHTML: '' } ),
                      this.heightSpinner.domNode,
-                     dom.create( 'span', { innerHTML: ' pixels' } )
+                     dom.create( 'span', { innerHTML: this.msg||' pixels' } )
                  ] );
 
         this.inherited( arguments );

diff --git a/src/JBrowse/View/FeatureGlyph/PairedReadCloud.js b/src/JBrowse/View/FeatureGlyph/PairedReadCloud.js
@@ -21,18 +21,19 @@ layoutFeature(viewArgs, layout, feature) {
     if (feature.pairedFeature()) {
         const tlen = Math.abs(feature.read1.get('template_length'))
 
-        // log view uses maximum to handle very large, linear uses upper percentile
 
         let k
         if(this.track.config.readCloudLogScale) {
             // max is set to upper percentile because it can handle things above this value
-            k = Math.log(tlen + 1) / Math.log(this.track.insertSizeStats.max + 1)
+            k = Math.log(tlen + 1) / Math.log(this.track.config.readCloudYScaleMax || this.track.insertSizeStats.max + 1)
+            k /= 2 // squish by 2 means theres space above the maxHeight for things larger than the estimated insert size stats/readcloud max
         } else {
-            // max set to literal max or a configurable insertSizeMax
-            k = tlen / (this.track.config.insertSizeMax || this.track.insertSizeStats.upper)
+            // max set to literal max or a configurable readCloudYScaleMax
+            k = tlen / (this.track.config.readCloudYScaleMax || this.track.insertSizeStats.upper)
+            k /= 3 // squish by 3 means theres space above the maxHeight for things larger than the estimated insert size stats, higher for linear
         }
+
         k *= this.track.config.maxHeight
-        k /= 3
 
         // use compact view for additional linear compression
         if(this.track.config.displayMode === 'compact') {

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -2,6 +2,7 @@ define( [
             'dojo/_base/declare',
             'dojo/_base/array',
             'dijit/MenuItem',
+            'JBrowse/View/Dialog/SetTrackHeight',
             'JBrowse/Util',
             'JBrowse/View/Track/CanvasFeatures',
             'JBrowse/View/Track/_AlignmentsMixin'
@@ -10,6 +11,7 @@ define( [
             declare,
             array,
             MenuItem,
+            Dialog,
             Util,
             CanvasFeatureTrack,
             AlignmentsMixin
@@ -212,24 +214,47 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
                 thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
             }
         });
-        c.children.push({
-            label: 'Show interchromosomal',
-            type: 'dijit/CheckedMenuItem',
-            checked: !!this.config.showInterchromosomalArcs,
-            onClick: function(event) {
-                thisB.config.showInterchromosomalArcs = this.get('checked');
-                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
-            }
-        });
-        c.children.push({
-            label: 'View read cloud log scale',
-            type: 'dijit/CheckedMenuItem',
-            checked: !!this.config.readCloudLogScale,
-            onClick: function(event) {
-                thisB.config.readCloudLogScale = this.get('checked');
-                thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+        if(this.config.glyph == 'JBrowse/View/FeatureGlyph/PairedReadCloud') {
+            var r = {
+                type: 'dijit/Menu',
+                label: 'Read cloud options',
+                children: []
             }
-        });
+            r.children.push({
+                label: 'Show interchromosomal',
+                type: 'dijit/CheckedMenuItem',
+                checked: !!this.config.showInterchromosomalArcs,
+                onClick: function(event) {
+                    thisB.config.showInterchromosomalArcs = this.get('checked');
+                    thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+                }
+            });
+            r.children.push({
+                label: 'View read cloud log scale',
+                type: 'dijit/CheckedMenuItem',
+                checked: !!this.config.readCloudLogScale,
+                onClick: function(event) {
+                    thisB.config.readCloudLogScale = this.get('checked');
+                    thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+                }
+            });
+            r.children.push({
+                label: 'Set read cloud Y-scale insert size',
+                onClick: function(event) {
+                    new Dialog({
+                        title: 'Set read cloud Y-scale in terms of the maximum expected insert size',
+                        msg: ' insert size (note: default estimated from sampling track data)',
+                        maxHeight: Infinity,
+                        height: thisB.config.readCloudYScaleMax || 50000,
+                        setCallback: ret => {
+                            thisB.config.readCloudYScaleMax = ret
+                            thisB.browser.publish('/jbrowse/v1/v/tracks/replace', [thisB.config]);
+                        }
+                    }).show()
+                }
+            });
+            displayOptions.push(r)
+        }
         return Promise.all([ this.inherited(arguments), this._alignmentsFilterTrackMenuOptions(), displayOptions ])
             .then( function( options ) {
                        var o = options.shift();