genoverse 3.2.0 → 4.0.1

package/js/Track/View/Sequence/Variation.js

@@ -1,115 +0,0 @@
-Genoverse.Track.View.SequenceVariation = Genoverse.Track.View.Sequence.extend({
-  featureHeight : 15,
-  featureMargin : { top: 0, right: 0, bottom: 4, left: 0 },
-  bump          : true,
-  showLegend    : false,
-
-  positionFeature: function (feature, params) {
-    var position = feature.position[params.scale];
-
-    if (feature.alt_allele) {
-      if (!position.positioned) {
-        position.reference = { end: position.start + feature.ref_allele.length * params.scale };
-      }
-
-      position.reference.x = position.reference.end - params.scaledStart;
-    }
-
-    this.base(feature, params);
-  },
-
-  bumpFeature: function (bounds, feature) {
-    if (feature.alt_allele) {
-      this.base.apply(this, arguments);
-    }
-  },
-
-  draw: function (features, featureContext, labelContext, scale) {
-    var drawing = { seq: [], snv: [] };
-
-    for (var i = 0; i < features.length; i++) {
-      drawing[features[i].alt_allele ? 'snv' : 'seq'].push(features[i]);
-    }
-
-    this.base(drawing.seq, featureContext, labelContext, scale);
-    this.highlightSNVs(drawing.snv, featureContext, scale);
-    this.base(drawing.snv, featureContext, labelContext, scale);
-    this.outlineSNVs(drawing.snv, featureContext, scale); // Redraw the outline for SNVs, since the feature will have been drawn on top of some of the outline created by highlightSNVs
-  },
-
-  highlightSNVs: function (features, context, scale) {
-    var position, positionX, positionY;
-
-    for (var i = 0; i < features.length; i++) {
-      position  = features[i].position[scale];
-      positionX = [ position.X, position.reference.x, position.X + position.width ];
-
-      if (positionX[2] < 0 || positionX[0] > this.width) {
-        continue;
-      }
-
-      if (positionX[0] < 0 || positionX[2] > this.width) {
-        this.truncateForDrawing(positionX);
-      }
-
-      positionY = [ 0, position.Y - this.featureMargin.bottom / 2, position.Y, position.Y + this.featureHeight ];
-
-      if (!features[i].highlightColor) {
-        this.setHighlightColor(features[i]);
-      }
-
-      context.strokeStyle = context.fillStyle = features[i].highlightColor;
-      context.lineWidth   = 2;
-
-      context.beginPath();
-      context.moveTo(positionX[0], positionY[0]);
-      context.lineTo(positionX[1], positionY[0]);
-      context.lineTo(positionX[1], positionY[1]);
-      context.lineTo(positionX[2], positionY[2]);
-      context.lineTo(positionX[2], positionY[3]);
-      context.lineTo(positionX[0], positionY[3]);
-      context.closePath();
-      context.stroke();
-
-      context.lineWidth   = 1;
-      context.globalAlpha = 0.5;
-
-      context.fill();
-
-      context.globalAlpha = 1;
-    }
-  },
-
-  outlineSNVs: function (features, context, scale) {
-    var position, positionX, positionY;
-
-    for (var i = 0; i < features.length; i++) {
-      position  = features[i].position[scale];
-      positionX = [ position.X, position.X + position.width ];
-      positionY = [ position.Y, position.Y + this.featureHeight ];
-
-      context.strokeStyle = features[i].highlightColor;
-
-      context.lineWidth = 2;
-
-      context.beginPath();
-      context.moveTo(positionX[1], positionY[0]);
-      context.lineTo(positionX[1], positionY[1]);
-      context.lineTo(positionX[0], positionY[1]);
-      context.lineTo(positionX[0], positionY[0]);
-      context.stroke();
-
-      context.lineWidth = 1;
-    }
-  },
-
-  truncateForDrawing: function (positionX) {
-    for (var i in positionX) {
-      positionX[i] = Math.min(Math.max(positionX[i], -1), this.width + 1);
-    }
-  },
-
-  setHighlightColor: function (feature) {
-    feature.highlightColor = feature.alt_allele === '-' || feature.alt_allele.length < feature.ref_allele.length ? '#D31D00' : '#1DD300';
-  }
-});

package/js/Track/View/Transcript/Ensembl.js

@@ -1,12 +0,0 @@
-Genoverse.Track.View.Transcript.Ensembl = Genoverse.Track.View.Transcript.extend({
-  setFeatureColor: function (feature) {
-    Genoverse.Track.View.Gene.Ensembl.prototype.setFeatureColor(feature);
-
-    for (var i = 0; i < (feature.subFeatures || []).length; i++) {
-      if (feature.subFeatures[i].utr) {
-        feature.subFeatures[i].color       = false;
-        feature.subFeatures[i].borderColor = feature.color;
-      }
-    }
-  }
-});

package/js/Track/View/Transcript.js

@@ -1,28 +0,0 @@
-Genoverse.Track.View.Transcript = Genoverse.Track.View.extend({
-  featureHeight       : 12,
-  utrHeight           : 7,
-  labels              : true,
-  repeatLabels        : true,
-  bump                : true,
-  subFeatureJoinStyle : 'curve',
-
-  scaleFeatures: function (features, scale) {
-    var subFeatures, j;
-
-    for (var i = 0; i < features.length; i++) {
-      subFeatures = features[i].subFeatures || [];
-
-      if (subFeatures.length) {
-        for (j = 0; j < subFeatures.length; j++) {
-          if (subFeatures[j].utr) {
-            subFeatures[j].height = this.utrHeight;
-          }
-        }
-
-        features[i].height = Math.max.apply(Math, subFeatures.map(function (c) { return c.fake ? 0 : c.height || 0; }).concat(this.featureHeight));
-      }
-    }
-
-    return this.base(features, scale);
-  }
-});

package/js/Track/library/File/BAM.js

@@ -1,30 +0,0 @@
-Genoverse.Track.File.BAM = Genoverse.Track.File.extend({
-  name      : 'BAM',
-  indexExt  : '.bai',
-  threshold : 100000,
-  largeFile : true,
-  model     : Genoverse.Track.Model.File.BAM,
-  view      : Genoverse.Track.View.Sequence.extend({
-    bump       : true,
-    autoHeight : true
-  }),
-
-  click: function () {
-    var menu = this.base.apply(this, arguments);
-
-    if (menu) {
-      menu.addClass('gv-wrap-values');
-    }
-
-    return menu;
-  },
-
-  populateMenu: function (feature) {
-    var f = $.extend({ title: feature.readName }, feature);
-
-    delete f.sequence;
-    delete f.id;
-
-    return this.base(f);
-  }
-});

package/js/Track/library/File/BED.js

@@ -1,24 +0,0 @@
-Genoverse.Track.File.BED = Genoverse.Track.File.extend({
-  name                : 'BED',
-  model               : Genoverse.Track.Model.File.BED,
-  bump                : true,
-  featureHeight       : 10,
-  thickHeight         : 10,
-  thinHeight          : 7,
-  subFeatureJoinStyle : 'curve',
-
-  populateMenu: function (feature) {
-    var fields = [ false, false, false, 'name', 'score', 'strand', 'thickStart', 'thickEnd', 'itemRgb', 'blockCount', 'blockSizes', 'blockStarts' ]; // First three fields are chr, start, end which are covered by Location
-
-    return feature.originalFeature.reduce(function (menu, val, i) {
-      if (fields[i]) {
-        menu[fields[i]] = val;
-      }
-
-      return menu;
-    }, {
-      title    : '<a target="_blank" href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED feature details</a>',
-      Location : feature.chr + ':' + feature.start + '-' + feature.end
-    });
-  }
-});

package/js/Track/library/File/BIGBED.js

@@ -1,47 +0,0 @@
-Genoverse.Track.File.BIGBED = Genoverse.Track.File.BED.extend({
-  name  : 'bigbed',
-  model : Genoverse.Track.Model.File.BED.extend({
-    getData: function (chr, start, end) {
-      var model    = this;
-      var deferred = $.Deferred();
-
-      if (!this.bigbedFile) {
-        this.bigbedFile = this.bigbedFile || (this.url ? new dallianceLib.URLFetchable(this.url) : new dallianceLib.BlobFetchable(this.track.dataFile));
-      }
-
-      var d = $.Deferred().done(function () {
-        model.bwReader.getValues(chr, start, end, function (features, error) {
-          if (!error) {
-            features.sort(function (a, b) { return a.start - b.start; });
-
-            if (features.length) {
-              model.receiveData(features, chr, features[0].start, features[features.length - 1].end);
-            } else {
-              model.receiveData(features, chr, start, end);
-            }
-          }
-
-          deferred.resolveWith(model);
-        });
-      });
-
-      if (this.bwReader) {
-        d.resolve();
-      } else {
-        new BWReader(this.bigbedFile, function (bwReader) {
-          if (bwReader) {
-            model.bwReader = bwReader;
-            d.resolve();
-          } else {
-            model.receiveData([], chr, start, end);
-            return deferred.resolveWith(model);
-          }
-        });
-      }
-
-      return deferred;
-    }
-  })
-});
-
-Genoverse.Track.File.BB = Genoverse.Track.File.BIGBED;

package/js/Track/library/File/BIGWIG.js

@@ -1,52 +0,0 @@
-Genoverse.Track.File.BIGWIG = Genoverse.Track.Graph.Bar.extend({
-  name   : 'bigwig',
-  height : 100,
-
-  setDefaults: function () {
-    this.bwReader = null; // Not part of model since it needs to be shared between bar and line graphs
-    this.base.apply(this, arguments);
-  },
-
-  getData: function (chr, start, end) {
-    var model    = this;
-    var deferred = $.Deferred();
-
-    if (!this.bigwigFile) {
-      this.bigwigFile = this.bigwigFile || (this.url ? new dallianceLib.URLFetchable(this.url) : new dallianceLib.BlobFetchable(this.track.dataFile));
-    }
-
-    var d = $.Deferred().done(function () {
-      model.prop('bwReader').getValues(chr, start, end, function (features, error) {
-        if (!error) {
-          features.sort(function (a, b) { return a.start - b.start; });
-
-          if (features.length) {
-            model.receiveData(features, chr, features[0].start, features[features.length - 1].end);
-          } else {
-            model.receiveData(features, chr, start, end);
-          }
-        }
-
-        deferred.resolveWith(model);
-      });
-    });
-
-    if (this.prop('bwReader')) {
-      d.resolve();
-    } else {
-      new BWReader(this.bigwigFile, function (bwReader) {
-        if (bwReader) {
-          model.prop('bwReader', bwReader);
-          d.resolve();
-        } else {
-          model.receiveData([], chr, start, end);
-          return deferred.resolveWith(model);
-        }
-      });
-    }
-
-    return deferred;
-  }
-});
-
-Genoverse.Track.File.BW = Genoverse.Track.File.BIGWIG;

package/js/Track/library/File/GFF.js

@@ -1,9 +0,0 @@
-Genoverse.Track.File.GFF = Genoverse.Track.File.extend({
-  name          : 'GFF',
-  model         : Genoverse.Track.Model.File.GFF,
-  bump          : true,
-  height        : 100,
-  featureHeight : 5
-});
-
-Genoverse.Track.File.GTF = Genoverse.Track.File.GFF;

package/js/Track/library/File/WIG.js

@@ -1,5 +0,0 @@
-Genoverse.Track.File.WIG = Genoverse.Track.Graph.Bar.extend({
-  model  : Genoverse.Track.Model.File.WIG,
-  name   : 'wig',
-  height : 100
-});

package/js/Track/library/Gene.js

@@ -1,37 +0,0 @@
-Genoverse.Track.Gene = Genoverse.Track.extend({
-  id     : 'genes',
-  name   : 'Genes',
-  height : 200,
-  legend : true,
-
-  populateMenu: function (feature) {
-    var url  = 'https://www.ensembl.org/Homo_sapiens/' + (feature.feature_type === 'transcript' ? 'Transcript' : 'Gene') + '/Summary?' + (feature.feature_type === 'transcript' ? 't' : 'g') + '=' + feature.id;
-    var menu = {
-      title    : '<a target="_blank" href="' + url + '">' + (feature.external_name ? feature.external_name + ' (' + feature.id + ')' : feature.id) + '</a>',
-      Location : feature.chr + ':' + feature.start + '-' + feature.end,
-      Source   : feature.source,
-      Biotype  : feature.biotype
-    };
-
-    if (feature.feature_type === 'transcript') {
-      menu.Gene = '<a target="_blank" href="https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=' + feature.Parent + '">' + feature.Parent + '</a>';
-    }
-
-    return menu;
-  },
-
-  // Different settings for different zoom level
-  2000000: { // This one applies when > 2M base-pairs per screen
-    labels: false
-  },
-  100000: { // more than 100K but less then 2M
-    labels : true,
-    model  : Genoverse.Track.Model.Gene.Ensembl,
-    view   : Genoverse.Track.View.Gene.Ensembl
-  },
-  1: { // > 1 base-pair, but less then 100K
-    labels : true,
-    model  : Genoverse.Track.Model.Transcript.Ensembl,
-    view   : Genoverse.Track.View.Transcript.Ensembl
-  }
-});

package/js/Track/library/Graph/Bar.js

@@ -1,235 +0,0 @@
-Genoverse.Track.Controller.Graph.Bar = {
-  getClickedFeatures: function (x, y) {
-    var yZero     = this.prop('marginTop') - (this.prop('range')[0] * this.track.getYScale());
-    var scale     = this.scale;
-    var tolerance = scale > 1 ? 0 : 1;
-
-    // Bars with negative values are stored in featurePositions with h < 0.
-    // While this works to a certain degree (fillRect allows negative height, drawing upwards from y), it makes them hard to search for in the RTree - to find such a feature you need to search with y = -h and h = y - h + 1
-    // It is therefore easier to search featuresByChr (i.e. the genomic positions) for a feature overlapping the x of the click, and then filter those results for y position manually.
-    var features = this.prop('featuresByChr')[this.browser.chr].search({
-      x : (x - (tolerance / 2)) / scale,
-      y : 0,
-      w : (1 + tolerance) / scale,
-      h : 1
-    });
-
-    if (features.length) {
-      if (
-        (y <  yZero && features.filter(function (f) { return f.position[scale].bounds.y + f.position[scale].bounds.h <= y && f.position[scale].bounds.y >= y; }).length === 0) ||
-        (y >= yZero && this.featurePositions.search({ x: x, y: y, w: 1, h: 1 }).length === 0)
-      ) {
-        features = [];
-      }
-    }
-
-    return features.length ? [ this.model.sortFeatures(features) ] : [];
-  },
-
-  populateMenu: function (features) {
-    if (!features.length) {
-      return [];
-    }
-
-    var start = features[0].start;
-    var end   = features[features.length - 1].end;
-    var avg   = features[0].start !== features[features.length - 1].start;
-    var menu  = { title: features[0].chr + ':' + (start === end ? start : start + '-' + end) };
-    var values, i;
-
-    function getValues(_features) {
-      var vals = _features.map(function (f) { return f.height; }).sort(function (a, b) { return a - b; });
-
-      return {
-        avg : vals.reduce(function (n, v) { return n + v; }, 0) / vals.length,
-        min : vals[0],
-        max : vals[vals.length - 1]
-      };
-    }
-
-    if (avg) {
-      if (features.length === 1) {
-        values = getValues(features);
-
-        menu['Average value'] = values.avg;
-        menu['Min value']     = values.min;
-        menu['Max value']     = values.max;
-      } else {
-        menu = [ menu ];
-
-        var datasets = this.prop('datasets');
-        var featuresByDataset;
-
-        if (datasets.length) {
-          featuresByDataset = datasets.reduce(function (hash, d) { hash[d.name] = []; return hash; }, {});
-
-          for (i = 0; i < features.length; i++) {
-            featuresByDataset[features[i].dataset].push(features[i]);
-          }
-        } else {
-          datasets          = [{ name: '' }];
-          featuresByDataset = { '': features };
-        }
-
-        for (i = 0; i < datasets.length; i++) {
-          values = getValues(featuresByDataset[datasets[i].name]);
-
-          menu.push($.extend({
-            Average : values.avg,
-            Min     : values.min,
-            Max     : values.max
-          }, datasets[i].name ? { title: datasets[i].name } : {}));
-        }
-      }
-    } else if (features.length === 1) {
-      menu.Value = features[0].height;
-    } else {
-      for (i = 0; i < features.length; i++) {
-        menu[features[i].dataset] = features[i].height;
-      }
-    }
-
-    return menu;
-  }
-};
-
-Genoverse.Track.Model.Graph.Bar = Genoverse.Track.Model.Graph.extend({
-  insertFeature: function (feature) {
-    var datasets = this.prop('datasets');
-
-    if (datasets.length) {
-      feature.legend = feature.dataset;
-      feature.color  = (datasets.filter(function (s) { return s.name === feature.dataset; })[0] || { color: this.color }).color;
-    }
-
-    feature.id = feature.id || [ feature.chr, feature.start, feature.end, feature.dataset || '' ].join(':');
-
-    return this.base.apply(this, arguments);
-  }
-});
-
-Genoverse.Track.View.Graph.Bar = Genoverse.Track.View.Graph.extend({
-  scaleFeatures: function (features, scale) {
-    var yScale = this.track.getYScale();
-    var zeroY  = this.prop('marginTop') - this.prop('range')[0] * yScale;
-
-    features = this.base(features, scale);
-
-    for (var i = 0; i < features.length; i++) {
-      features[i].position[scale].height = features[i].height * yScale;
-      features[i].position[scale].y      = zeroY;
-    }
-
-    return features;
-  },
-
-  draw: function (features, featureContext, labelContext, scale) {
-    var datasets     = this.featureDataSets(features);
-    var marginBottom = this.prop('margin');
-    var binSize      = scale < 1 ? Math.ceil(1 / scale) : 0;
-    var conf, set, setFeatures, j, binnedFeatures, binStart, bin, f;
-
-    var defaults = {
-      color       : this.color,
-      globalAlpha : this.prop('globalAlpha')
-    };
-
-    for (var i = 0; i < datasets.list.length; i++) {
-      conf        = $.extend({}, defaults, datasets.list[i]);
-      set         = datasets.list[i].name;
-      setFeatures = $.extend(true, [], datasets.features[set] || []);
-
-      if (!setFeatures.length) {
-        continue;
-      }
-
-      if (binSize) {
-        binnedFeatures = [];
-        j              = 0;
-
-        while (j < setFeatures.length) {
-          binStart = setFeatures[j].start;
-          bin      = [];
-
-          while (setFeatures[j] && setFeatures[j].start - binStart < binSize) {
-            bin.push(setFeatures[j++]);
-          }
-
-          f = $.extend(true, {}, bin[0], {
-            height : bin.reduce(function (a, b) { return a + b.height; }, 0) / bin.length,
-            end    : bin[bin.length - 1].end
-          });
-
-          [ 'H', 'W', 'height', 'width' ].forEach(function (attr) { // eslint-disable-line no-loop-func
-            f.position[scale][attr] = bin.reduce(function (a, b) { return a + b.position[scale][attr]; }, 0) / bin.length;
-          });
-
-          binnedFeatures.push(f);
-        }
-
-        setFeatures = binnedFeatures;
-      }
-
-      for (j = 0; j < setFeatures.length; j++) {
-        setFeatures[j].color = conf.color;
-      }
-
-      featureContext.globalAlpha = conf.globalAlpha;
-
-      this.base(setFeatures, featureContext, labelContext, scale);
-    }
-
-    // Don't allow features to be drawn in the margins
-    featureContext.clearRect(0, 0,                                  this.width, this.prop('marginTop') - 1);
-    featureContext.clearRect(0, this.prop('height') - marginBottom, this.width, marginBottom);
-  }
-});
-
-Genoverse.Track.Graph.Bar = Genoverse.Track.Graph.extend({
-  type      : 'Bar',
-  model     : Genoverse.Track.Model.Graph.Bar,
-  view      : Genoverse.Track.View.Graph.Bar,
-  threshold : 500000,
-
-  10000: $.extend( // Switch to line graph at 10000bp region
-    Object.keys(Genoverse.Track.Graph.Line.prototype).reduce(function (hash, key) {
-      if (Genoverse.Track.Graph.Line.prototype.hasOwnProperty(key) && !Base.prototype[key]) {
-        hash[key] = Genoverse.Track.Graph.Line.prototype[key];
-      }
-
-      return hash;
-    }, {}), {
-      fill  : true,
-      model : Genoverse.Track.Model.Graph.Line.extend({
-        parseData: function (data, chr, start, end) {
-          var coords = [];
-          var j;
-
-          for (var i = 0; i < data.length; i++) {
-            for (j = data[i].start; j < data[i].end; j++) {
-              coords.push([ j, data[i].height ]);
-            }
-          }
-
-          return this.base([{ chr: chr, start: start, end: end, coords: coords }], chr, start, end);
-        }
-      })
-    }
-  ),
-  50000: $.extend( // Switch to sparser line graph at 50000bp region
-    Object.keys(Genoverse.Track.Graph.Line.prototype).reduce(function (hash, key) {
-      if (Genoverse.Track.Graph.Line.prototype.hasOwnProperty(key) && !Base.prototype[key]) {
-        hash[key] = Genoverse.Track.Graph.Line.prototype[key];
-      }
-
-      return hash;
-    }, {}), {
-      fill  : true,
-      model : Genoverse.Track.Model.Graph.Line.extend({
-        parseData: function (data, chr, start, end) {
-          return this.base([{ chr: chr, start: start, end: end, coords: data.map(function (d) { return [ d.start, d.height ]; }) }], chr, start, end);
-        }
-      })
-    }
-  )
-});