higlass 1.11.7 → 1.11.10

package/app/scripts/api.js

@@ -15,6 +15,7 @@ const forceUpdate = (self) => {
 };
 
 const createApi = function api(context, pubSub) {
+  /** @type {import('./HiGlassComponent').default} */
   const self = context;
 
   let pubSubs = [];
@@ -112,10 +113,38 @@ const createApi = function api(context, pubSub) {
       },
 
       /**
-       * Reload all of the tiles
+       * Reload all or specific tiles for viewId/trackId
+       *
+       * @param {array} target Should be an array of type
+       *                       ({ viewId: string, trackId: string } | string).
+       *                       If the array is just strings, it's interpreted
+       *                       as a list of views whose tracks to reload.
        */
-      reload() {
-        console.warn('Not implemented yet!');
+      reload(target) {
+        /** @type {{ viewId: string, trackId: string}[]} */
+        let tracks;
+        if (!target) {
+          tracks = self.iterateOverTracks();
+        } else {
+          tracks = target.flatMap((d) =>
+            typeof d === 'string' ? self.iterateOverTracksInView(d) : d,
+          );
+        }
+
+        for (const { viewId, trackId } of tracks) {
+          const selectedTrack = self.getTrackObject(viewId, trackId);
+          // iterate over childTracks if CombinedTrack
+          for (const track of selectedTrack.childTracks || [selectedTrack]) {
+            // reload tiles for tracks with tiles.
+            if (track.fetchedTiles) {
+              track.removeTiles(Object.keys(track.fetchedTiles));
+              track.fetching.clear();
+              track.refreshTiles();
+            }
+            // second argument forces re-render
+            track.rerender(track.options, true);
+          }
+        }
       },
 
       /**
@@ -473,13 +502,14 @@ const createApi = function api(context, pubSub) {
        *
        * @param {string} viewUid The identifier of the view to zoom
        * @param {string} geneName The name of gene symbol to search
+       * @param {string} padding The padding (base pairs) around a given gene for the navigation
        * @param {Number} animateTime The time to spend zooming to the specified location
        * @example
        * // Zoom to the location near 'MYC'
-       * hgApi.zoomToGene('view1', 'MYC', 2000);
+       * hgApi.zoomToGene('view1', 'MYC', 100, 2000);
        */
-      zoomToGene(viewUid, geneName, animateTime = 0) {
-        self.zoomToGene(viewUid, geneName, animateTime);
+      zoomToGene(viewUid, geneName, padding = 0, animateTime = 0) {
+        self.zoomToGene(viewUid, geneName, padding, animateTime);
       },
 
       /**
@@ -647,6 +677,10 @@ const createApi = function api(context, pubSub) {
       /**
        * Return the track's javascript object. This is useful for subscribing to
        * data events (dataChanged)
+       *
+       * @param {string} viewId The id of the view containing the track
+       * @param {string} trackId The id of the track within the view
+       * @return {obj} The HiGlass track object for this track
        */
       getTrackObject(viewId, trackId) {
         let newViewId = viewId;
@@ -664,7 +698,7 @@ const createApi = function api(context, pubSub) {
        * Set or get an option.
        * @param   {string}  key  The name of the option you want get or set
        * @param   {*}  value  If not `undefined`, `key` will be set to `value`
-       * @return  {[type]}  When `value` is `undefined` the current value of
+       * @return  {obj}  When `value` is `undefined` the current value of
        *   `key` will be returned.
        */
       option(key, value) {

package/app/scripts/configs/available-for-plugins.js

@@ -28,14 +28,20 @@ import * as configs from '.';
 import * as utils from '../utils';
 
 // Tracks
+import Annotations1dTrack from '../Annotations1dTrack';
 import Annotations2dTrack from '../Annotations2dTrack';
 import ArrowheadDomainsTrack from '../ArrowheadDomainsTrack';
 import BarTrack from '../BarTrack';
 import BedLikeTrack from '../BedLikeTrack';
 import CNVIntervalTrack from '../CNVIntervalTrack';
+import Chromosome2DAnnotations from '../Chromosome2DAnnotations';
+import Chromosome2DLabels from '../Chromosome2DLabels';
+import ChromosomeGrid from '../ChromosomeGrid';
 import CombinedTrack from '../CombinedTrack';
+import CrossRule from '../CrossRule';
 import DivergentBarTrack from '../DivergentBarTrack';
 import HeatmapTiledPixiTrack from '../HeatmapTiledPixiTrack';
+import Horizontal1dHeatmapTrack from '../Horizontal1dHeatmapTrack';
 import Horizontal2DDomainsTrack from '../Horizontal2DDomainsTrack';
 import HorizontalChromosomeLabels from '../HorizontalChromosomeLabels';
 import HorizontalGeneAnnotationsTrack from '../HorizontalGeneAnnotationsTrack';
@@ -43,6 +49,8 @@ import HorizontalHeatmapTrack from '../HorizontalHeatmapTrack';
 import HorizontalLine1DPixiTrack from '../HorizontalLine1DPixiTrack';
 import HorizontalMultivecTrack from '../HorizontalMultivecTrack';
 import HorizontalPoint1DPixiTrack from '../HorizontalPoint1DPixiTrack';
+import HorizontalRule from '../HorizontalRule';
+import HorizontalTiled1DPixiTrack from '../HorizontalTiled1DPixiTrack';
 import HorizontalTiledPlot from '../HorizontalTiledPlot';
 import HorizontalTrack from '../HorizontalTrack';
 import Id2DTiledPixiTrack from '../Id2DTiledPixiTrack';
@@ -51,8 +59,11 @@ import IdVertical1DTiledPixiTrack from '../IdVertical1DTiledPixiTrack';
 import LeftAxisTrack from '../LeftAxisTrack';
 import MapboxTilesTrack from '../MapboxTilesTrack';
 import MoveableTrack from '../MoveableTrack';
+import OSMTileIdsTrack from '../OSMTileIdsTrack';
 import OSMTilesTrack from '../OSMTilesTrack';
+import OverlayTrack from '../OverlayTrack';
 import PixiTrack from '../PixiTrack';
+import RasterTilesTrack from '../RasterTilesTrack';
 import SVGTrack from '../SVGTrack';
 import SquareMarkersTrack from '../SquareMarkersTrack';
 import Tiled1DPixiTrack from '../Tiled1DPixiTrack';
@@ -60,8 +71,13 @@ import TiledPixiTrack from '../TiledPixiTrack';
 import TopAxisTrack from '../TopAxisTrack';
 import Track from '../Track';
 import ValueIntervalTrack from '../ValueIntervalTrack';
+import VerticalRule from '../VerticalRule';
 import VerticalTiled1DPixiTrack from '../VerticalTiled1DPixiTrack';
 import VerticalTrack from '../VerticalTrack';
+import ViewportTracker2D from '../ViewportTracker2D';
+import ViewportTracker2DPixi from '../ViewportTracker2DPixi';
+import ViewportTrackerHorizontal from '../ViewportTrackerHorizontal';
+import ViewportTrackerVertical from '../ViewportTrackerVertical';
 
 // Factories
 import ContextMenuItem from '../ContextMenuItem';
@@ -75,6 +91,11 @@ import * as services from '../services';
 import ChromosomeInfo from '../ChromosomeInfo';
 import SearchField from '../SearchField';
 
+// Data Fetchers
+import GBKDataFetcher from '../data-fetchers/genbank-fetcher';
+import LocalDataFetcher from '../data-fetchers/local-tile-fetcher';
+import getDataFetcher from '../data-fetchers/get-data-fetcher';
+
 const libraries = {
   d3Array,
   d3Axis,
@@ -96,14 +117,20 @@ const libraries = {
 };
 
 const tracks = {
+  Annotations1dTrack,
   Annotations2dTrack,
   ArrowheadDomainsTrack,
   BarTrack,
   BedLikeTrack,
   CNVIntervalTrack,
+  Chromosome2DAnnotations,
+  Chromosome2DLabels,
+  ChromosomeGrid,
   CombinedTrack,
+  CrossRule,
   DivergentBarTrack,
   HeatmapTiledPixiTrack,
+  Horizontal1dHeatmapTrack,
   Horizontal2DDomainsTrack,
   HorizontalChromosomeLabels,
   HorizontalGeneAnnotationsTrack,
@@ -111,6 +138,8 @@ const tracks = {
   HorizontalLine1DPixiTrack,
   HorizontalMultivecTrack,
   HorizontalPoint1DPixiTrack,
+  HorizontalRule,
+  HorizontalTiled1DPixiTrack,
   HorizontalTiledPlot,
   HorizontalTrack,
   Id2DTiledPixiTrack,
@@ -119,8 +148,11 @@ const tracks = {
   LeftAxisTrack,
   MapboxTilesTrack,
   MoveableTrack,
+  OSMTileIdsTrack,
   OSMTilesTrack,
+  OverlayTrack,
   PixiTrack,
+  RasterTilesTrack,
   SVGTrack,
   SquareMarkersTrack,
   Tiled1DPixiTrack,
@@ -128,8 +160,13 @@ const tracks = {
   TopAxisTrack,
   Track,
   ValueIntervalTrack,
+  VerticalRule,
   VerticalTiled1DPixiTrack,
   VerticalTrack,
+  ViewportTracker2D,
+  ViewportTracker2DPixi,
+  ViewportTrackerHorizontal,
+  ViewportTrackerVertical,
 };
 
 const factories = {
@@ -143,10 +180,18 @@ const chromosomes = {
   SearchField,
 };
 
+const dataFetchers = {
+  DataFetcher,
+  GBKDataFetcher,
+  LocalDataFetcher,
+  getDataFetcher,
+};
+
 export default {
   chromosomes,
   libraries,
   tracks,
+  dataFetchers,
   factories,
   services,
   utils,

package/app/scripts/configs/options-info.js

@@ -329,6 +329,10 @@ export const OPTIONS_INFO = {
     name: 'Fill color',
     inlineOptions: AVAILABLE_COLORS,
   },
+  rectangleDomainFillOpacity: {
+    name: 'Fill opacity',
+    inlineOptions: OPACITY_OPTIONS,
+  },
   rectangleDomainOpacity: {
     name: 'Opacity',
     inlineOptions: OPACITY_OPTIONS,

package/app/scripts/configs/tracks-info.js

@@ -950,6 +950,7 @@ export const TRACKS_INFO = [
       'trackBorderWidth',
       'trackBorderColor',
       'rectangleDomainFillColor',
+      'rectangleDomainFillOpacity',
       'rectangleDomainStrokeColor',
       'rectangleDomainOpacity',
       'minSquareSize',
@@ -965,6 +966,7 @@ export const TRACKS_INFO = [
       trackBorderWidth: 0,
       trackBorderColor: 'black',
       rectangleDomainFillColor: 'grey',
+      rectangleDomainFillOpacity: 0.4,
       rectangleDomainStrokeColor: 'black',
       rectangleDomainOpacity: 0.6,
       minSquareSize: 'none',

package/app/scripts/icons.js

@@ -1,4 +1,6 @@
+import React from 'react';
 import { select } from 'd3-selection';
+import '../styles/ViewHeader.module.scss';
 
 export const COG = {
   id: 'cog',
@@ -369,3 +371,18 @@ export const svgArrowheadDomainsIcon = parser.parseFromString(
   arrowHeadDomainsStr,
   'text/xml',
 ).documentElement;
+
+export function SearchIcon({ theStyle }) {
+  return (
+    <svg
+      styleName={theStyle}
+      viewBox="0 0 12 13"
+      xmlns="http://www.w3.org/2000/svg"
+    >
+      <g fill="none" stroke="#6c6c6c" strokeWidth="2">
+        <path d="M11.29 11.71l-4-4" />
+        <circle cx="5" cy="5" r="4" />
+      </g>
+    </svg>
+  );
+}

package/app/scripts/utils/ndarray-assign.js

@@ -1,14 +1,19 @@
-import cwise from 'cwise';
-
 const ndarrayAssign = (target, source) => {
   const numSource = +source;
   const isScalar = !Number.isNaN(numSource);
 
   if (isScalar) {
-    cwise({
-      args: ['array', 'scalar'],
-      body: 'function assigns(a, s) { a = s; }',
-    })(target, numSource);
+    if (target.dimension === 1) {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        target.set(i, numSource);
+      }
+    } else {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        for (let j = 0; j < target.shape[1]; ++j) {
+          target.set(i, j, numSource);
+        }
+      }
+    }
   } else {
     const ty = target.shape[0];
     const tx = target.shape[1];
@@ -26,10 +31,17 @@ const ndarrayAssign = (target, source) => {
       return;
     }
 
-    cwise({
-      args: ['array', 'array'],
-      body: 'function assign(a, b) { a = b; }',
-    })(target, source);
+    if (target.dimension === 1) {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        target.set(i, source.get(i));
+      }
+    } else {
+      for (let i = 0; i < target.shape[0]; ++i) {
+        for (let j = 0; j < target.shape[1]; ++j) {
+          target.set(i, j, source.get(i, j));
+        }
+      }
+    }
   }
 };
 

package/app/scripts/utils/ndarray-to-list.js

@@ -1,16 +1,22 @@
-import cwise from 'cwise';
-
 const ndarrayToList = (arr) => {
   const size = arr.shape.reduce((s, x) => s * x, 1);
   const list = new Array(size);
 
-  cwise({
-    args: ['array', 'scalar', 'scalar'],
-    body: (a, l, i) => {
-      l[i] = a; // eslint-disable-line
-      i++; // eslint-disable-line
-    },
-  })(arr, list, 0);
+  if (arr.dimension === 1) {
+    let l = 0;
+    for (let i = 0; i < arr.shape[0]; ++i) {
+      list[l] = arr.get(i);
+      l++;
+    }
+  } else {
+    let l = 0;
+    for (let i = 0; i < arr.shape[0]; ++i) {
+      for (let j = 0; j < arr.shape[1]; ++j) {
+        list[l] = arr.get(i, j);
+        l++;
+      }
+    }
+  }
 
   return list;
 };

package/app/styles/ViewHeader.module.scss

@@ -19,8 +19,7 @@ $unit: 24px;
   border: 0;
   border-radius: $unit / 8;
   background: $gray-lighter;
-  transition: height $fast $ease,
-              margin $fast $ease;
+  transition: height $fast $ease, margin $fast $ease;
 }
 
 .multitrack-header-dark {
@@ -123,14 +122,20 @@ $unit: 24px;
   width: $unit;
   height: 100%;
   padding: $unit / 4;
-  transition: background $fast $ease,
-              color $fast $ease;
+  transition: background $fast $ease, color $fast $ease;
+
+  g {
+    stroke: $gray;
+  }
 
   &:hover,
   &:active,
   &:focus {
     color: $white;
     background: $active;
+    g {
+      stroke: $white;
+    }
   }
 
   &:last-child {
@@ -145,7 +150,7 @@ $unit: 24px;
 }
 
 .multitrack-header-icon-squeazed {
-  width: $unit / 1.2  5;
+  width: $unit / 1.2 5;
   padding-left: $unit / 8;
   padding-right: $unit / 8;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "higlass",
-  "version": "1.11.7",
+  "version": "1.11.10",
   "description": "HiGlass Hi-C / genomic / large data viewer",
   "author": "Peter Kerpedjiev <pkerpedjiev@gmail.com>",
   "main": "dist/hglib.js",
@@ -47,7 +47,6 @@
     "ajv": "^6.10.0",
     "box-intersect": "^1.0.1",
     "css-element-queries": "github:marcj/css-element-queries",
-    "cwise": "^1.0.10",
     "d3-array": "^1.2.1",
     "d3-axis": "^1.0.4",
     "d3-brush": "github:flekschas/d3-brush",
@@ -71,7 +70,7 @@
     "path": "^0.12.7",
     "prismjs": "^1.16.0",
     "prop-types": "^15.6.0",
-    "pub-sub-es": "^1.2.1",
+    "pub-sub-es": "^2.0.1",
     "react": "^16.6.3",
     "react-autocomplete": "github:tiemevanveen/react-autocomplete#fix-176",
     "react-bootstrap": "0.32.1",

package/app/scripts/CollapsePanel.js

@@ -1,38 +0,0 @@
-/* jshint esnext: true */
-import React from 'react';
-import PropTypes from 'prop-types';
-import { Collapse, ControlLabel, Panel } from 'react-bootstrap';
-
-const CollapsePanel = (props) => (
-  <div>
-    <ControlLabel>
-      <a
-        className={`collapse-toggle-icon ${props.collapsedClass(
-          props.collapsed,
-        )}`}
-        onClick={() => props.toggleCollapse()}
-        role="button"
-        tabIndex={0}
-      >
-        {props.name}
-      </a>
-    </ControlLabel>
-    <Collapse in={!props.collapsed}>
-      <Panel>{props.children}</Panel>
-    </Collapse>
-  </div>
-);
-
-CollapsePanel.propTypes = {
-  children: PropTypes.node.isRequired,
-  collapsed: PropTypes.bool.isRequired,
-  collapsedClass: PropTypes.func.isRequired,
-  toggleCollapse: PropTypes.func.isRequired,
-  name: PropTypes.string,
-};
-
-CollapsePanel.defaultProps = {
-  name: 'Advanced Options',
-};
-
-export default CollapsePanel;

package/app/scripts/SeriesOptions.js

@@ -1,70 +0,0 @@
-import PropTypes from 'prop-types';
-import React from 'react';
-import { Collapse, Panel, Checkbox } from 'react-bootstrap';
-
-import CollapsePanel from './CollapsePanel';
-import TilesetFinder from './TilesetFinder';
-
-export class SeriesOptions extends React.Component {
-  constructor(props) {
-    super(props);
-
-    this.state = {
-      advancedVisible: true,
-    };
-  }
-
-  handleNormalizeTilesetChanged() {}
-
-  handleNormalizeCheckboxChanged(e) {
-    this.setState({
-      normalizeChecked: e.target.checked,
-    });
-  }
-
-  toggleAdvancedVisible() {
-    this.setState((prevState) => ({
-      advancedVisible: !prevState.advancedVisible,
-    }));
-  }
-
-  render() {
-    // console.log('trackType:', this.props.trackType);
-
-    return (
-      <CollapsePanel
-        collapsed={this.state.advancedVisible}
-        toggleCollapse={this.toggleAdvancedVisible.bind(this)}
-      >
-        <Checkbox
-          ref={(c) => {
-            this.normalizeCheckbox = c;
-          }}
-          onChange={this.handleNormalizeCheckboxChanged.bind(this)}
-        >
-          Normalize By
-        </Checkbox>
-
-        <Collapse in={this.state.normalizeChecked}>
-          <Panel>
-            <TilesetFinder
-              onTrackChosen={(value) =>
-                this.props.onTrackChosen(value, this.props.position)
-              }
-              selectedTilesetChanged={this.handleNormalizeTilesetChanged.bind(
-                this,
-              )}
-            />
-          </Panel>
-        </Collapse>
-      </CollapsePanel>
-    );
-  }
-}
-
-SeriesOptions.propTypes = {
-  onTrackChosen: PropTypes.func,
-  position: PropTypes.string,
-};
-
-export default SeriesOptions;

package/dist/hglib.css

@@ -1 +0,0 @@
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ease}.ContextMenu-module_context-menu-item-1HeVv:hover{background:#337ab7;color:#fff}.ContextMenu-module_context-menu-hr-3yapb{margin-top:5px;margin-bottom:5px;border:0;border-top:1px solid rgba(0,0,0,.1)}.ContextMenu-module_play-icon-R4pIO{width:12px;height:12px;position:absolute;right:5px}.ContextMenu-module_context-menu-span-8EUfZ{margin-right:20px;vertical-align:middle;display:inline-block;line-height:normal;white-space:nowrap}.ContextMenu-module_context-menu-thumbnail-2vHLD{margin-right:10px;border:1px solid #888}.ContextMenu-module_context-menu-thumbnail-inline-1iOcg{display:inline-block;margin-right:10px;vertical-align:middle}.TrackControl-module_track-control-2zDf3,.TrackControl-module_track-control-vertical-2McB_{position:absolute;z-index:1;display:-ms-flexbox;display:flex;background:hsla(0,0%,100%,.75);right:2px;top:2px;border-radius:2.5px;-webkit-box-shadow:0 0 0 1px rgba(0,0,0,.05),0 0 3px 0 rgba(0,0,0,.1);box-shadow:0 0 0 1px rgba(0,0,0,.05),0 0 3px 0 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