@jbrowse/plugin-hic 2.15.0 → 2.15.2

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Files changed (11) hide show
  1. package/dist/HicRenderer/HicRenderer.d.ts +1 -2
  2. package/dist/HicRenderer/HicRenderer.js +26 -74
  3. package/dist/HicRenderer/makeImageData.d.ts +10 -0
  4. package/dist/HicRenderer/makeImageData.js +81 -0
  5. package/dist/LinearHicDisplay/model.d.ts +18 -14
  6. package/esm/HicRenderer/HicRenderer.d.ts +1 -2
  7. package/esm/HicRenderer/HicRenderer.js +3 -74
  8. package/esm/HicRenderer/makeImageData.d.ts +10 -0
  9. package/esm/HicRenderer/makeImageData.js +75 -0
  10. package/esm/LinearHicDisplay/model.d.ts +18 -14
  11. package/package.json +2 -2
package/dist/HicRenderer/HicRenderer.d.ts CHANGED
@@ -28,7 +28,6 @@ export type ResultsSerialized = ServerSideResultsSerialized;
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  export type ResultsDeserialized = ServerSideResultsDeserialized;
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  export default class HicRenderer extends ServerSideRendererType {
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  supportsSVG: boolean;
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- makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
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  render(renderProps: RenderArgsDeserialized): Promise<{
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  height: any;
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  width: number;
@@ -38,7 +37,7 @@ export default class HicRenderer extends ServerSideRendererType {
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  } | {
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  height: any;
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  width: number;
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- reactElement: import("react").JSX.Element;
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+ reactElement: React.JSX.Element;
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  html?: string;
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  } | {
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  height: any;
package/dist/HicRenderer/HicRenderer.js CHANGED
@@ -1,101 +1,53 @@
1
1
  "use strict";
2
+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ var desc = Object.getOwnPropertyDescriptor(m, k);
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+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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+ desc = { enumerable: true, get: function() { return m[k]; } };
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+ }
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+ Object.defineProperty(o, k2, desc);
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+ }) : (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ o[k2] = m[k];
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+ }));
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+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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+ Object.defineProperty(o, "default", { enumerable: true, value: v });
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+ }) : function(o, v) {
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+ o["default"] = v;
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+ });
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+ var __importStar = (this && this.__importStar) || function (mod) {
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+ if (mod && mod.__esModule) return mod;
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+ var result = {};
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+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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+ __setModuleDefault(result, mod);
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+ return result;
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+ };
2
25
  var __importDefault = (this && this.__importDefault) || function (mod) {
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26
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
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  };
5
28
  Object.defineProperty(exports, "__esModule", { value: true });
6
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  const ServerSideRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType"));
7
- const util_1 = require("@jbrowse/core/util");
8
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  const offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils");
9
31
  const operators_1 = require("rxjs/operators");
10
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  const configuration_1 = require("@jbrowse/core/configuration");
11
33
  const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
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- const colord_1 = require("@jbrowse/core/util/colord");
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34
  const rxjs_1 = require("rxjs");
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- const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
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- const viridis_1 = __importDefault(require("./viridis"));
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- const d3_interpolate_1 = require("@mui/x-charts-vendor/d3-interpolate");
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  class HicRenderer extends ServerSideRendererType_1.default {
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  constructor() {
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  super(...arguments);
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  this.supportsSVG = true;
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  }
22
- async makeImageData(ctx, props) {
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- const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, } = props;
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- const region = regions[0];
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- const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
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- const res = await dataAdapter.getResolution(bpPerPx / resolution);
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- const width = (region.end - region.start) / bpPerPx;
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- const w = res / (bpPerPx * Math.sqrt(2));
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- const baseColor = (0, colord_1.colord)((0, configuration_1.readConfObject)(config, 'baseColor'));
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- const offset = Math.floor(region.start / res);
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- if (features.length) {
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- let maxScore = 0;
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- let minBin = 0;
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- let maxBin = 0;
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- await (0, util_1.abortBreakPoint)(signal);
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- for (const { bin1, bin2, counts } of features) {
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- maxScore = Math.max(counts, maxScore);
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- minBin = Math.min(Math.min(bin1, bin2), minBin);
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- maxBin = Math.max(Math.max(bin1, bin2), maxBin);
40
- }
41
- await (0, util_1.abortBreakPoint)(signal);
42
- const colorSchemes = {
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- juicebox: ['rgba(0,0,0,0)', 'red'],
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- fall: (0, d3_interpolate_1.interpolateRgbBasis)([
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- 'rgb(255, 255, 255)',
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- 'rgb(255, 255, 204)',
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- 'rgb(255, 237, 160)',
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- 'rgb(254, 217, 118)',
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- 'rgb(254, 178, 76)',
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- 'rgb(253, 141, 60)',
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- 'rgb(252, 78, 42)',
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- 'rgb(227, 26, 28)',
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- 'rgb(189, 0, 38)',
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- 'rgb(128, 0, 38)',
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- 'rgb(0, 0, 0)',
56
- ]),
57
- viridis: viridis_1.default,
58
- };
59
- const m = useLogScale ? maxScore : maxScore / 20;
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- // @ts-expect-error
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- const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
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- const scale = useLogScale
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- ? (0, d3_scale_1.scaleSequentialLog)(x1).domain([1, m])
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- : (0, d3_scale_1.scaleSequential)(x1).domain([0, m]);
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- ctx.save();
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- if (region.reversed === true) {
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- ctx.scale(-1, 1);
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- ctx.translate(-width, 0);
69
- }
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- ctx.rotate(-Math.PI / 4);
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- let start = Date.now();
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- for (const { bin1, bin2, counts } of features) {
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- ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', {
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- count: counts,
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- maxScore,
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- baseColor,
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- scale,
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- useLogScale,
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- });
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- ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
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- if (+Date.now() - start > 400) {
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- await (0, util_1.abortBreakPoint)(signal);
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- start = +Date.now();
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- }
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- }
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- ctx.restore();
87
- }
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- return undefined;
89
- }
90
40
  async render(renderProps) {
91
41
  const { config, regions, bpPerPx } = renderProps;
92
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  const region = regions[0];
93
43
  const width = (region.end - region.start) / bpPerPx;
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44
  const height = (0, configuration_1.readConfObject)(config, 'maxHeight');
95
45
  const features = await this.getFeatures(renderProps);
96
- const res = await (0, offscreenCanvasUtils_1.renderToAbstractCanvas)(width, height, renderProps, ctx => this.makeImageData(ctx, {
46
+ const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
47
+ const res = await (0, offscreenCanvasUtils_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData(ctx, {
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48
  ...renderProps,
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  features,
50
+ pluginManager: this.pluginManager,
99
51
  }));
100
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  const results = await super.render({
101
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  ...renderProps,
package/dist/HicRenderer/makeImageData.d.ts ADDED
@@ -0,0 +1,10 @@
1
+ import { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
2
+ import { Region } from '@jbrowse/core/util/types';
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+ import PluginManager from '@jbrowse/core/PluginManager';
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+ import { RenderArgsDeserializedWithFeatures } from './HicRenderer';
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+ export interface RenderArgs extends ServerSideRenderArgs {
6
+ regions: Region[];
7
+ }
8
+ export declare function makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures & {
9
+ pluginManager: PluginManager;
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+ }): Promise<undefined>;
package/dist/HicRenderer/makeImageData.js ADDED
@@ -0,0 +1,81 @@
1
+ "use strict";
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.makeImageData = makeImageData;
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+ const util_1 = require("@jbrowse/core/util");
8
+ const configuration_1 = require("@jbrowse/core/configuration");
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+ const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
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+ const colord_1 = require("@jbrowse/core/util/colord");
11
+ const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
12
+ const d3_interpolate_1 = require("@mui/x-charts-vendor/d3-interpolate");
13
+ const viridis_1 = __importDefault(require("./viridis"));
14
+ async function makeImageData(ctx, props) {
15
+ const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
16
+ const region = regions[0];
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+ const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
18
+ const res = await dataAdapter.getResolution(bpPerPx / resolution);
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+ const width = (region.end - region.start) / bpPerPx;
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+ const w = res / (bpPerPx * Math.sqrt(2));
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+ const baseColor = (0, colord_1.colord)((0, configuration_1.readConfObject)(config, 'baseColor'));
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+ const offset = Math.floor(region.start / res);
23
+ if (features.length) {
24
+ let maxScore = 0;
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+ let minBin = 0;
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+ let maxBin = 0;
27
+ await (0, util_1.abortBreakPoint)(signal);
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+ for (const { bin1, bin2, counts } of features) {
29
+ maxScore = Math.max(counts, maxScore);
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+ minBin = Math.min(Math.min(bin1, bin2), minBin);
31
+ maxBin = Math.max(Math.max(bin1, bin2), maxBin);
32
+ }
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+ await (0, util_1.abortBreakPoint)(signal);
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+ const colorSchemes = {
35
+ juicebox: ['rgba(0,0,0,0)', 'red'],
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+ fall: (0, d3_interpolate_1.interpolateRgbBasis)([
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+ 'rgb(255, 255, 255)',
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+ 'rgb(255, 255, 204)',
39
+ 'rgb(255, 237, 160)',
40
+ 'rgb(254, 217, 118)',
41
+ 'rgb(254, 178, 76)',
42
+ 'rgb(253, 141, 60)',
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+ 'rgb(252, 78, 42)',
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+ 'rgb(227, 26, 28)',
45
+ 'rgb(189, 0, 38)',
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+ 'rgb(128, 0, 38)',
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+ 'rgb(0, 0, 0)',
48
+ ]),
49
+ viridis: viridis_1.default,
50
+ };
51
+ const m = useLogScale ? maxScore : maxScore / 20;
52
+ // @ts-expect-error
53
+ const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
54
+ const scale = useLogScale
55
+ ? (0, d3_scale_1.scaleSequentialLog)(x1).domain([1, m])
56
+ : (0, d3_scale_1.scaleSequential)(x1).domain([0, m]);
57
+ ctx.save();
58
+ if (region.reversed === true) {
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+ ctx.scale(-1, 1);
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+ ctx.translate(-width, 0);
61
+ }
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+ ctx.rotate(-Math.PI / 4);
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+ let start = Date.now();
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+ for (const { bin1, bin2, counts } of features) {
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+ ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', {
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+ count: counts,
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+ maxScore,
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+ baseColor,
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+ scale,
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+ useLogScale,
71
+ });
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+ ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
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+ if (+Date.now() - start > 400) {
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+ await (0, util_1.abortBreakPoint)(signal);
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+ start = +Date.now();
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+ }
77
+ }
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+ ctx.restore();
79
+ }
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+ return undefined;
81
+ }
package/dist/LinearHicDisplay/model.d.ts CHANGED
@@ -33,7 +33,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
33
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  }, {
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  renderInProgress: AbortController | undefined;
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  filled: boolean;
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- reactElement: import("react").ReactElement | undefined;
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+ reactElement: React.ReactElement /**
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+ * #getter
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+ */ | undefined;
37
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  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
38
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  layout: any;
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  status: string;
@@ -46,10 +48,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
46
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  * #method
47
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  */: unknown;
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  reload: () => void;
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- message: import("react").ReactNode;
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+ message: React.ReactNode;
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  filled?: boolean;
51
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  status?: string;
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- reactElement?: import("react").ReactElement;
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+ reactElement?: React.ReactElement;
53
55
  };
54
56
  }) => import("react").JSX.Element | undefined;
55
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  renderProps: any;
@@ -60,7 +62,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
60
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  setLoading(abortController: AbortController): void;
61
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  setMessage(messageText: string): void;
62
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  setRendered(props: {
63
- reactElement: import("react").ReactElement;
65
+ reactElement: React.ReactElement;
64
66
  features: Map<string, import("@jbrowse/core/util").Feature>;
65
67
  layout: any;
66
68
  maxHeightReached: boolean;
@@ -109,7 +111,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
109
111
  error: unknown;
110
112
  message: string | undefined;
111
113
  } & {
112
- readonly RenderingComponent: import("react").FC<{
114
+ readonly RenderingComponent: React.FC<{
113
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  model: {
114
116
  id: string;
115
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  type: string;
@@ -132,7 +134,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
132
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  onHorizontalScroll?: () => void;
133
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  blockState?: Record<string, any>;
134
136
  }>;
135
- readonly DisplayBlurb: import("react").FC<{
137
+ readonly DisplayBlurb: React.FC<{
136
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  model: {
137
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  id: string;
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  type: string;
@@ -155,7 +157,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
155
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  readonly parentTrack: any;
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  renderProps(): any;
157
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  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
158
- readonly DisplayMessageComponent: undefined | import("react").FC<any>;
160
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
159
161
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
160
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  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
161
163
  regionCannotBeRendered(): null;
@@ -201,13 +203,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
201
203
  featureIdUnderMouse: undefined | string;
202
204
  contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
203
205
  } & {
206
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
204
207
  readonly blockType: "dynamicBlocks" | "staticBlocks";
205
208
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
206
209
  } & {
207
210
  readonly renderDelay: number;
208
- readonly TooltipComponent: import("react").FC<any>;
211
+ readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
209
212
  readonly selectedFeatureId: string | undefined;
210
- readonly DisplayMessageComponent: undefined | import("react").FC<any>;
211
213
  } & {
212
214
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
213
215
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -307,7 +309,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
307
309
  }, {
308
310
  renderInProgress: AbortController | undefined;
309
311
  filled: boolean;
310
- reactElement: import("react").ReactElement | undefined;
312
+ reactElement: React.ReactElement /**
313
+ * #getter
314
+ */ | undefined;
311
315
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
312
316
  layout: any;
313
317
  status: string;
@@ -320,10 +324,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
320
324
  * #method
321
325
  */: unknown;
322
326
  reload: () => void;
323
- message: import("react").ReactNode;
327
+ message: React.ReactNode;
324
328
  filled?: boolean;
325
329
  status?: string;
326
- reactElement?: import("react").ReactElement;
330
+ reactElement?: React.ReactElement;
327
331
  };
328
332
  }) => import("react").JSX.Element | undefined;
329
333
  renderProps: any;
@@ -334,7 +338,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
334
338
  setLoading(abortController: AbortController): void;
335
339
  setMessage(messageText: string): void;
336
340
  setRendered(props: {
337
- reactElement: import("react").ReactElement;
341
+ reactElement: React.ReactElement;
338
342
  features: Map<string, import("@jbrowse/core/util").Feature>;
339
343
  layout: any;
340
344
  maxHeightReached: boolean;
@@ -376,8 +380,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
376
380
  type: string;
377
381
  id: string;
378
382
  configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
379
- rpcDriverName: string | undefined;
380
383
  heightPreConfig: number | undefined;
384
+ rpcDriverName: string | undefined;
381
385
  userBpPerPxLimit: number | undefined;
382
386
  userByteSizeLimit: number | undefined;
383
387
  } & import("mobx-state-tree")._NotCustomized>;
package/esm/HicRenderer/HicRenderer.d.ts CHANGED
@@ -28,7 +28,6 @@ export type ResultsSerialized = ServerSideResultsSerialized;
28
28
  export type ResultsDeserialized = ServerSideResultsDeserialized;
29
29
  export default class HicRenderer extends ServerSideRendererType {
30
30
  supportsSVG: boolean;
31
- makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;
32
31
  render(renderProps: RenderArgsDeserialized): Promise<{
33
32
  height: any;
34
33
  width: number;
@@ -38,7 +37,7 @@ export default class HicRenderer extends ServerSideRendererType {
38
37
  } | {
39
38
  height: any;
40
39
  width: number;
41
- reactElement: import("react").JSX.Element;
40
+ reactElement: React.JSX.Element;
42
41
  html?: string;
43
42
  } | {
44
43
  height: any;
package/esm/HicRenderer/HicRenderer.js CHANGED
@@ -1,96 +1,25 @@
1
1
  import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
2
- import { abortBreakPoint } from '@jbrowse/core/util';
3
2
  import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils';
4
3
  import { toArray } from 'rxjs/operators';
5
4
  import { readConfObject } from '@jbrowse/core/configuration';
6
5
  import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
7
- import { colord } from '@jbrowse/core/util/colord';
8
6
  import { firstValueFrom } from 'rxjs';
9
- import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
10
- import interpolateViridis from './viridis';
11
- import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
12
7
  export default class HicRenderer extends ServerSideRendererType {
13
8
  constructor() {
14
9
  super(...arguments);
15
10
  this.supportsSVG = true;
16
11
  }
17
- async makeImageData(ctx, props) {
18
- const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, } = props;
19
- const region = regions[0];
20
- const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
21
- const res = await dataAdapter.getResolution(bpPerPx / resolution);
22
- const width = (region.end - region.start) / bpPerPx;
23
- const w = res / (bpPerPx * Math.sqrt(2));
24
- const baseColor = colord(readConfObject(config, 'baseColor'));
25
- const offset = Math.floor(region.start / res);
26
- if (features.length) {
27
- let maxScore = 0;
28
- let minBin = 0;
29
- let maxBin = 0;
30
- await abortBreakPoint(signal);
31
- for (const { bin1, bin2, counts } of features) {
32
- maxScore = Math.max(counts, maxScore);
33
- minBin = Math.min(Math.min(bin1, bin2), minBin);
34
- maxBin = Math.max(Math.max(bin1, bin2), maxBin);
35
- }
36
- await abortBreakPoint(signal);
37
- const colorSchemes = {
38
- juicebox: ['rgba(0,0,0,0)', 'red'],
39
- fall: interpolateRgbBasis([
40
- 'rgb(255, 255, 255)',
41
- 'rgb(255, 255, 204)',
42
- 'rgb(255, 237, 160)',
43
- 'rgb(254, 217, 118)',
44
- 'rgb(254, 178, 76)',
45
- 'rgb(253, 141, 60)',
46
- 'rgb(252, 78, 42)',
47
- 'rgb(227, 26, 28)',
48
- 'rgb(189, 0, 38)',
49
- 'rgb(128, 0, 38)',
50
- 'rgb(0, 0, 0)',
51
- ]),
52
- viridis: interpolateViridis,
53
- };
54
- const m = useLogScale ? maxScore : maxScore / 20;
55
- // @ts-expect-error
56
- const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
57
- const scale = useLogScale
58
- ? scaleSequentialLog(x1).domain([1, m])
59
- : scaleSequential(x1).domain([0, m]);
60
- ctx.save();
61
- if (region.reversed === true) {
62
- ctx.scale(-1, 1);
63
- ctx.translate(-width, 0);
64
- }
65
- ctx.rotate(-Math.PI / 4);
66
- let start = Date.now();
67
- for (const { bin1, bin2, counts } of features) {
68
- ctx.fillStyle = readConfObject(config, 'color', {
69
- count: counts,
70
- maxScore,
71
- baseColor,
72
- scale,
73
- useLogScale,
74
- });
75
- ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
76
- if (+Date.now() - start > 400) {
77
- await abortBreakPoint(signal);
78
- start = +Date.now();
79
- }
80
- }
81
- ctx.restore();
82
- }
83
- return undefined;
84
- }
85
12
  async render(renderProps) {
86
13
  const { config, regions, bpPerPx } = renderProps;
87
14
  const region = regions[0];
88
15
  const width = (region.end - region.start) / bpPerPx;
89
16
  const height = readConfObject(config, 'maxHeight');
90
17
  const features = await this.getFeatures(renderProps);
91
- const res = await renderToAbstractCanvas(width, height, renderProps, ctx => this.makeImageData(ctx, {
18
+ const { makeImageData } = await import('./makeImageData');
19
+ const res = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData(ctx, {
92
20
  ...renderProps,
93
21
  features,
22
+ pluginManager: this.pluginManager,
94
23
  }));
95
24
  const results = await super.render({
96
25
  ...renderProps,
package/esm/HicRenderer/makeImageData.d.ts ADDED
@@ -0,0 +1,10 @@
1
+ import { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
2
+ import { Region } from '@jbrowse/core/util/types';
3
+ import PluginManager from '@jbrowse/core/PluginManager';
4
+ import { RenderArgsDeserializedWithFeatures } from './HicRenderer';
5
+ export interface RenderArgs extends ServerSideRenderArgs {
6
+ regions: Region[];
7
+ }
8
+ export declare function makeImageData(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures & {
9
+ pluginManager: PluginManager;
10
+ }): Promise<undefined>;
package/esm/HicRenderer/makeImageData.js ADDED
@@ -0,0 +1,75 @@
1
+ import { abortBreakPoint } from '@jbrowse/core/util';
2
+ import { readConfObject } from '@jbrowse/core/configuration';
3
+ import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
4
+ import { colord } from '@jbrowse/core/util/colord';
5
+ import { scaleSequential, scaleSequentialLog, } from '@mui/x-charts-vendor/d3-scale';
6
+ import { interpolateRgbBasis } from '@mui/x-charts-vendor/d3-interpolate';
7
+ import interpolateViridis from './viridis';
8
+ export async function makeImageData(ctx, props) {
9
+ const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
10
+ const region = regions[0];
11
+ const { dataAdapter } = await getAdapter(pluginManager, sessionId, adapterConfig);
12
+ const res = await dataAdapter.getResolution(bpPerPx / resolution);
13
+ const width = (region.end - region.start) / bpPerPx;
14
+ const w = res / (bpPerPx * Math.sqrt(2));
15
+ const baseColor = colord(readConfObject(config, 'baseColor'));
16
+ const offset = Math.floor(region.start / res);
17
+ if (features.length) {
18
+ let maxScore = 0;
19
+ let minBin = 0;
20
+ let maxBin = 0;
21
+ await abortBreakPoint(signal);
22
+ for (const { bin1, bin2, counts } of features) {
23
+ maxScore = Math.max(counts, maxScore);
24
+ minBin = Math.min(Math.min(bin1, bin2), minBin);
25
+ maxBin = Math.max(Math.max(bin1, bin2), maxBin);
26
+ }
27
+ await abortBreakPoint(signal);
28
+ const colorSchemes = {
29
+ juicebox: ['rgba(0,0,0,0)', 'red'],
30
+ fall: interpolateRgbBasis([
31
+ 'rgb(255, 255, 255)',
32
+ 'rgb(255, 255, 204)',
33
+ 'rgb(255, 237, 160)',
34
+ 'rgb(254, 217, 118)',
35
+ 'rgb(254, 178, 76)',
36
+ 'rgb(253, 141, 60)',
37
+ 'rgb(252, 78, 42)',
38
+ 'rgb(227, 26, 28)',
39
+ 'rgb(189, 0, 38)',
40
+ 'rgb(128, 0, 38)',
41
+ 'rgb(0, 0, 0)',
42
+ ]),
43
+ viridis: interpolateViridis,
44
+ };
45
+ const m = useLogScale ? maxScore : maxScore / 20;
46
+ // @ts-expect-error
47
+ const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
48
+ const scale = useLogScale
49
+ ? scaleSequentialLog(x1).domain([1, m])
50
+ : scaleSequential(x1).domain([0, m]);
51
+ ctx.save();
52
+ if (region.reversed === true) {
53
+ ctx.scale(-1, 1);
54
+ ctx.translate(-width, 0);
55
+ }
56
+ ctx.rotate(-Math.PI / 4);
57
+ let start = Date.now();
58
+ for (const { bin1, bin2, counts } of features) {
59
+ ctx.fillStyle = readConfObject(config, 'color', {
60
+ count: counts,
61
+ maxScore,
62
+ baseColor,
63
+ scale,
64
+ useLogScale,
65
+ });
66
+ ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
67
+ if (+Date.now() - start > 400) {
68
+ await abortBreakPoint(signal);
69
+ start = +Date.now();
70
+ }
71
+ }
72
+ ctx.restore();
73
+ }
74
+ return undefined;
75
+ }
package/esm/LinearHicDisplay/model.d.ts CHANGED
@@ -33,7 +33,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
33
33
  }, {
34
34
  renderInProgress: AbortController | undefined;
35
35
  filled: boolean;
36
- reactElement: import("react").ReactElement | undefined;
36
+ reactElement: React.ReactElement /**
37
+ * #getter
38
+ */ | undefined;
37
39
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
38
40
  layout: any;
39
41
  status: string;
@@ -46,10 +48,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
46
48
  * #method
47
49
  */: unknown;
48
50
  reload: () => void;
49
- message: import("react").ReactNode;
51
+ message: React.ReactNode;
50
52
  filled?: boolean;
51
53
  status?: string;
52
- reactElement?: import("react").ReactElement;
54
+ reactElement?: React.ReactElement;
53
55
  };
54
56
  }) => import("react").JSX.Element | undefined;
55
57
  renderProps: any;
@@ -60,7 +62,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
60
62
  setLoading(abortController: AbortController): void;
61
63
  setMessage(messageText: string): void;
62
64
  setRendered(props: {
63
- reactElement: import("react").ReactElement;
65
+ reactElement: React.ReactElement;
64
66
  features: Map<string, import("@jbrowse/core/util").Feature>;
65
67
  layout: any;
66
68
  maxHeightReached: boolean;
@@ -109,7 +111,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
109
111
  error: unknown;
110
112
  message: string | undefined;
111
113
  } & {
112
- readonly RenderingComponent: import("react").FC<{
114
+ readonly RenderingComponent: React.FC<{
113
115
  model: {
114
116
  id: string;
115
117
  type: string;
@@ -132,7 +134,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
132
134
  onHorizontalScroll?: () => void;
133
135
  blockState?: Record<string, any>;
134
136
  }>;
135
- readonly DisplayBlurb: import("react").FC<{
137
+ readonly DisplayBlurb: React.FC<{
136
138
  model: {
137
139
  id: string;
138
140
  type: string;
@@ -155,7 +157,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
155
157
  readonly parentTrack: any;
156
158
  renderProps(): any;
157
159
  readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
158
- readonly DisplayMessageComponent: undefined | import("react").FC<any>;
160
+ readonly DisplayMessageComponent: undefined | React.FC<any>;
159
161
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
160
162
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
161
163
  regionCannotBeRendered(): null;
@@ -201,13 +203,13 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
201
203
  featureIdUnderMouse: undefined | string;
202
204
  contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
203
205
  } & {
206
+ readonly DisplayMessageComponent: import("react").FC<any> | undefined;
204
207
  readonly blockType: "dynamicBlocks" | "staticBlocks";
205
208
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
206
209
  } & {
207
210
  readonly renderDelay: number;
208
- readonly TooltipComponent: import("react").FC<any>;
211
+ readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
209
212
  readonly selectedFeatureId: string | undefined;
210
- readonly DisplayMessageComponent: undefined | import("react").FC<any>;
211
213
  } & {
212
214
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
213
215
  readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -307,7 +309,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
307
309
  }, {
308
310
  renderInProgress: AbortController | undefined;
309
311
  filled: boolean;
310
- reactElement: import("react").ReactElement | undefined;
312
+ reactElement: React.ReactElement /**
313
+ * #getter
314
+ */ | undefined;
311
315
  features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
312
316
  layout: any;
313
317
  status: string;
@@ -320,10 +324,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
320
324
  * #method
321
325
  */: unknown;
322
326
  reload: () => void;
323
- message: import("react").ReactNode;
327
+ message: React.ReactNode;
324
328
  filled?: boolean;
325
329
  status?: string;
326
- reactElement?: import("react").ReactElement;
330
+ reactElement?: React.ReactElement;
327
331
  };
328
332
  }) => import("react").JSX.Element | undefined;
329
333
  renderProps: any;
@@ -334,7 +338,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
334
338
  setLoading(abortController: AbortController): void;
335
339
  setMessage(messageText: string): void;
336
340
  setRendered(props: {
337
- reactElement: import("react").ReactElement;
341
+ reactElement: React.ReactElement;
338
342
  features: Map<string, import("@jbrowse/core/util").Feature>;
339
343
  layout: any;
340
344
  maxHeightReached: boolean;
@@ -376,8 +380,8 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
376
380
  type: string;
377
381
  id: string;
378
382
  configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
379
- rpcDriverName: string | undefined;
380
383
  heightPreConfig: number | undefined;
384
+ rpcDriverName: string | undefined;
381
385
  userBpPerPxLimit: number | undefined;
382
386
  userByteSizeLimit: number | undefined;
383
387
  } & import("mobx-state-tree")._NotCustomized>;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-hic",
3
- "version": "2.15.0",
3
+ "version": "2.15.2",
4
4
  "description": "JBrowse 2 hic adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -55,5 +55,5 @@
55
55
  "publishConfig": {
56
56
  "access": "public"
57
57
  },
58
- "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
58
+ "gitHead": "8a58cefbfe39af4c97bcb6ead354d72c9fef9224"
59
59
  }