genoverse 3.2.0 → 4.0.1

package/{js → src/js}/Track/Model/Stranded.js

@@ -1,9 +1,11 @@
-Genoverse.Track.Model.Stranded = Genoverse.Track.Model.extend({
+import Model from '../Model';
+
+export default Model.extend({
   init: function (reset) {
     this.base(reset);
 
     if (!reset) {
-      var otherTrack = this.prop('forwardTrack');
+      const otherTrack = this.prop('forwardTrack');
 
       if (otherTrack) {
         this.featuresByChr = otherTrack.prop('featuresByChr');
@@ -13,16 +15,17 @@ Genoverse.Track.Model.Stranded = Genoverse.Track.Model.extend({
     }
   },
 
-  parseURL: function () {
+  parseURL: function (...args) {
     if (!this.urlParams.strand) {
       this.urlParams.strand = this.prop('featureStrand');
     }
 
-    return this.base.apply(this, arguments);
+    return this.base(...args);
   },
 
-  findFeatures: function () {
-    var strand = this.track.featureStrand;
-    return $.grep(this.base.apply(this, arguments), function (feature) { return feature.strand === strand; });
-  }
+  findFeatures: function (...args) {
+    const strand = this.track.featureStrand;
+
+    return this.base(...args).filter(feature => feature.strand === strand);
+  },
 });

package/src/js/Track/Model/Transcript/Ensembl.js

@@ -0,0 +1,73 @@
+import Model from '../Transcript';
+
+// Ensembl REST API Transcript model
+export default Model.extend({
+  url              : '//rest.ensembl.org/overlap/region/human/__CHR__:__START__-__END__?feature=transcript;feature=exon;feature=cds;content-type=application/json',
+  dataRequestLimit : 5000000, // As per e! REST API restrictions
+
+  setDefaults: function (...args) {
+    this.geneIds   = {};
+    this.seenGenes = 0;
+
+    this.base(...args);
+  },
+
+  // The url above responds in json format, data is an array
+  // See rest.ensembl.org/documentation/info/overlap_region for more details
+  parseData: function (data, chr) {
+    const featuresById = this.featuresById;
+    const ids          = [];
+
+    data.filter(d => d.feature_type === 'transcript').forEach(
+      (feature, i) => {
+        if (!featuresById[feature.id]) {
+          this.geneIds[feature.Parent] = this.geneIds[feature.Parent] || ++this.seenGenes;
+
+          feature.chr         = feature.chr || chr;
+          feature.label       = parseInt(feature.strand, 10) === 1 ? `${feature.external_name || feature.id} >` : `< ${feature.external_name || feature.id}`;
+          feature.sort        = (this.geneIds[feature.Parent] * 1e10) + (feature.logic_name.indexOf('ensembl_havana') === 0 ? 0 : 2e9) + (feature.biotype === 'protein_coding' ? 0 : 1e9) + feature.start + i;
+          feature.cdsStart    = Infinity;
+          feature.cdsEnd      = -Infinity;
+          feature.exons       = {};
+          feature.subFeatures = [];
+
+          this.insertFeature(feature);
+        }
+
+        ids.push(feature.id);
+      }
+    );
+
+    data.filter(d => d.feature_type === 'cds' && featuresById[d.Parent]).forEach(
+      (cds) => {
+        featuresById[cds.Parent].cdsStart = Math.min(featuresById[cds.Parent].cdsStart, cds.start);
+        featuresById[cds.Parent].cdsEnd   = Math.max(featuresById[cds.Parent].cdsEnd,   cds.end);
+      }
+    );
+
+    data.filter(d => d.feature_type === 'exon' && featuresById[d.Parent] && !featuresById[d.Parent].exons[d.id]).forEach(
+      (exon) => {
+        if (exon.end < featuresById[exon.Parent].cdsStart || exon.start > featuresById[exon.Parent].cdsEnd) {
+          featuresById[exon.Parent].subFeatures.push({ utr: true, ...exon });
+        } else {
+          if (exon.start < featuresById[exon.Parent].cdsStart) {
+            featuresById[exon.Parent].subFeatures.push({ utr: true, ...exon, end: featuresById[exon.Parent].cdsStart });
+          }
+
+          featuresById[exon.Parent].subFeatures.push({
+            ...exon,
+            start  : Math.max(exon.start, featuresById[exon.Parent].cdsStart),
+            end    : Math.min(exon.end,   featuresById[exon.Parent].cdsEnd),
+            strand : featuresById[exon.Parent].strand,
+          });
+
+          if (exon.end > featuresById[exon.Parent].cdsEnd) {
+            featuresById[exon.Parent].subFeatures.push({ utr: true, ...exon, start: featuresById[exon.Parent].cdsEnd });
+          }
+        }
+      }
+    );
+
+    ids.forEach(id => featuresById[id].subFeatures.sort((a, b) => a.start - b.start));
+  },
+});

package/{js → src/js}/Track/Model/Transcript.js

@@ -1,5 +1,7 @@
+import Model from '../Model';
+
 // Abstract Transcript model
 // see sub-models for more specific examples
-Genoverse.Track.Model.Transcript = Genoverse.Track.Model.extend({
+export default Model.extend({
 
 });

package/{js → src/js}/Track/Model.js

@@ -1,4 +1,8 @@
-Genoverse.Track.Model = Base.extend({
+import Base          from 'basejs';
+import RTree         from 'rtree';
+import wrapFunctions from '../lib/wrap-functions';
+
+export default Base.extend({
   dataType           : 'json',
   allData            : false,
   dataBuffer         : undefined, // e.g. { start: 0, end: 0 } - basepairs to extend data region for, when getting data from the origin
@@ -11,8 +15,15 @@ Genoverse.Track.Model = Base.extend({
   showServerErrors   : false,     // if true, error messages return from the server by getData requests will be shown on the track
 
   constructor: function (properties) {
-    $.extend(this, properties);
-    Genoverse.wrapFunctions(this);
+    Object.entries(properties).forEach(
+      ([ key, val ]) => {
+        if (typeof val !== 'undefined') {
+          this[key] = val;
+        }
+      }
+    );
+
+    wrapFunctions(this, 'Model');
     this.init();
   },
 
@@ -20,9 +31,7 @@ Genoverse.Track.Model = Base.extend({
     this.setDefaults(reset);
 
     if (reset) {
-      for (var i in this.featuresById) {
-        delete this.featuresById[i].position;
-      }
+      Object.values(this.featuresById).forEach((feature) => { delete feature.position; });
     }
 
     if (!reset || this.data) {
@@ -52,7 +61,7 @@ Genoverse.Track.Model = Base.extend({
   },
 
   setChrProps: function () {
-    var chr = this.browser.chr;
+    const chr = this.browser.chr;
 
     this.dataRangesByChr = this.dataRangesByChr || {};
     this.featuresByChr   = this.featuresByChr   || {};
@@ -78,26 +87,28 @@ Genoverse.Track.Model = Base.extend({
   },
 
   getData: function (chr, start, end, done) {
+    const jQuery = this.browser.jQuery;
+
     start = Math.max(1, start);
     end   = Math.min(this.browser.getChromosomeSize(chr), end);
 
-    var deferred = $.Deferred();
+    const deferred = jQuery.Deferred();
 
     if (typeof this.data !== 'undefined') {
-      this.receiveData(typeof this.data.sort === 'function' ? this.data.sort(function (a, b) { return a.start - b.start; }) : this.data, chr, start, end);
-      return deferred.resolveWith(this);
+      this.receiveData(typeof this.data.sort === 'function' ? this.data.sort((a, b) => a.start - b.start) : this.data, chr, start, end);
+
+      return deferred.resolve();
     }
 
-    var model  = this;
-    var bins   = [];
-    var length = end - start + 1;
+    const bins   = [];
+    const length = end - start + 1;
 
     if (!this.url) {
-      return deferred.resolveWith(this);
+      return deferred.resolve();
     }
 
     if (this.dataRequestLimit && length > this.dataRequestLimit) {
-      var i = Math.ceil(length / this.dataRequestLimit);
+      let i = Math.ceil(length / this.dataRequestLimit);
 
       while (i--) {
         bins.push([ start, i ? start += this.dataRequestLimit - 1 : end ]);
@@ -107,39 +118,45 @@ Genoverse.Track.Model = Base.extend({
       bins.push([ start, end ]);
     }
 
-    $.when.apply($, $.map(bins, function (bin) {
-      var request = $.ajax({
-        url       : model.parseURL(chr, bin[0], bin[1]),
-        data      : model.urlParams,
-        dataType  : model.dataType,
-        context   : model,
-        xhrFields : model.xhrFields,
-        success   : function (data) {
-          this.receiveData(data, chr, bin[0], bin[1]);
-        },
-        error: function (xhr, statusText) {
-          this.track.controller.showError(
-            this.showServerErrors && (xhr.responseJSON || {}).message
-              ? xhr.responseJSON.message
-              : statusText + ' while getting the data, see console for more details',
-            arguments
+    jQuery.when(
+      ...bins.map(
+        (bin) => {
+          const request = jQuery.ajax({
+            url       : this.parseURL(chr, bin[0], bin[1]),
+            data      : this.urlParams,
+            dataType  : this.dataType,
+            xhrFields : this.xhrFields,
+          }).then(
+            (data) => {
+              this.receiveData(data, chr, bin[0], bin[1]);
+            }
+          ).catch(
+            (xhr, statusText, ...args) => {
+              this.track.controller.showError(
+                this.showServerErrors && xhr.responseJSON?.message
+                  ? xhr.responseJSON.message
+                  : `${statusText} while getting the data, see console for more details`,
+                [ xhr, statusText, ...args ]
+              );
+            }
+          ).always(
+            () => {
+              this.dataLoading = this.dataLoading.filter(loading => request !== loading);
+            }
           );
-        },
-        complete: function (xhr) {
-          this.dataLoading = $.grep(this.dataLoading, function (t) { return xhr !== t; });
-        }
-      });
 
-      request.coords = [ chr, bin[0], bin[1] ]; // store actual chr, start and end on the request, in case they are needed
+          request.coords = [ chr, bin[0], bin[1] ]; // store actual chr, start and end on the request, in case they are needed
 
-      if (typeof done === 'function') {
-        request.done(done);
-      }
+          if (typeof done === 'function') {
+            request.done(done);
+          }
 
-      model.dataLoading.push(request);
+          this.dataLoading.push(request);
 
-      return request;
-    })).done(function () { deferred.resolveWith(model); });
+          return request;
+        }
+      )
+    ).done(deferred.resolve);
 
     return deferred;
   },
@@ -177,17 +194,15 @@ Genoverse.Track.Model = Base.extend({
   * and call this.insertFeature(feature)
   */
   parseData: function (data, chr, start) { // end is also passed in, but not used in this case
-    var feature;
-
     // Example of parseData function when data is an array of hashes like { start: ..., end: ... }
-    for (var i = 0; i < data.length; i++) {
-      feature = data[i];
+    data.forEach(
+      (feature, i) => {
+        feature.chr  = feature.chr || chr;
+        feature.sort = start + i;
 
-      feature.chr  = feature.chr || chr;
-      feature.sort = start + i;
-
-      this.insertFeature(feature);
-    }
+        this.insertFeature(feature);
+      }
+    );
   },
 
   updateData: function (data) {
@@ -208,20 +223,22 @@ Genoverse.Track.Model = Base.extend({
     start = Math.max(1, start);
     end   = Math.min(this.browser.getChromosomeSize(chr), end);
 
-    var ranges = this.dataRanges(chr).search({ x: start, w: end - start + 1, y: 0, h: 1 }).sort(function (a, b) { return a[0] - b[0]; });
+    const ranges = this.dataRanges(chr).search({ x: start, w: end - start + 1, y: 0, h: 1 }).sort((a, b) => a[0] - b[0]);
 
     if (!ranges.length) {
       return false;
     }
 
-    var s = ranges.length === 1 ? ranges[0][0] : 9e99;
-    var e = ranges.length === 1 ? ranges[0][1] : -9e99;
+    let s = ranges.length === 1 ? ranges[0][0] : 9e99;
+    let e = ranges.length === 1 ? ranges[0][1] : -9e99;
+
+    for (let i = 0; i < ranges.length - 1; i++) {
+      const [ s0, s1 ] = ranges[i];
+      const [ e0, e1 ] = ranges[i + 1];
 
-    for (var i = 0; i < ranges.length - 1; i++) {
-      // s0 <= s1 && ((e0 >= e1) || (e0 + 1 >= s1))
-      if (ranges[i][0] <= ranges[i + 1][0] && ((ranges[i][1] >= ranges[i + 1][1]) || (ranges[i][1] + 1 >= ranges[i + 1][0]))) {
-        s = Math.min(s, ranges[i][0]);
-        e = Math.max(e, ranges[i][1], ranges[i + 1][1]);
+      if (s0 <= s1 && ((e0 >= e1) || (e0 + 1 >= s1))) {
+        s = Math.min(s, s0);
+        e = Math.max(e, e0, e1);
       } else {
         return false;
       }
@@ -237,67 +254,82 @@ Genoverse.Track.Model = Base.extend({
 
     // Make sure we have a unique ID, this method is not efficient, so better supply your own id
     if (!feature.id) {
-      feature.id = feature.ID || this.hashCode(JSON.stringify($.extend({}, feature, { sort: '' }))); // sort is dependant on the browser's region, so will change on zoom
+      feature.id = feature.ID || this.hashCode(JSON.stringify({ ...feature, sort: '' })); // sort is dependant on the browser's region, so will change on zoom
     }
 
-    var features = this.features(feature.chr);
+    const features = this.features(feature.chr);
 
     if (features && !this.featuresById[feature.id]) {
       if (feature.subFeatures) {
-        feature.subFeatures.sort(function (a, b) { return a.start - b.start; });
-
-        for (var i = 0; i < feature.subFeatures.length; i++) {
-          feature.subFeatures[i].start = Math.min(Math.max(feature.subFeatures[i].start, feature.start), feature.end);
-          feature.subFeatures[i].end   = Math.max(Math.min(feature.subFeatures[i].end,   feature.end),   feature.start);
-        }
+        feature.subFeatures.sort(
+          (a, b) => a.start - b.start
+        ).forEach(
+          (subFeature) => {
+            subFeature.start = Math.min(Math.max(subFeature.start, feature.start), feature.end);
+            subFeature.end   = Math.max(Math.min(subFeature.end,   feature.end),   feature.start);
+          }
+        );
 
         // Add "fake" sub-features at the start and end of the feature - this will allow joins to be drawn when there are no sub-features in the current region.
         feature.subFeatures.unshift({ start: feature.start, end: feature.start, fake: true });
-        feature.subFeatures.push({    start: feature.end,   end: feature.end,   fake: true });
+        feature.subFeatures.push({ start: feature.end, end: feature.end, fake: true });
       }
 
       features.insert({ x: feature.start, y: 0, w: feature.end - feature.start + 1, h: 1 }, feature);
+
       this.featuresById[feature.id] = feature;
     }
   },
 
   findFeatures: function (chr, start, end) {
-    var features = this.features(chr).search({ x: start - this.dataBuffer.start, y: 0, w: end - start + this.dataBuffer.start + this.dataBuffer.end + 1, h: 1 });
-    var filters  = this.prop('featureFilters') || [];
-
-    for (var i = 0; i < filters.length; i++) {
-      features = $.grep(features, $.proxy(filters[i], this));
-    }
+    let features = this.features(chr).search({
+      x : start - this.dataBuffer.start,
+      y : 0,
+      w : end - start + this.dataBuffer.start + this.dataBuffer.end + 1,
+      h : 1,
+    });
+
+    (this.prop('featureFilters') || []).forEach(
+      (filter) => {
+        features = features.filter(feature => filter.call(this, feature));
+      }
+    );
 
     return this.sortFeatures(features);
   },
 
   sortFeatures: function (features) {
-    return features.sort(function (a, b) { return a.sort - b.sort; });
+    return features.sort((a, b) => a.sort - b.sort);
   },
 
-  abort: function () {
-    for (var i = 0; i < this.dataLoading.length; i++) {
-      this.dataLoading[i].abort();
+  hashCode: function (string) {
+    let hash = 0;
+
+    if (string.length) {
+      for (let i = 0; i < string.length; i++) {
+        const c = string.charCodeAt(i);
+
+        hash  = ((hash << 5) - hash) + c;
+        hash &= hash; // Convert to 32bit integer
+      }
     }
 
-    this.dataLoading = [];
+    return String(hash);
   },
 
-  hashCode: function (string) {
-    var hash = 0;
-    var c;
+  abort: function () {
+    this.dataLoading.forEach(loading => loading.abort());
 
-    if (!string.length) {
-      return hash;
-    }
+    this.dataLoading = [];
+  },
 
-    for (var i = 0; i < string.length; i++) {
-      c     = string.charCodeAt(i);
-      hash  = ((hash << 5) - hash) + c;
-      hash &= hash; // Convert to 32bit integer
-    }
+  destroy: function () {
+    this.abort();
 
-    return '' + hash;
-  }
+    // Force garbage collection
+    delete this.data;
+    delete this.dataRangesByChr;
+    delete this.featuresByChr;
+    delete this.featuresById;
+  },
 });

package/{js → src/js}/Track/View/Gene/Ensembl.js

@@ -1,6 +1,8 @@
-Genoverse.Track.View.Gene.Ensembl = Genoverse.Track.View.Gene.extend({
+import View from '../Gene';
+
+export default View.extend({
   setFeatureColor: function (feature) {
-    var processedTranscript = {
+    const processedTranscript = {
       'sense_intronic'           : 1,
       'sense_overlapping'        : 1,
       'processed_transcript'     : 1,
@@ -12,7 +14,7 @@ Genoverse.Track.View.Gene.Ensembl = Genoverse.Track.View.Gene.extend({
       'non_coding'               : 1,
       'ambiguous_orf'            : 1,
       'disrupted_domain'         : 1,
-      '3prime_overlapping_ncrna' : 1
+      '3prime_overlapping_ncrna' : 1,
     };
 
     feature.color = '#000000';
@@ -42,5 +44,5 @@ Genoverse.Track.View.Gene.Ensembl = Genoverse.Track.View.Gene.extend({
     }
 
     feature.labelColor = feature.labelColor || feature.color;
-  }
+  },
 });

package/src/js/Track/View/Gene.js

@@ -0,0 +1,8 @@
+import View from '../View';
+
+export default View.extend({
+  featureHeight : 5,
+  labels        : true,
+  repeatLabels  : true,
+  bump          : true,
+});

package/{js → src/js}/Track/View/Sequence.js

@@ -1,14 +1,15 @@
-Genoverse.Track.View.Sequence = Genoverse.Track.View.extend({
+import View from '../View';
+
+export default View.extend({
   featureMargin : { top: 0, right: 0, bottom: 0, left: 0 },
   colors        : { 'default': '#CCCCCC', A: '#73E973', T: '#DE4C61', G: '#FFFF77', C: '#688EC0' },
   labelColors   : { 'default': '#000000', T: '#FFFFFF', C: '#FFFFFF' },
   labels        : 'overlay',
 
-  setDefaults: function () {
-    this.base.apply(this, arguments);
+  setDefaults: function (...args) {
+    this.base(...args);
 
-    var lowerCase = this.prop('lowerCase');
-    var key;
+    const lowerCase = this.prop('lowerCase');
 
     this.labelYOffset = typeof this.labelYOffset === 'number' ? this.labelYOffset : (this.featureHeight + 1) / 2;
     this.widestLabel  = typeof this.widestLabel  === 'string' ? this.widestLabel : lowerCase ? 'g' : 'G';
@@ -17,13 +18,11 @@ Genoverse.Track.View.Sequence = Genoverse.Track.View.extend({
     this.labelWidth[this.widestLabel] = Math.ceil(this.context.measureText(this.widestLabel).width) + 1;
 
     if (lowerCase) {
-      for (key in this.colors) {
-        this.colors[key.toLowerCase()] = this.colors[key];
-      }
-
-      for (key in this.labelColors) {
-        this.labelColors[key.toLowerCase()] = this.labelColors[key];
-      }
+      [ this.colors, this.labelColors ].forEach(
+        colorObject => Object.entries(colorObject).forEach(([ letter, color ]) => {
+          colorObject[letter.toLowerCase()] = color;
+        })
+      );
     }
   },
 
@@ -31,25 +30,22 @@ Genoverse.Track.View.Sequence = Genoverse.Track.View.extend({
     featureContext.textBaseline = 'middle';
     featureContext.textAlign    = 'center';
 
-    var width = Math.max(scale, this.minScaledWidth);
+    const width = Math.max(scale, this.minScaledWidth);
 
-    for (var i = 0; i < features.length; i++) {
-      this.drawSequence(features[i], featureContext, scale, width);
-    }
+    features.forEach(feature => this.drawSequence(feature, featureContext, scale, width));
   },
 
   drawSequence: function (feature, context, scale, width) {
-    var drawLabels = this.labelWidth[this.widestLabel] < width - 1;
-    var start, bp;
+    const drawLabels = this.labelWidth[this.widestLabel] < width - 1;
 
-    for (var i = 0; i < feature.sequence.length; i++) {
-      start = feature.position[scale].X + i * scale;
+    for (let i = 0; i < feature.sequence.length; i++) {
+      const start = feature.position[scale].X + i * scale;
 
       if (start < -scale || start > context.canvas.width) {
         continue;
       }
 
-      bp = feature.sequence.charAt(i);
+      const bp = feature.sequence.charAt(i);
 
       context.fillStyle = this.colors[bp] || this.colors.default;
       context.fillRect(start, feature.position[scale].Y, width, this.featureHeight);
@@ -59,5 +55,5 @@ Genoverse.Track.View.Sequence = Genoverse.Track.View.extend({
         context.fillText(bp, start + (width / 2), feature.position[scale].Y + this.labelYOffset);
       }
     }
-  }
+  },
 });