higlass 1.13.0 → 1.13.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (22) hide show
  1. package/app/scripts/Autocomplete.jsx +1 -0
  2. package/app/scripts/CustomTrackDialog.jsx +4 -0
  3. package/app/scripts/GenomePositionSearchBox.jsx +1 -0
  4. package/app/scripts/ListWrapper.jsx +1 -0
  5. package/app/scripts/PixiTrack.js +106 -42
  6. package/app/scripts/SortableList.jsx +1 -0
  7. package/app/scripts/TiledPlot.jsx +2 -0
  8. package/app/scripts/Track.js +153 -45
  9. package/app/scripts/TrackRenderer.jsx +54 -53
  10. package/app/scripts/hocs/with-modal.jsx +1 -0
  11. package/app/scripts/hocs/with-pub-sub.jsx +4 -1
  12. package/app/scripts/hocs/with-theme.jsx +1 -0
  13. package/app/scripts/icons.jsx +6 -0
  14. package/app/scripts/services/tile-proxy.js +1 -1
  15. package/app/scripts/types.ts +26 -0
  16. package/app/scripts/utils/type-guards.js +24 -0
  17. package/dist/esm.html +283 -0
  18. package/dist/hglib.js +42 -82877
  19. package/dist/hglib.min.js +86 -105
  20. package/dist/higlass.mjs +207 -0
  21. package/dist/index.html +6 -6
  22. package/package.json +10 -3
package/app/scripts/types.ts CHANGED
@@ -1,5 +1,7 @@
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  /* eslint-disable */
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+ import type { THEME_DARK, THEME_LIGHT } from "./configs";
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+
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  export type Scale = import("d3-scale").ScaleContinuousNumeric<number, number>;
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  export type TrackPosition = typeof import('./configs/primitives').TRACK_LOCATIONS[number];
@@ -77,3 +79,27 @@ export interface TrackObject {
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  movedY(extent: number): void;
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  zoomedY(yPosition: number, wheelDelta: number): void;
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  }
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+
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+ export type Theme = typeof THEME_DARK | typeof THEME_LIGHT;
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+
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+ type TilesetInfoBase = {
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+ name: string;
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+ coordSystem: string;
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+ min_pos: number[];
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+ max_pos: number[];
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+ max_zoom: number;
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+ tile_size?: number;
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+ max_tile_width?: number;
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+ transforms?: { name: string, value: string }[];
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+ }
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+
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+ export type LegacyTilesetInfo = TilesetInfoBase & {
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+ max_width: number;
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+ bins_per_dimension?: number;
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+ }
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+
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+ export type ResolutionsTilesetInfo = TilesetInfoBase & {
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+ resolutions: number[];
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+ }
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+
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+ export type TilesetInfo = LegacyTilesetInfo | ResolutionsTilesetInfo;
package/app/scripts/utils/type-guards.js CHANGED
@@ -15,3 +15,27 @@ export function isCombinedTrackConfig(trackConfig) {
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  export function isWheelEvent(event) {
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  return 'deltaY' in event && 'deltaMode' in event;
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  }
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+
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+ /**
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+ * @param {unknown} obj
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+ * @returns {obj is {}}
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+ */
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+ export function isObject(obj) {
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+ return obj !== null && typeof obj === 'object';
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+ }
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+
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+ /**
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+ * @param {import('../types').TilesetInfo | undefined} info
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+ * @returns {info is import('../types').LegacyTilesetInfo}
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+ */
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+ export function isLegacyTilesetInfo(info) {
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+ return isObject(info) && 'max_width' in info;
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+ }
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+
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+ /**
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+ * @param {import('../types').TilesetInfo | undefined} info
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+ * @returns {info is import('../types').ResolutionsTilesetInfo}
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+ */
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+ export function isResolutionsTilesetInfo(info) {
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+ return isObject(info) && 'resolutions' in info;
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+ }
package/dist/esm.html ADDED
@@ -0,0 +1,283 @@
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta charset="utf-8">
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+ <meta name="viewport" content="width=device-width,initial-scale=1">
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+ <title>HiGlass</title>
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+ <style type="text/css">
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+ #demo {
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+ position: absolute;
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+ left: 1rem;
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+ top: 1rem;
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+ bottom: 1rem;
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+ right: 1rem;
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+ overflow: hidden;
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+ }
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+ </style>
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+ <link rel="stylesheet" href="./hglib.css">
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+ <script type="importmap">
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+ {
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+ "imports": {
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+ "react": "https://esm.sh/react@17",
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+ "react-dom": "https://esm.sh/react-dom@17",
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+ "pixi.js": "https://esm.sh/pixi.js@6"
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+ }
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+ }
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+ </script>
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+ <script type="module">
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+ import * as hglib from "./higlass.mjs";
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+ globalThis.hglib = hglib;
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+ </script>
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+
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+ </head>
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+
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+ <body>
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+ <div id="demo"></div>
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+ </body>
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+
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+ <script type="module">
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+ const viewConfig = {
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+ zoomFixed: false,
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+ views: [
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+ {
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+ layout: {
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+ w: 12,
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+ h: 7,
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+ x: 0,
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+ y: 0
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+ },
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+ uid: 'aa',
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+ initialYDomain: [
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+ 2534823997.9776945,
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+ 2547598956.834603
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+ ],
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+ initialXDomain: [
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+ 2521015726.4619913,
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+ 2558682921.8435397
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+ ],
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+ tracks: {
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+ left: [],
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+ top: [
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+ {
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+ uid: 'genes',
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+ tilesetUid: 'OHJakQICQD6gTD7skx4EWA',
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-gene-annotations',
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+ height: 48,
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+ options: {
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+ labelColor: 'black',
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+ plusStrandColor: 'black',
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+ labelPosition: 'hidden',
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+ minusStrandColor: 'black',
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+ fontSize: 11,
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ geneAnnotationHeight: 10,
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+ geneLabelPosition: 'outside',
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+ geneStrandSpacing: 4
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+ },
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+ },
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+ {
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+ uid: 'line1',
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+ tilesetUid: 'PjIJKXGbSNCalUZO21e_HQ',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#4a35fc',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ }
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+ },
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+ {
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+ uid: 'line2',
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+ tilesetUid: 'PdAaSdibTLK34hCw7ubqKA',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#d104fa',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'line3',
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+ tilesetUid: 'e0DYtZBSTqiMLHoaimsSpg',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: '#ff0000',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'line4',
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+ tilesetUid: 'cE0nGyd0Q_yVYSyBUe89Ww',
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+ height: 20,
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+ server: 'http://higlass.io/api/v1',
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+ type: 'horizontal-line',
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+ options: {
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+ valueScaling: 'linear',
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+ lineStrokeWidth: 2,
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+ lineStrokeColor: 'orange',
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+ labelPosition: 'topLeft',
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+ labelColor: 'black',
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+ axisPositionHorizontal: 'right',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ labelTextOpacity: 0.4,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: false
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+ },
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+ },
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+ {
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+ uid: 'chroms',
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+ height: 18,
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+ chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
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+ type: 'horizontal-chromosome-labels',
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+ options: {
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+ color: '#777777',
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+ stroke: '#FFFFFF',
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+ fontSize: 11,
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+ fontIsLeftAligned: true,
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+ showMousePosition: true,
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+ mousePositionColor: '#000000'
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+ },
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+ }
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+ ],
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+ right: [],
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+ center: [
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+ {
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+ uid: 'center',
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+ type: 'combined',
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+ contents: [
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+ {
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+ server: 'http://higlass.io/api/v1',
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+ tilesetUid: 'dVBREuC2SvO01uXYMUh2aQ',
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+ type: 'heatmap',
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+ uid: 'Yqetzqw6Qfy-hREAJhAXEA',
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+ options: {
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+ backgroundColor: '#eeeeee',
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+ labelPosition: 'topLeft',
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+ labelTextOpacity: 0.4,
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+ colorRange: [
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+ 'white',
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+ 'rgba(245,166,35,1.0)',
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+ 'rgba(208,2,27,1.0)',
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+ 'black'
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+ ],
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+ maxZoom: null,
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+ colorbarPosition: 'topRight',
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+ trackBorderWidth: 0,
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+ trackBorderColor: 'black',
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+ heatmapValueScaling: 'log',
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+ showMousePosition: true,
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+ mousePositionColor: '#000000',
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+ showTooltip: true,
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+ scaleStartPercent: '0.00000',
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+ scaleEndPercent: '1.00000',
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+ showMousePositionGlobally: true,
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+ },
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+ }
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+ ],
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+ }
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+ ],
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+ bottom: [],
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+ whole: [],
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+ gallery: []
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+ },
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+ chromInfoPath: '//s3.amazonaws.com/pkerp/data/hg19/chromSizes.tsv',
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+ genomePositionSearchBox: {
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+ visible: true,
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+ chromInfoServer: 'http://higlass.io/api/v1',
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+ chromInfoId: 'hg19',
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+ autocompleteServer: 'http://higlass.io/api/v1',
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+ autocompleteId: 'OHJakQICQD6gTD7skx4EWA'
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+ }
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+ }
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+ ],
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+ editable: true,
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+ viewEditable: true,
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+ tracksEditable: true,
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+ exportViewUrl: '/api/v1/viewconfs',
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+ zoomLocks: {
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+ locksByViewUid: {},
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+ locksDict: {}
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+ },
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+ trackSourceServers: [
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+ 'http://higlass.io/api/v1'
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+ ],
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+ locationLocks: {
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+ locksByViewUid: {
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+ aa: 'PkNgAl3mSIqttnSsCewngw',
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+ ewZvJwlDSei_dbpIAkGMlg: 'PkNgAl3mSIqttnSsCewngw'
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+ },
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+ locksDict: {
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+ PkNgAl3mSIqttnSsCewngw: {
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+ aa: [
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+ 1550000000,
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+ 1550000000,
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+ 3380588.876772046
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+ ],
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+ ewZvJwlDSei_dbpIAkGMlg: [
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+ 1550000000.0000002,
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+ 1549999999.9999993,
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+ 3380588.876772046
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+ ],
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+ uid: 'PkNgAl3mSIqttnSsCewngw'
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+ }
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+ }
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+ },
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+ valueScaleLocks: {
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+ locksByViewUid: {},
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+ locksDict: {}
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+ }
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+ };
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+
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+ const hgApi = window.hgApi = hglib.viewer(
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+ document.getElementById('demo'),
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+ viewConfig,
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+ { bounded: true },
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+ );
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+
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+ hgApi.setBroadcastMousePositionGlobally(true);
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+
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+ hgApi.on('viewConfig', () => {
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+ console.log('View Config changed');
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+ });
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+
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+ </script>
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+ </html>