Some updates

* Reduced default console message level.
* Changed auto-scale in bigWig display.
* Fixed interaction-track-dom.

Author: Xiaoyi Cao

give/html/components/bower_components/genemo-data-components/basic-func/basicFunc.js

@@ -109,10 +109,12 @@ var GIVe = (function (give) {
           !!(navigator.userAgent.match(/Trident/) ||
              navigator.userAgent.match(/rv 11/)))) {
           // IE detected (should be IE 11), fix the json return issue
-          console.log('You are currently using IE 11 to visit this site. ' +
-          'Some part of the site may behave differently and if you encounter ' +
-          'any problems, please use the info on \'About us\' page to ' +
-          'contact us.')
+          give._verboseConsole(
+            'You are currently using IE 11 to visit this site. ' +
+            'Some part of the site may behave differently and if you encounter ' +
+            'any problems, please use the info on \'About us\' page to ' +
+            'contact us.', give.VERBOSE_MAJ_ERROR
+          )
           responses = JSON.parse(responses)
         }
         responseFunc.call(thisVar, responses, xhr.status)
@@ -194,6 +196,22 @@ var GIVe = (function (give) {
     }
   }
 
+  give._findPercentile = function (dataArr, upperPercentile, lowerPercentile) {
+    function numberComp (a, b) {
+      return a - b
+    }
+    lowerPercentile = lowerPercentile || upperPercentile
+    var sortedArr = dataArr.sort(numberComp)
+    return {
+      upper: sortedArr[parseInt(sortedArr.length * (1 - upperPercentile))],
+      lower: sortedArr[parseInt(sortedArr.length * lowerPercentile)]
+    }
+  }
+
+  give._maxDecimalDigits = function (number, digits) {
+    return Number(Math.round(number + 'e' + digits) + 'e-' + digits)
+  }
+
   window.addEventListener('WebComponentsReady', function (e) {
     give.fireCoreSignal('content-dom-ready', null)
     give.fireSignal(give.TASKSCHEDULER_EVENT_NAME, {flag: 'web-component-ready'})

give/html/components/bower_components/genemo-data-components/basic-func/constants-template.js

@@ -8,7 +8,7 @@ var GIVe = (function (give) {
   give.VERBOSE_DEBUG = 4
   give.VERBOSE_DEBUG_MORE = 5
 
-  give.verboseLvl = give.VERBOSE_DEBUG
+  give.verboseLvl = give.VERBOSE_MAJ_ERROR
 
   give.Host = 'https://www.givengine.org'
 

give/html/components/bower_components/genemo-data-components/chrom-b-plus-tree/chromBPlusTreeNode.js

@@ -78,7 +78,8 @@ var GIVe = (function (give) {
     function (revdepth, start, end, summaryCtor, nextNode, prevNode, bFactor, isroot) {
     // start and length is for the corresponding region
       if (isNaN(bFactor) || parseInt(bFactor) !== bFactor || bFactor <= 2) {
-        console.log('Default branching factor is chosen instead of ' + bFactor)
+        give._verboseConsole('Default branching factor is chosen instead of ' +
+          bFactor, give.VERBOSE_DEBUG)
         bFactor = give.ChromBPlusTreeNode._DEFAULT_B_FACTOR
       }
       if (typeof revdepth !== 'number' || isNaN(revdepth)) {

give/html/components/bower_components/genemo-visual-components/chart-area/track-doms/bigwig-track-dom.html

@@ -21,6 +21,25 @@
           give.TrackDOMBehavior
         ],
         properties: {
+          upperPercentile: {
+            type: Number,
+            value: 0.01
+          },
+
+          lowerPercentile: {
+            type: Number,
+            value: 0.01
+          },
+
+          numOfDigits: {
+            type: Number,
+            value: 2
+          },
+
+          includeZero: {
+            type: Boolean,
+            value: true
+          }
         },
         created: function () {
           this.MARGIN = 2
@@ -199,29 +218,30 @@
           var vwindow = this.mainSvg.viewWindow
 
           if (this.track.data.hasOwnProperty(vwindow.chr)) {
-            var updateExtreme = function (dataSegment) {
-              var yvalue = dataSegment.data.value
-              if (Math.ceil(yvalue) > this.windowMax) {
-                this.windowMax = Math.ceil(yvalue)
-              }
-              if (Math.floor(yvalue) < this.windowMin) {
-                this.windowMin = Math.floor(yvalue)
-              }
-            }.bind(this)
+            this.dataPoints = this._generateSmoothedPoints()
 
             if (this.autoScale) {
               this.windowMax = Number.NEGATIVE_INFINITY
-              this.windowMin = Number.POSITIVE_INFINITY
-              this.track.data[vwindow.chr].traverse(vwindow, updateExtreme, null,
-                this.getResolution(vwindow), this, false)
+              this.windowMin = this.includeZero ? 0 : Number.POSITIVE_INFINITY
+              try {
+                var extremities = give._findPercentile(this.dataPoints.map(
+                  function (dataEntry) {
+                    return dataEntry.data.value
+                  }, this), this.upperPercentile, this.lowerPercentile)
+                if (this.windowMax < extremities.upper) {
+                  this.windowMax = extremities.upper
+                }
+                if (this.windowMin > extremities.lower) {
+                  this.windowMin = extremities.lower
+                }
+              } catch (e) {
+              }
               if (this.windowMax === Number.NEGATIVE_INFINITY) {
                 this.windowMax = 1
                 this.windowMin = 0
               }
             }
 
-            this.dataPoints = this._generateSmoothedPoints()
-
             if (mode === 0) {
               this.drawPeak(this.dataPoints)
             }
@@ -716,10 +736,12 @@
 
           // then the text
             this.drawText(this.textMargin - this.MARGIN - this.scaleTickLength - this.TEXT_MARGIN_GAP,
-                  this.drawingBoundary.top + this.textSize * 0.4, this.windowMax.toString(),
+                  this.drawingBoundary.top + this.textSize * 0.4,
+                  give._maxDecimalDigits(this.windowMax, this.numOfDigits).toString(),
                   'end', null, this.textSvg)
             this.drawText(this.textMargin - this.MARGIN - this.scaleTickLength - this.TEXT_MARGIN_GAP,
-                  this.drawingBoundary.bottom - this.textSize * 0.4, this.windowMin.toString(),
+                  this.drawingBoundary.bottom - this.textSize * 0.4,
+                  give._maxDecimalDigits(this.windowMin, this.numOfDigits).toString(),
                   'end', null, this.textSvg)
           }
         },

give/html/components/bower_components/genemo-visual-components/chart-area/track-doms/interaction-track-dom.html

@@ -27,7 +27,7 @@
 
           subTrackGap: {
             type: Number,
-            value: 4    // em
+            value: 6    // em
           },
 
           // data structure for interaction tracks:
@@ -89,6 +89,8 @@
           this.numOfSubs = properties.numOfSubs
           this.bufferWindow = []
           this.percentiles = this.track.getSetting('thresholdPercentile')
+
+          this._pendingVWs = []
         },
 
         initSvgComponents: function () {
@@ -203,6 +205,66 @@
           this.initSubSvgHolders()
         },
 
+        drawDataFireWrapper: function (newVWindow) {
+          // fire track-ready event to its container (to calculate size and do other stuff)
+          this.changeViewWindow(newVWindow)
+          this.drawData()
+          this._setIsReady(true)
+          this.fire('track-ready', {ID: this.track.getID()})
+          if (this.callbackAfterDraw) {
+            this.callbackAfterDraw()
+            delete this.callbackAfterDraw
+          }
+        },
+
+        drawDataDebounceWrapper: function (newVWindow) {
+          // debounce wrapper for drawData()
+          this.debounce(this.updateJobName, this.drawDataFireWrapper.bind(
+            this, newVWindow), this._drawDebounceInt)
+        },
+
+        checkDataAndUpdate: function (newVWindow) {
+          // Steps:
+          //     * run this.track.getData with drawData (debounced) as callback
+          //    * whenever drawData (debounced) is done, run updateCache
+          //    Meanwhile, run fetch data (debounced) without visible callback
+          //    * Otherwise, run fetch data with drawData (debounced) as callback
+
+          newVWindow = newVWindow || this._pendingVWs
+
+          if (this.isDebouncerActive(this.cacheUpdateJobName)) {
+            this.cancelDebouncer(this.cacheUpdateJobName)
+          }
+
+          if (!Array.isArray(newVWindow)) {
+            newVWindow = [newVWindow]
+          }
+
+          // this is to set up cache loading functions as call back after draw
+          this.callbackAfterDraw = this.debounce.bind(
+            this, this.cacheUpdateJobName, this.track.getData.bind(
+              this.track,
+              newVWindow.map(function (range) {
+                return range.getExtension(
+                  give.TrackDOMBehaviorImpl.CacheRangeSpanProportion,
+                  null, true, this.track.ref
+                )
+              }, this), this.getResolution(newVWindow), null, this.id
+            ), this._cacheDebounceInt)
+          this.track.getData(
+            newVWindow.map(function (range) {
+              return range.getExtension(
+                give.TrackDOMBehaviorImpl.DefaultRangeSpanProportion,
+                null, true, this.track.ref
+              )
+            }, this),
+            this.getResolution(newVWindow),
+            this.drawDataDebounceWrapper.bind(
+              this, newVWindow
+            ), this.id
+          )
+        },
+
         updateTracks: function (viewWindow, index, threshold) {
           // viewWindow: give.ChromRegion object or an array of give.ChromRegion objects
           // index: if viewWindow is a single give.ChromRegion Object, index will be the index
@@ -215,18 +277,18 @@
             if (viewWindow) {
               if (Array.isArray(viewWindow)) {
                 // then it must have enough elements
-                viewWindow.forEach(this.changeViewWindow, this)
+                this._pendingVWs = viewWindow
               } else {
-                this.changeViewWindow(viewWindow, index)
+                this._pendingVWs[index] = viewWindow
               }
             }
 
-            if (this.subSvgs.every(function (subSvg) {
-              return subSvg.viewWindow
+            if (this._pendingVWs.every(function (pendingVWindow) {
+              return pendingVWindow
             }, this)) {
               // Get data clipped by viewWindow by calling getData()
               //    May also include data preparation
-              this.checkDataAndUpdate()
+              this.checkDataAndUpdate(this._pendingVWs)
               // Update detailed content by calling drawData()
               //    Will be debounced to prevent lagging
             }
@@ -245,10 +307,15 @@
         },
 
         changeViewWindow: function (viewWindow, index) {
-          if (typeof (viewWindow) === 'string') {
-            this.subSvgs[index].viewWindow = new give.ChromRegion(viewWindow, this.track.ref)
+          if (Array.isArray(viewWindow)) {
+            viewWindow.forEach(this.changeViewWindow, this)
           } else {
-            this.subSvgs[index].viewWindow = viewWindow.clipRegion(this.track.ref).clone()
+            if (typeof (viewWindow) === 'string') {
+              this.subSvgs[index].viewWindow = new give.ChromRegion(viewWindow, this.track.ref)
+            } else {
+              this.subSvgs[index].viewWindow = viewWindow.clipRegion(this.track.ref).clone()
+            }
+            this._pendingVWs[index] = this.subSvgs[index].viewWindow
           }
         },
 

give/html/components/bower_components/genemo-visual-components/chart-area/track-doms/track-dom-behavior.html

@@ -861,19 +861,25 @@
           this.cancelDebouncer(this.cacheUpdateJobName)
         }
 
+        var newVWArr = Array.isArray(newVWindow) ? newVWindow : [newVWindow]
+
         // this is to set up cache loading functions as call back after draw
         this.callbackAfterDraw = this.debounce.bind(
           this, this.cacheUpdateJobName, this.track.getData.bind(
-            this.track, newVWindow.getExtension(
-              give.TrackDOMBehaviorImpl.CacheRangeSpanProportion,
-              null, true, this.track.ref
-            ), this.getResolution(newVWindow), null, this.id
+            this.track, newVWArr.map(function (range) {
+              return range.getExtension(
+                give.TrackDOMBehaviorImpl.CacheRangeSpanProportion,
+                null, true, this.track.ref
+              )
+            }, this), this.getResolution(newVWindow), null, this.id
           ), this._cacheDebounceInt)
         this.track.getData(
-          newVWindow.getExtension(
-            give.TrackDOMBehaviorImpl.DefaultRangeSpanProportion,
-            null, true, this.track.ref
-          ), this.getResolution(newVWindow),
+          newVWArr.map(function (range) {
+            return range.getExtension(
+              give.TrackDOMBehaviorImpl.DefaultRangeSpanProportion,
+              null, true, this.track.ref
+            )
+          }, this), this.getResolution(newVWindow),
           this.drawDataDebounceWrapper.bind(
             this, newVWindow
           ), this.id)
@@ -946,7 +952,7 @@
         if (typeof (viewWindow) === 'string') {
           return new give.ChromRegion(viewWindow, this.track.ref)
         } else {
-          return viewWindow.clipRegion(this.track.ref).clone()
+          return viewWindow.clone().clipRegion(this.track.ref)
         }
         // this.set('viewWindowString', newValue);
       },