clean up

Author: turner

js/bam/alignmentTrack.js

@@ -889,7 +889,6 @@ class AlignmentTrack extends TrackBase {
      *
      * @param menuItem
      * @param showCheck
-     * @returns {{init: undefined, name: undefined, click: clickHandler, element: (jQuery|HTMLElement|jQuery.fn.init)}}
      */
     colorByCB(menuItem, showCheck) {
 
@@ -953,7 +952,6 @@ class AlignmentTrack extends TrackBase {
      *
      * @param menuItem
      * @param showCheck
-     * @returns {{init: undefined, name: undefined, click: clickHandler, element: (jQuery|HTMLElement|jQuery.fn.init)}}
      */
     groupByCB(menuItem, showCheck) {
 

js/cnvpytor/cnvpytorTrack.js

@@ -237,9 +237,9 @@ class CNVPytorTrack extends TrackBase {
         items.push('<hr/>')
         items.push("Bin Sizes")
         for (let rd_bin of this.available_bins) {
-            const checkBox = createCheckbox(rd_bin, rd_bin === this.bin_size)
+
             items.push({
-                element: checkBox,
+                element: createCheckbox(rd_bin, rd_bin === this.bin_size),
                 click: async function binSizesHandler() {
                     this.bin_size = rd_bin
                     // data loader image
@@ -257,9 +257,9 @@ class CNVPytorTrack extends TrackBase {
 
         let signal_dct = {"rd_snp": "RD and BAF Likelihood", "rd": "RD Signal", "snp": "BAF Likelihood"}
         for (let signal_name in signal_dct) {
-            const checkBox = createCheckbox(signal_dct[signal_name], signal_name === this.signal_name)
+
             items.push({
-                element: checkBox,
+                element: createCheckbox(signal_dct[signal_name], signal_name === this.signal_name),
                 click: async function signalTypeHandler() {
                     this.signal_name = signal_name
                     await this.recreate_tracks(this.bin_size)
@@ -275,9 +275,9 @@ class CNVPytorTrack extends TrackBase {
         items.push('<hr/>')
         items.push("CNV caller")
         for (let cnv_caller of this.available_callers) {
-            const checkBox = createCheckbox(cnv_caller, cnv_caller === this.cnv_caller)
+
             items.push({
-                element: checkBox,
+                element: createCheckbox(cnv_caller, cnv_caller === this.cnv_caller),
                 click: async function cnvCallerHandler() {
                     this.cnv_caller = cnv_caller
                     // data loader image

js/feature/featureTrack.js

@@ -362,14 +362,12 @@ class FeatureTrack extends TrackBase {
 
             for (const colorScheme of ["function", "class"]) {
 
-                const element = createCheckbox(`Color by ${colorScheme}`, colorScheme === this.colorBy)
-
                 function colorSchemeHandler() {
                     this.colorBy = colorScheme
                     this.trackView.repaintViews()
                 }
 
-                menuItems.push({element, click: colorSchemeHandler})
+                menuItems.push({element:createCheckbox(`Color by ${colorScheme}`, colorScheme === this.colorBy), click: colorSchemeHandler})
             }
         }
 
@@ -384,16 +382,14 @@ class FeatureTrack extends TrackBase {
 
         for (const displayMode of ["COLLAPSED", "SQUISHED", "EXPANDED"]) {
 
-            const element = createCheckbox(lut[displayMode], displayMode === this.displayMode)
-
             function displayModeHandler() {
                 this.displayMode = displayMode
                 this.config.displayMode = displayMode
                 this.trackView.checkContentHeight()
                 this.trackView.repaintViews()
             }
 
-            menuItems.push({element, click: displayModeHandler})
+            menuItems.push({element:createCheckbox(lut[displayMode], displayMode === this.displayMode), click: displayModeHandler})
         }
 
         return menuItems

js/feature/segTrack.js

@@ -166,10 +166,10 @@ class SegTrack extends TrackBase {
         menuItems.push("DisplayMode:")
         const displayOptions = this.type === 'seg' || this.type === 'shoebox' ? ["SQUISHED", "EXPANDED", "FILL"] : ["SQUISHED", "EXPANDED"]
         for (let displayMode of displayOptions) {
-            const checkBox = createCheckbox(lut[displayMode], displayMode === this.displayMode)
+
             menuItems.push(
                 {
-                    element: checkBox,
+                    element: createCheckbox(lut[displayMode], displayMode === this.displayMode),
                     click: function displayModeHandler() {
                         this.displayMode = displayMode
                         this.config.displayMode = displayMode

js/feature/wigTrack.js

@@ -173,14 +173,13 @@ class WigTrack extends TrackBase {
         menuItems.push('<hr/>')
         menuItems.push("<div>Windowing function</div>")
         for (const wf of windowFunctions) {
-            const element = createCheckbox(wf, this.windowFunction === wf)
 
             function clickHandler() {
                 this.windowFunction = wf
                 this.trackView.updateViews()
             }
 
-            menuItems.push({element, click: clickHandler})
+            menuItems.push({element:createCheckbox(wf, this.windowFunction === wf), click: clickHandler})
         }
 
         return menuItems
@@ -195,14 +194,13 @@ class WigTrack extends TrackBase {
         menuItems.push("<div>Graph type</div>")
 
         for (const gt of graphType) {
-            const element = createCheckbox(gt, this.graphType === gt)
 
             function clickHandler() {
                 this.graphType = gt
                 this.trackView.repaintViews()
             }
 
-            menuItems.push({element, click: clickHandler})
+            menuItems.push({element:createCheckbox(gt, this.graphType === gt), click: clickHandler})
         }
 
         return menuItems