genoverse 3.2.0 → 4.0.0-beta1

package/js/Track/library/Graph/Line.js

@@ -1,296 +0,0 @@
-Genoverse.Track.Controller.Graph.Line = {
-  click: function () {
-    if (this.prop('showPopups')) {
-      this.prop('menus').hide(); // Hide first, because closeMenus causes fadeOut to happen, which doens't look great in this scenario
-      this.browser.closeMenus(this);
-      return Genoverse.Track.Controller.prototype.click.apply(this, arguments);
-    }
-  },
-
-  getClickedFeatures: function (x) {
-    var bounds    = { x: x, y: 0, w: 1, h: 9e99 };
-    var tolerance = this.scale > 1 ? 0 : 1 / this.scale;
-    var xMid      = bounds.x / this.scale;
-    var xRange    = tolerance ? [ Math.floor(xMid - tolerance), Math.ceil(xMid + tolerance) ] : [ Math.floor(xMid), Math.floor(xMid) ];
-    var features  = {};
-
-    this.featurePositions.search(bounds).forEach(function (f) {
-      if (!features[f.dataset]) {
-        features[f.dataset] = f;
-      }
-    });
-
-    return [
-      this.model.sortFeatures(Object.keys(features).map(function (k) {
-        return $.extend(true, {}, features[k], { clickedCoords: features[k].coords.filter(function (c) { return c[0] >= xRange[0] && c[0] <= xRange[1]; }) });
-      }))
-    ];
-  },
-
-  populateMenu: function (features) {
-    if (!features.length || !features[0].clickedCoords.length) {
-      return [];
-    }
-
-    var start = features[0].clickedCoords[0][0];
-    var end   = features[0].clickedCoords[features[0].clickedCoords.length - 1][0];
-    var avg   = start !== end;
-    var menu  = { title: features[0].chr + ':' + (start === end ? start : start + '-' + end) };
-    var m, values, i;
-
-    function getValues(coords) {
-      var vals = coords.map(function (c) { return c[1]; }).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[0].clickedCoords);
-
-        menu['Average value'] = values.avg;
-        menu['Min value']     = values.min;
-        menu['Max value']     = values.max;
-      } else {
-        menu = [ menu ];
-
-        for (i = 0; i < features.length; i++) {
-          values    = getValues(features[i].clickedCoords);
-          m         = { title: features[i].dataset };
-          m.Average = values.avg;
-          m.Min     = values.min;
-          m.Max     = values.max;
-
-          menu.push(m);
-        }
-      }
-    } else if (features.length === 1) {
-      menu.Value = features[0].clickedCoords[0][1];
-    } else {
-      for (i = 0; i < features.length; i++) {
-        menu[features[i].dataset] = features[i].clickedCoords[0][1];
-      }
-    }
-
-    return menu;
-  }
-};
-
-Genoverse.Track.Model.Graph.Line = Genoverse.Track.Model.Graph.extend({
-  parseData: function (data, chr, start, end) {
-    var features = [];
-    var feature, x;
-
-    function getX(f) {
-      return typeof f.x !== 'undefined' ? f.x : f.start + (f.start === f.end ? 0 : (f.end - f.start + 1) / 2);
-    }
-
-    data.sort(function (a, b) { return (a.start - b.start) || (a.x - b.x); });
-
-    for (var i = 0; i < data.length; i++) {
-      if (typeof data[i].y !== 'undefined' && !data[i].coords) {
-        x = getX(data[i]);
-
-        if (feature && feature.coords[feature.coords.length - 1][0] === x - 1) {
-          feature.coords.push([ x, data[i].y ]);
-          feature.end = x;
-        } else {
-          if (feature) {
-            features.push(feature);
-          }
-
-          feature = $.extend({ coords: [[ x, data[i].y ]], start: x, end: x }, data[i]);
-        }
-      } else {
-        if (feature) {
-          features.push(feature);
-          feature = undefined;
-        }
-
-        features.push(data[i]);
-      }
-    }
-
-    if (feature) {
-      features.push(feature);
-    }
-
-    return this.base(features, chr, start, end);
-  },
-
-  insertFeature: function (feature) {
-    var datasets = this.prop('datasets');
-
-    if (feature.coords) {
-      feature.coords = feature.coords.map(function (c, i) { return c.length > 1 ? c : [ feature.start + i, c ]; }).filter(function (c) { return c[0] >= feature.start && c[0] <= feature.end; });
-    } else if (feature.y) {
-      feature.coords = [[ feature.start + (feature.start === feature.end ? 0 : (feature.end - feature.start + 1) / 2), feature.y ]];
-    } else {
-      feature.coords = [];
-    }
-
-    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.Line = Genoverse.Track.View.Graph.extend({
-  featureHeight: 1,
-
-  positionFeatures: function (features, params) {
-    var scale  = params.scale;
-    var yScale = this.track.getYScale();
-    var margin = this.prop('marginTop');
-    var zeroY  = margin - this.prop('range')[0] * yScale;
-    var add    = (scale > 1 ? scale / 2 : 0) - params.scaledStart;
-
-    function setCoords(c) {
-      return [ c[0] * scale + add, c[1] * yScale + zeroY ];
-    }
-
-    for (var i = 0; i < features.length; i++) {
-      features[i].coordPositions = features[i].coords.map(setCoords);
-    }
-
-    params.featureHeight = this.prop('height');
-
-    return this.base(features, params);
-  },
-
-  draw: function (features, featureContext, labelContext, scale) {
-    if (!features.length) {
-      return;
-    }
-
-    var datasets     = this.featureDataSets(features);
-    var height       = this.prop('height');
-    var marginTop    = this.prop('marginTop');
-    var marginBottom = this.prop('margin');
-    var baseline     = Math.min(Math.max(marginTop, marginTop - this.prop('range')[0] * this.track.getYScale()), height - marginTop);
-    var binSize      = scale < 1 ? Math.floor(1 / scale) : 0;
-    var set, conf, feature, coords, binnedFeatures, lastBinSize, j, k, binStart, bin, l, prevFeature, prevCoords;
-
-    var defaults = {
-      color       : this.color,
-      fill        : this.prop('fill'),
-      lineWidth   : this.prop('lineWidth'),
-      globalAlpha : this.prop('globalAlpha')
-    };
-
-    for (var i = 0; i < datasets.list.length; i++) {
-      set  = datasets.list[i].name;
-      conf = $.extend({}, defaults, datasets.list[i]);
-
-      for (j = 0; j < (datasets.features[set] || []).length; j++) {
-        feature = datasets.features[set][j];
-        coords  = feature.coordPositions;
-
-        if (coords.length) {
-          if (binSize) {
-            binnedFeatures = [];
-            k              = 0;
-
-            while (k < coords.length) {
-              binStart = feature.coords[k][0];
-              bin      = [];
-
-              while (coords[k] && feature.coords[k][0] - binStart < binSize) {
-                bin.push(coords[k++]);
-              }
-
-              l      = bin.length;
-              bin    = bin.reduce(function (arr, b) { arr[0] += b[0]; arr[1] += b[1]; return arr; }, [ 0, 0 ]);
-              bin[0] = Math.round(bin[0] / l);
-
-              if (binnedFeatures.length && bin[0] === binnedFeatures[binnedFeatures.length - 1][0]) {
-                binnedFeatures[binnedFeatures.length - 1][1] = (binnedFeatures[binnedFeatures.length - 1][1] * lastBinSize + bin[1]) / (lastBinSize + l);
-              } else {
-                binnedFeatures.push([ bin[0], bin[1] / l ]);
-              }
-
-              lastBinSize = l;
-            }
-
-            coords = binnedFeatures;
-            feature.binnedCoords = coords;
-          }
-
-          featureContext.fillStyle = featureContext.strokeStyle = conf.color;
-          featureContext.lineWidth = conf.lineWidth;
-
-          if (conf.fill) {
-            featureContext.globalAlpha = conf.globalAlpha;
-          }
-
-          featureContext.beginPath();
-
-          if (conf.fill) {
-            featureContext.moveTo(coords[0][0], baseline);
-            featureContext.lineTo.apply(featureContext, coords[0]);
-          } else {
-            featureContext.moveTo.apply(featureContext, coords[0]);
-          }
-
-          for (k = 1; k < coords.length; k++) {
-            featureContext.lineTo.apply(featureContext, coords[k]);
-          }
-
-          featureContext.stroke();
-
-          if (conf.fill) {
-            featureContext.lineTo(coords[coords.length - 1][0], baseline);
-            featureContext.closePath();
-            featureContext.fill();
-          }
-
-          prevFeature = j ? datasets.features[set][j - i] : undefined;
-
-          if (prevFeature && prevFeature.end === feature.start - 1) {
-            featureContext.beginPath();
-
-            prevCoords = (binSize ? prevFeature.binnedCoords : prevFeature.coordPositions).slice(-1);
-
-            featureContext.moveTo.apply(featureContext, prevCoords[0]);
-            featureContext.lineTo.apply(featureContext, coords[0]);
-            featureContext.stroke();
-
-            if (conf.fill) {
-              featureContext.lineTo(coords[0][0], baseline);
-              featureContext.lineTo(prevCoords[0][0], baseline);
-
-              featureContext.closePath();
-              featureContext.fill();
-            }
-          }
-
-          if (conf.fill) {
-            featureContext.globalAlpha = 1;
-          }
-        }
-      }
-    }
-
-    // Don't allow features to be drawn in the margins
-    featureContext.clearRect(0, 0,                     this.width, marginTop - 1);
-    featureContext.clearRect(0, height - marginBottom, this.width, marginBottom);
-  }
-});
-
-Genoverse.Track.Graph.Line = Genoverse.Track.Graph.extend({
-  type       : 'Line',
-  showPopups : true, // If true, clicking on the track will show popups. If false, popups will not appear.
-  fill       : false,
-  lineWidth  : 1,
-  model      : Genoverse.Track.Model.Graph.Line,
-  view       : Genoverse.Track.View.Graph.Line
-});

package/js/Track/library/Legend.js

@@ -1,224 +0,0 @@
-Genoverse.Track.Controller.Legend = Genoverse.Track.Controller.Static.extend({
-  init: function () {
-    this.base();
-
-    this.container.addClass('gv-track-container-legend');
-
-    this.browser.legends[this.track.id] = this.track;
-
-    this.track.setTracks();
-  },
-
-  destroy: function () {
-    delete this.browser.legends[this.prop('id')];
-    this.base();
-  }
-});
-
-Genoverse.Track.Model.Legend = Genoverse.Track.Model.Static.extend({
-  findFeatures: function () {
-    var bounds   = { x: this.browser.scaledStart, y: 0, w: this.width };
-    var features = {};
-
-    $.each($.map(this.track.tracks, function (track) {
-      var featurePositions = track.prop('featurePositions');
-      bounds.h = track.prop('height');
-      return featurePositions ? featurePositions.search(bounds).concat(track.prop('labelPositions').search(bounds)) : [];
-    }), function () {
-      if (Array.isArray(this.legend)) {
-        this.legend.forEach(function (legend) { features[legend.label] = legend.color; });
-      } else if (this.legend) {
-        features[this.legend] = this.legendColor || this.color;
-      }
-    });
-
-    return this.sortFeatures($.map(features, function (color, text) { return [[ text, color ]]; }));
-  },
-
-  sortFeatures: function (features) {
-    // sort legend alphabetically
-    return features.sort(function (a, b) { return a[0].localeCompare(b[0]); });
-  }
-});
-
-Genoverse.Track.View.Legend = Genoverse.Track.View.Static.extend({
-  textColor     : '#000000',
-  labels        : 'overlay',
-  featureHeight : 12,
-
-  positionFeatures: function (f, params) {
-    if (params.positioned) {
-      return f;
-    }
-
-    var cols     = 2;
-    var pad      = 5;
-    var w        = 20;
-    var x        = 0;
-    var y        = 0;
-    var xScale   = this.width / cols;
-    var yScale   = this.fontHeight + pad;
-    var features = [];
-    var xOffest  = params.xOffset || 0;
-    var xPos, yPos, labelWidth;
-
-    for (var i = 0; i < f.length; i++) {
-      xPos       = (x * xScale) + pad;
-      yPos       = (y * yScale) + pad;
-      labelWidth = this.context.measureText(f[i][0]).width;
-
-      features.push(
-        { x: xPos + xOffest,           y: yPos, width: w,              height: this.featureHeight, color: f[i][1] },
-        { x: xPos + xOffest + pad + w, y: yPos, width: labelWidth + 1, height: this.featureHeight, color: false, labelColor: this.textColor, labelWidth: labelWidth, label: f[i][0] }
-      );
-
-      if (++x === cols) {
-        x = 0;
-        y++;
-      }
-    }
-
-    params.height     = this.prop('height', f.length ? ((y + (x ? 1 : 0)) * yScale) + pad : 0);
-    params.width      = this.width;
-    params.positioned = true;
-
-    return this.base(features, params);
-  }
-});
-
-Genoverse.Track.Legend = Genoverse.Track.Static.extend({
-  unsortable  : true,
-  lockToTrack : true, // Always put the legend just below the last track that the legend is for
-  removable   : false,
-
-  controller : Genoverse.Track.Controller.Legend,
-  model      : Genoverse.Track.Model.Legend,
-  view       : Genoverse.Track.View.Legend,
-
-  setDefaults: function () {
-    this.order = typeof this.order !== 'undefined' ? this.order : 9e99;
-    this.id    = this.id   || 'legend';
-    this.type  = this.type || 'legend';
-    this.base();
-  },
-
-  setEvents: function () {
-    this.browser.on({
-      'afterAddTracks afterRemoveTracks': function () {
-        for (var i in this.legends) {
-          this.legends[i].setTracks();
-        }
-
-        this.sortTracks();
-      },
-      afterRemoveTracks: function (tracks) {
-        var i;
-
-        for (i in tracks) {
-          if (tracks[i].legendTrack && tracks[i].legendTrack.tracks.length === 0) {
-            tracks[i].legendTrack.remove();
-          }
-        }
-
-        for (i in this.legends) {
-          this.legends[i].controller.makeImage({});
-        }
-      },
-      afterUpdateTrackOrder: function (e, ui) {
-        var track       = ui.item.data('track');
-        var legendTrack = this.legends[track.id] || track.legendTrack;
-
-        // If a legend track, or a track with a sortable legend has been reordered, its lockToTrack status is ignored from now on.
-        // This allows a legend to initially be locked to a track, but then to be reordered once the browser has been initialized
-        if (legendTrack && legendTrack.lockToTrack && legendTrack.unsortable === false) {
-          legendTrack.lockToTrack = false;
-        }
-
-        for (var i in this.legends) {
-          this.legends[i].updateOrder();
-        }
-
-        this.sortTracks();
-      }
-    });
-
-    this.browser.on({
-      afterPositionFeatures: function (features, params) {
-        var legend = this.prop('legendTrack');
-
-        if (legend) {
-          setTimeout(function () { legend.controller.makeImage(params); }, 1);
-        }
-      },
-      afterResize: function (height, userResize) {
-        var legend = this.prop('legendTrack');
-
-        if (legend && userResize === true) {
-          legend.controller.makeImage({});
-        }
-      },
-      afterCheckHeight: function () {
-        var legend = this.prop('legendTrack');
-
-        if (legend) {
-          legend.controller.makeImage({});
-        }
-      },
-      afterSetMVC: function () {
-        var legend = this.prop('legendTrack');
-
-        if (legend && legend.tracks.length) {
-          legend.disable();
-
-          if (this.legend !== false) {
-            legend.enable();
-          }
-        }
-      }
-    }, this);
-  },
-
-  setTracks: function () {
-    var legend = this;
-    var type   = this.type;
-
-    this.tracks = $.map(this.browser.tracks.filter(function (t) {
-      if (t.legendType === type) {
-        t.legendTrack = t.legendTrack || legend;
-        return true;
-      }
-
-      return false;
-    }), function (track) {
-      return [ track ].concat(track.prop('childTracks'), track.prop('parentTrack')).filter(function (t) { return t && t !== legend && !t.prop('disabled'); });
-    });
-
-    this.updateOrder();
-
-    if (typeof this.controller === 'object') {
-      this[this.tracks.length ? 'enable' : 'disable']();
-    } else {
-      this.disabled = !this.tracks.length;
-    }
-  },
-
-  updateOrder: function () {
-    if (this.lockToTrack) {
-      var tracks = this.tracks.filter(function (t) { return !t.prop('parentTrack'); });
-
-      if (tracks.length) {
-        this.order = tracks[tracks.length - 1].order + 0.1;
-      }
-    }
-  },
-
-  enable: function () {
-    this.base();
-    this.controller.makeImage({});
-  },
-
-  disable: function () {
-    delete this.controller.stringified;
-    this.base();
-  }
-});

package/js/Track/library/Static.js

@@ -1,78 +0,0 @@
-Genoverse.Track.Controller.Static = Genoverse.Track.Controller.extend({
-  addDomElements: function () {
-    this.base();
-
-    this.image = $('<img>').appendTo(this.imgContainer);
-
-    this.container.toggleClass('gv-track-container gv-track-container-static').prepend(this.imgContainer);
-    this.scrollContainer.add(this.messageContainer).remove();
-  },
-
-  reset: function () {
-    delete this.stringified;
-    this.base.apply(this, arguments);
-  },
-
-  setWidth: function (width) {
-    this.base(width);
-    this.image.width = this.width;
-  },
-
-  makeFirstImage: function () {
-    this.base.apply(this, arguments);
-    this.container.css('left', 0);
-    this.imgContainer.show();
-  },
-
-  makeImage: function (params) {
-    if (this.prop('disabled')) {
-      return $.Deferred().resolve();
-    }
-
-    var features = this.view.positionFeatures(this.model.findFeatures(params.chr, params.start, params.end), params);
-
-    if (features) {
-      var string = JSON.stringify(features);
-
-      if (this.stringified !== string) {
-        var height = this.prop('height');
-
-        params.width         = this.width;
-        params.featureHeight = height;
-
-        this.render(features, this.image.data(params));
-        this.imgContainer.children(':last').show();
-        this.resize(height, undefined, false);
-
-        this.stringified = string;
-      }
-    }
-
-    return $.Deferred().resolve();
-  }
-});
-
-Genoverse.Track.Model.Static = Genoverse.Track.Model.extend({
-  url            : false,
-  checkDataRange : function () { return true; }
-});
-
-Genoverse.Track.View.Static = Genoverse.Track.View.extend({
-  featureMargin   : { top: 0, right: 1, bottom: 0, left: 1 },
-  positionFeature : $.noop,
-  scaleFeatures   : function (features) { return features; },
-
-  draw: function (features, featureContext, labelContext, scale) {
-    for (var i = 0; i < features.length; i++) {
-      this.drawFeature(features[i], featureContext, labelContext, scale);
-    }
-  }
-});
-
-Genoverse.Track.Static = Genoverse.Track.extend({
-  controls   : 'off',
-  resizable  : false,
-  controller : Genoverse.Track.Controller.Static,
-  model      : Genoverse.Track.Model.Static,
-  view       : Genoverse.Track.View.Static
-});