genoverse 3.2.0 → 4.0.1

package/js/Track/Controller/Stranded.js

@@ -1,73 +0,0 @@
-Genoverse.Track.Controller.Stranded = Genoverse.Track.Controller.extend({
-  constructor: function (properties) {
-    this.base(properties);
-
-    if (typeof this._makeImage === 'function') {
-      return;
-    }
-
-    var strand        = this.prop('strand');
-    var featureStrand = this.prop('featureStrand');
-
-    if (strand === -1) {
-      this._makeImage = this.track.makeReverseImage ? $.proxy(this.track.makeReverseImage, this) : this.makeImage;
-      this.makeImage  = $.noop;
-    } else {
-      strand = this.prop('strand', 1);
-
-      this._makeImage = this.makeImage;
-      this.makeImage  = this.makeForwardImage;
-
-      var track = this.track;
-
-      setTimeout(function () {
-        track.reverseTrack = track.browser.addTrack(track.constructor.extend({
-          id           : track.id ? track.id + 'Reverse' : undefined,
-          strand       : -1,
-          url          : false,
-          order        : typeof track.orderReverse === 'number' ? track.orderReverse : track.order,
-          forwardTrack : track
-        }));
-
-        $.each(track.controller._deferredReverseTrackImages, function (i, args) { track.controller._makeReverseTrackImage.apply(track.controller, args); });
-        delete track.controller._deferredReverseTrackImages;
-      }, 1);
-    }
-
-    if (!featureStrand) {
-      this.prop('featureStrand', strand);
-    }
-  },
-
-  makeForwardImage: function (params) {
-    this._makeReverseTrackImage(params, this._makeImage(params));
-  },
-
-  _makeReverseTrackImage: function (params, deferred) {
-    var reverseTrack = this.prop('reverseTrack');
-
-    if (!reverseTrack) {
-      this._deferredReverseTrackImages = (this._deferredReverseTrackImages || []).concat([[ params, deferred ]]);
-      return;
-    }
-
-    if (deferred && typeof deferred.done === 'function') {
-      deferred.done(function () {
-        reverseTrack.controller._makeImage(params, deferred);
-      });
-    } else {
-      reverseTrack.controller._makeImage(params, deferred);
-    }
-  },
-
-  destroy: function () {
-    if (this.removing) {
-      return;
-    }
-
-    this.removing = true;
-
-    this.browser.removeTrack(this.prop('forwardTrack') || this.prop('reverseTrack'));
-    this.base();
-  }
-});

package/js/Track/Model/File/BAM.js

@@ -1,44 +0,0 @@
-Genoverse.Track.Model.File.BAM = Genoverse.Track.Model.File.extend({
-  getData: function (chr, start, end) {
-    var model    = this;
-    var deferred = $.Deferred();
-
-    if (!this.bamFile) {
-      if (this.url) {
-        this.bamFile = new dallianceLib.URLFetchable(this.url);
-        this.baiFile = new dallianceLib.URLFetchable(this.url + this.prop('indexExt'));
-      } else if (this.dataFile && this.indexFile) {
-        this.bamFile = new dallianceLib.BlobFetchable(this.dataFile);
-        this.baiFile = new dallianceLib.BlobFetchable(this.indexFile);
-      } else {
-        return deferred.rejectWith(model, [ 'BAM files must be accompanied by a .bai index file' ]);
-      }
-    }
-
-    dallianceLib.makeBam(this.bamFile, this.baiFile, null, function (bam, makeBamError) {
-      if (makeBamError) {
-        console.error(makeBamError); // eslint-disable-line no-console
-      } else {
-        bam.fetch(chr, start, end, function (features, fetchBamError) {
-          if (fetchBamError) {
-            console.error(fetchBamError); // eslint-disable-line no-console
-          } else {
-            model.receiveData(features, chr, start, end);
-            deferred.resolveWith(model);
-          }
-        });
-      }
-    });
-
-    return deferred;
-  },
-
-  insertFeature: function (feature) {
-    feature.id       = feature.chr + ':' + feature.readName + ':' + feature.pos;
-    feature.start    = feature.pos + 1;
-    feature.end      = feature.start + feature.seq.length;
-    feature.sequence = feature.seq;
-
-    return this.base(feature);
-  }
-});

package/js/Track/Model/File/BED.js

@@ -1,116 +0,0 @@
-Genoverse.Track.Model.File.BED = Genoverse.Track.Model.File.extend({
-  parseData: function (data, chr) {
-    var lines       = typeof data === 'string' ? data.split('\n') : data;
-    var thinHeight  = this.prop('thinHeight');
-    var thickHeight = this.prop('thickHeight');
-    var fields, len, feature, subfeatures, subfeature, blockSizes, blockStarts, j, thinFeature, thinFeature1, thinFeature2, thickFeature;
-
-    function filterNumber(n) {
-      return !isNaN(n);
-    }
-
-    for (var i = 0; i < lines.length; i++) {
-      fields = lines[i].split('\t').filter(function (f) { return f; });
-
-      if (fields.length < 3 || fields[0] === 'track' || fields[0] === 'browser') {
-        continue;
-      }
-
-      len = fields.length;
-
-      if (fields[0] === String(chr) || fields[0].toLowerCase() === 'chr' + chr || fields[0].match('[^1-9]' + chr + '$')) {
-        feature = {
-          chr             : chr,
-          start           : parseInt(fields[1], 10) + 1,
-          end             : parseInt(fields[2], 10),
-          name            : fields[3],
-          color           : '#000000',
-          originalFeature : fields
-        };
-
-        if (len > 3) { feature.score  = parseFloat(fields[4], 10); }
-        if (len > 5) { feature.strand = fields[5];                 }
-
-        if (len > 7) {
-          feature.thickStart = parseInt(fields[6], 10) + 1;
-          feature.thickEnd   = parseInt(fields[7], 10);
-          feature.drawThick  = fields[6] !== fields[7];
-        }
-
-        if (fields[8]) {
-          feature.color = 'rgb(' + fields[8] + ')';
-        } else {
-          feature.color = this.scoreColor(isNaN(feature.score) ? 1000 : feature.score);
-        }
-
-        if (len === 12) { // subfeatures present
-          feature.blockCount = parseInt(fields[9], 10);
-
-          subfeatures = [];
-          blockSizes  = fields[10].split(',').filter(filterNumber);
-          blockStarts = fields[11].split(',').filter(filterNumber);
-
-          for (j = 0; j < blockSizes.length; j++) {
-            subfeature = {
-              start  : feature.start + parseInt(blockStarts[j], 10),
-              height : thinHeight // if subfeature lies entirely left / right to [ thickStart, thickEnd ]
-            };
-
-            subfeature.end = subfeature.start + parseInt(blockSizes[j], 10) - 1;
-
-            if (feature.drawThick && subfeature.start <= feature.thickEnd && subfeature.end >= feature.thickStart) {
-              // some kind of an overlap for sure
-              if (subfeature.start >= feature.thickStart && subfeature.end <= feature.thickEnd) {
-                // subfeature within thickBlock, draw thick
-                subfeature.height = thickHeight;
-                subfeatures.push(subfeature);
-              } else if (subfeature.start < feature.thickStart && subfeature.end <= feature.thickEnd) {
-                // left overlap, split subfeature into 2 - thin | thick
-                thinFeature  = $.extend({}, subfeature, { end: feature.thickStart });
-                thickFeature = $.extend({}, subfeature, { start: feature.thickStart, height: thickHeight });
-
-                subfeatures = subfeatures.concat([ thinFeature, thickFeature ]);
-              } else if (subfeature.start >= feature.thickStart && subfeature.end > feature.thickEnd) {
-                // right overlap, split subfeature into 2 - thick | thin
-                thinFeature  = $.extend({}, subfeature, { start: feature.thickEnd });
-                thickFeature = $.extend({}, subfeature, { end: feature.thickEnd, height: thickHeight });
-
-                subfeatures = subfeatures.concat([ thickFeature, thinFeature ]);
-              } else {
-                // thickBlock lies within subfeature, split into 3 - thin | thick | thin
-                // the least possible case but lets be prepared for the outliers
-                thinFeature1 = $.extend({}, subfeature, { end: feature.thickStart });
-                thinFeature2 = $.extend({}, subfeature, { start: feature.thickEnd });
-                thickFeature = { start: feature.thickStart, end: feature.thickEnd, height: thickHeight };
-
-                subfeatures = subfeatures.concat([ thinFeature1, thickFeature, thinFeature2 ]);
-              }
-            } else {
-              // no thick block
-              subfeatures.push(subfeature);
-            }
-          }
-
-          if (subfeatures.length) {
-            feature.subFeatures = subfeatures;
-          }
-        }
-
-        this.insertFeature(feature);
-      }
-    }
-  },
-
-  // As per https://genome.ucsc.edu/FAQ/FAQformat.html#format1 specification
-  scoreColor: function (score) {
-    if (score <= 166) { return 'rgb(219,219,219)'; }
-    if (score <= 277) { return 'rgb(186,186,186)'; }
-    if (score <= 388) { return 'rgb(154,154,154)'; }
-    if (score <= 499) { return 'rgb(122,122,122)'; }
-    if (score <= 611) { return 'rgb(94,94,94)';    }
-    if (score <= 722) { return 'rgb(67,67,67)';    }
-    if (score <= 833) { return 'rgb(42,42,42)';    }
-    if (score <= 944) { return 'rgb(21,21,21)';    }
-    return '#000000';
-  }
-});

package/js/Track/Model/File/GFF.js

@@ -1,40 +0,0 @@
-Genoverse.Track.Model.File.GFF = Genoverse.Track.Model.File.extend({
-  parseData: function (text, chr) {
-    var lines = text.split('\n');
-
-    for (var i = 0; i < lines.length; i++) {
-      if (!lines[i].length || lines[i].indexOf('#') === 0) {
-        continue;
-      }
-
-      var fields = lines[i].split('\t');
-
-      if (fields.length < 5) {
-        continue;
-      }
-
-      var seqId = fields[0].toLowerCase();
-
-      if (
-        seqId === String(chr)             ||
-        seqId === 'chr' + chr             ||
-        seqId.match('[^1-9]' + chr + '$') ||
-        seqId.match('^' + chr + '\\b')
-      ) {
-        this.insertFeature({
-          id     : fields.slice(0, 5).join('|'),
-          chr    : chr,
-          start  : parseInt(fields[3], 10),
-          end    : parseInt(fields[4], 10),
-          source : fields[1],
-          type   : fields[2],
-          score  : fields[5],
-          strand : fields[6] === '-' ? -1 : 1,
-          label  : fields[1] + ' ' + fields[2] + ' ' + fields[3] + '-' + fields[4]
-        });
-      }
-    }
-  }
-});
-
-Genoverse.Track.Model.File.GTF = Genoverse.Track.Model.File.GFF;

package/js/Track/Model/File/VCF.js

@@ -1,101 +0,0 @@
-Genoverse.Track.Model.File.VCF = Genoverse.Track.Model.File.extend({
-  getData: function (chr, start, end) {
-    var deferred = $.Deferred();
-    var model    = this;
-
-    if (!this.prop('gz')) {
-      return this.base.apply(this, arguments);
-    }
-
-    if (!this.vcfFile) {
-      if (this.url) {
-        this.vcfFile = new dallianceLib.URLFetchable(this.url);
-        this.tbiFile = new dallianceLib.URLFetchable(this.url + this.prop('indexExt'));
-      } else if (this.dataFile && this.indexFile) {
-        this.vcfFile = new dallianceLib.BlobFetchable(this.dataFile);
-        this.tbiFile = new dallianceLib.BlobFetchable(this.indexFile);
-      } else {
-        return deferred.rejectWith(model, [ 'GZipped VCF files must be accompanied by a .tbi index file' ]);
-      }
-    }
-
-    this.makeVCF(this.vcfFile, this.tbiFile).then(function (vcf) {
-      model.cachedVCF = vcf;
-
-      vcf.getRecords(chr, start, end, function (records) {
-        model.receiveData(records, chr, start, end);
-        deferred.resolveWith(model);
-      });
-    });
-
-    return deferred;
-  },
-
-  makeVCF: function (vcfFile, tbiFile) {
-    var deferred = $.Deferred();
-
-    if (this.cachedVCF) {
-      deferred.resolve(this.cachedVCF);
-    } else {
-      var vcf = new VCFReader(vcfFile, tbiFile);
-
-      vcf.readTabix(function (tabix) {
-        vcf.tabix = tabix;
-        deferred.resolve(vcf);
-      });
-    }
-
-    return deferred;
-  },
-
-  parseData: function (text, chr) {
-    var lines   = text.split('\n');
-    var maxQual = this.allData ? this.prop('maxQual') || 0 : false;
-
-    for (var i = 0; i < lines.length; i++) {
-      if (!lines[i].length || lines[i].indexOf('#') === 0) {
-        continue;
-      }
-
-      var fields = lines[i].split('\t');
-
-      if (fields.length < 5) {
-        continue;
-      }
-
-      if (fields[0] === String(chr) || fields[0] === 'chr' + chr) {
-        var id      = fields.slice(0, 3).join('|');
-        var start   = parseInt(fields[1], 10);
-        var alleles = fields[4].split(',');
-
-        alleles.unshift(fields[3]);
-
-        for (var j = 0; j < alleles.length; j++) {
-          var end = start + alleles[j].length - 1;
-
-          this.insertFeature({
-            id              : id + '|' + alleles[j],
-            sort            : j,
-            chr             : chr,
-            start           : start,
-            end             : end,
-            width           : end - start,
-            allele          : j === 0 ? 'REF' : 'ALT',
-            sequence        : alleles[j],
-            label           : alleles[j],
-            labelColor      : '#FFFFFF',
-            originalFeature : fields
-          });
-        }
-
-        if (maxQual !== false) {
-          maxQual = Math.max(maxQual, fields[5]);
-        }
-      }
-    }
-
-    if (maxQual) {
-      this.prop('maxQual', maxQual);
-    }
-  }
-});

package/js/Track/Model/File/WIG.js

@@ -1,67 +0,0 @@
-Genoverse.Track.Model.File.WIG = Genoverse.Track.Model.Graph.Bar.extend({
-  dataType: 'text',
-
-  getData: function () {
-    if (!this.url) {
-      this.isLocal  = true;
-      this.dataFile = this.track.dataFile;
-
-      return Genoverse.Track.Model.File.prototype.getData.apply(this, arguments);
-    }
-
-    return this.base.apply(this, arguments);
-  },
-
-  parseData: function (text, chr, s, e) {
-    var lines    = text.split('\n');
-    var features = [];
-    var fields, chrom, start, step, span, line, feature, i;
-
-    while (lines.length && (line = lines.shift())) {
-      if (line.indexOf('#') !== -1 || line.indexOf('browser') !== -1 || line.indexOf('track') !== -1) {
-        continue;
-      } else {
-        break;
-      }
-    }
-
-    if (line) {
-      fields = line.split(/\s+/);
-      chrom  = parseInt(fields[1].split('=')[1].replace('chr', ''), 10);
-
-      if (fields[0] === 'fixedStep') {
-        start = parseInt(fields[2].split('=')[1], 10);
-        step  = parseInt(fields[3].split('=')[1], 10);
-        span  = fields[4] ? parseInt(fields[4].split('=')[1], 10) : 1;
-
-        for (i = 0; i < lines.length; i++) {
-          features.push({
-            chr    : chrom,
-            start  : start,
-            end    : start + span,
-            height : parseFloat(lines[i])
-          });
-
-          start += step;
-        }
-      } else if (fields[0] === 'variableStep') {
-        span = fields[2] ? parseInt(fields[2].split('=')[1], 10) : 1;
-
-        for (i = 0; i < lines.length; i++) {
-          fields  = lines[i].split(/\s+/);
-          feature = {
-            chr    : chrom,
-            start  : parseInt(fields[0], 10),
-            height : parseFloat(fields[1])
-          };
-
-          feature.end = feature.start + span;
-
-          features.push(feature);
-        }
-      }
-    }
-
-    return this.base.call(this, features, chr, s, e);
-  }
-});

package/js/Track/Model/File.js

@@ -1,36 +0,0 @@
-Genoverse.Track.Model.File = Genoverse.Track.Model.extend({
-  dataType: 'text',
-
-  init: function () {
-    if (this.isLocal) {
-      this.url = false;
-    }
-
-    if (!(this.largeFile || this.indexFile)) {
-      this.allData = true;
-    }
-
-    this.base.apply(this, arguments);
-  },
-
-  getData: function (chr) {
-    var model = this;
-
-    if (this.isLocal && this.dataFile) {
-      var reader   = new FileReader();
-      var deferred = $.Deferred();
-
-      reader.onload = function (e) {
-        deferred.done(function () {
-          this.receiveData(e.target.result, chr, 1, this.browser.getChromosomeSize(chr));
-        }).resolveWith(model);
-      };
-
-      reader.readAsText(this.dataFile);
-
-      return deferred;
-    }
-
-    return this.base.apply(this, arguments);
-  }
-});

package/js/Track/Model/Gene/Ensembl.js

@@ -1,22 +0,0 @@
-// Ensembl REST API Gene model
-Genoverse.Track.Model.Gene.Ensembl = Genoverse.Track.Model.Gene.extend({
-  url              : '//rest.ensembl.org/overlap/region/human/__CHR__:__START__-__END__?feature=gene;content-type=application/json',
-  dataRequestLimit : 5000000, // As per e! REST API restrictions
-
-  // The url above responds in json format, data is an array
-  // We assume that parents always preceed children in data array, gene -> transcript -> exon
-  // See rest.ensembl.org/documentation/info/feature_region for more details
-  parseData: function (data, chr) {
-    for (var i = 0; i < data.length; i++) {
-      var feature = data[i];
-
-      if (feature.feature_type === 'gene' && !this.featuresById[feature.id]) {
-        feature.chr         = feature.chr || chr;
-        feature.label       = parseInt(feature.strand, 10) === 1 ? (feature.external_name || feature.id) + ' >' : '< ' + (feature.external_name || feature.id);
-        feature.transcripts = [];
-
-        this.insertFeature(feature);
-      }
-    }
-  }
-});

package/js/Track/Model/Sequence/Ensembl.js

@@ -1,4 +0,0 @@
-Genoverse.Track.Model.Sequence.Ensembl = Genoverse.Track.Model.Sequence.extend({
-  url              : '//rest.ensembl.org/sequence/region/human/__CHR__:__START__-__END__?content-type=text/plain', // Example url
-  dataRequestLimit : 10000000 // As per e! REST API restrictions
-});

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

@@ -1,67 +0,0 @@
-// Ensembl REST API Transcript model
-Genoverse.Track.Model.Transcript.Ensembl = Genoverse.Track.Model.Transcript.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 () {
-    this.geneIds   = {};
-    this.seenGenes = 0;
-
-    this.base.apply(this, arguments);
-  },
-
-  // 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) {
-    var model        = this;
-    var featuresById = this.featuresById;
-    var ids          = [];
-
-    data.filter(function (d) { return d.feature_type === 'transcript'; }).forEach(function (feature, i) {
-      if (!featuresById[feature.id]) {
-        model.geneIds[feature.Parent] = model.geneIds[feature.Parent] || ++model.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        = (model.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 = [];
-
-        model.insertFeature(feature);
-      }
-
-      ids.push(feature.id);
-    });
-
-    data.filter(function (d) { return d.feature_type === 'cds' && featuresById[d.Parent]; }).forEach(function (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(function (d) { return d.feature_type === 'exon' && featuresById[d.Parent] && !featuresById[d.Parent].exons[d.id]; }).forEach(function (exon) {
-      if (exon.end < featuresById[exon.Parent].cdsStart || exon.start > featuresById[exon.Parent].cdsEnd) {
-        featuresById[exon.Parent].subFeatures.push($.extend({ utr: true }, exon));
-      } else {
-        if (exon.start < featuresById[exon.Parent].cdsStart) {
-          featuresById[exon.Parent].subFeatures.push($.extend({ utr: true }, exon, { end: featuresById[exon.Parent].cdsStart }));
-        }
-
-        featuresById[exon.Parent].subFeatures.push($.extend({}, exon, {
-          start  : Math.max(exon.start, featuresById[exon.Parent].cdsStart),
-          end    : Math.min(exon.end,   featuresById[exon.Parent].cdsEnd),
-          strand : featuresById[exon.Parent].strand
-        }));
-
-        if (exon.end > featuresById[exon.Parent].cdsEnd) {
-          featuresById[exon.Parent].subFeatures.push($.extend({ utr: true }, exon, { start: featuresById[exon.Parent].cdsEnd }));
-        }
-      }
-    });
-
-    ids.forEach(function (id) {
-      featuresById[id].subFeatures.sort(function (a, b) { return a.start - b.start; });
-    });
-  }
-});

package/js/Track/View/Gene.js

@@ -1,6 +0,0 @@
-Genoverse.Track.View.Gene = Genoverse.Track.View.extend({
-  featureHeight : 5,
-  labels        : true,
-  repeatLabels  : true,
-  bump          : true
-});