@jbrowse/plugin-hic 2.17.0 → 2.18.0

package/dist/HicAdapter/HicAdapter.d.ts

@@ -1,8 +1,9 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Region } from '@jbrowse/core/util/types';
 interface HicOptions extends BaseOptions {
     resolution?: number;
     bpPerPx?: number;

package/dist/HicAdapter/HicAdapter.js

@@ -4,10 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const hic_straw_1 = __importDefault(require("hic-straw"));
-const util_1 = require("@jbrowse/core/util");
-// locals
 const HicFilehandle_1 = require("./HicFilehandle");
 class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -22,7 +21,6 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getHeader(opts) {
         const { chromosomes, ...rest } = await this.setup(opts);
-        // @ts-expect-error
         const norms = await this.hic.getNormalizationOptions();
         return { ...rest, norms };
     }
@@ -54,14 +52,13 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
-    // don't do feature stats estimation, similar to bigwigadapter
     async getMultiRegionFeatureDensityStats(_regions) {
         return {
             featureDensity: 0,
         };
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = HicAdapter;

package/dist/HicAdapter/HicFilehandle.d.ts

@@ -1,6 +1,6 @@
-import { FileLocation } from '@jbrowse/core/util';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { FileLocation } from '@jbrowse/core/util';
 import type { GenericFilehandle } from 'generic-filehandle';
-import PluginManager from '@jbrowse/core/PluginManager';
 declare class HicFilehandle {
     private filehandle;
     constructor(filehandle: GenericFilehandle);

package/dist/HicAdapter/HicFilehandle.js

@@ -1,13 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.openHicFilehandle = openHicFilehandle;
-const io_1 = require("@jbrowse/core/util/io");
 const buffer_1 = require("buffer");
-// wraps generic-filehandle so the read function only takes a position and
-// length
-//
-// in some ways, generic-filehandle wishes it was just this but it has
-// to adapt to the node.js fs promises API
+const io_1 = require("@jbrowse/core/util/io");
 class HicFilehandle {
     constructor(filehandle) {
         this.filehandle = filehandle;

package/dist/HicAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     hicLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const HicAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     resolutionMultiplier: {
         type: string;
         defaultValue: number;

package/dist/HicAdapter/configSchema.js

@@ -1,15 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config HicAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HicAdapter = (0, configuration_1.ConfigurationSchema)('HicAdapter', {
-    /**
-     * #slot
-     */
     hicLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -17,9 +10,6 @@ const HicAdapter = (0, configuration_1.ConfigurationSchema)('HicAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     resolutionMultiplier: {
         type: 'number',
         defaultValue: 1,

package/dist/HicAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function HicAdapterF(pluginManager: PluginManager): void;

package/dist/HicRenderer/HicRenderer.d.ts

@@ -1,7 +1,8 @@
-import ServerSideRendererType, { RenderArgs as ServerSideRenderArgs, RenderArgsDeserialized as ServerSideRenderArgsDeserialized, ResultsSerialized as ServerSideResultsSerialized, ResultsDeserialized as ServerSideResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
-import { Region } from '@jbrowse/core/util/types';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import ServerSideRendererType from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { RenderArgs as ServerSideRenderArgs, RenderArgsDeserialized as ServerSideRenderArgsDeserialized, ResultsDeserialized as ServerSideResultsDeserialized, ResultsSerialized as ServerSideResultsSerialized } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { Region } from '@jbrowse/core/util/types';
 interface HicFeature {
     bin1: number;
     bin2: number;

package/dist/HicRenderer/HicRenderer.js

@@ -26,12 +26,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const ServerSideRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType"));
-const offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils");
-const operators_1 = require("rxjs/operators");
 const configuration_1 = require("@jbrowse/core/configuration");
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const ServerSideRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType"));
+const offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils");
 const rxjs_1 = require("rxjs");
+const operators_1 = require("rxjs/operators");
 class HicRenderer extends ServerSideRendererType_1.default {
     constructor() {
         super(...arguments);
@@ -70,9 +70,6 @@ class HicRenderer extends ServerSideRendererType_1.default {
         const features = await (0, rxjs_1.firstValueFrom)(dataAdapter
             .getFeatures(regions[0], args)
             .pipe((0, operators_1.toArray)()));
-        // cast to any to avoid return-type conflict, because the
-        // types of features returned by our getFeatures are quite
-        // different from the base interface
         return features;
     }
 }

package/dist/HicRenderer/components/HicRendering.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
+import type { Region } from '@jbrowse/core/util/types';
 declare const HicRendering: (props: {
     blockKey: string;
     width: number;

package/dist/HicRenderer/components/HicRendering.js

@@ -9,7 +9,6 @@ const mobx_react_1 = require("mobx-react");
 const HicRendering = (0, mobx_react_1.observer)(function HicRendering(props) {
     const { width, height } = props;
     const canvasWidth = Math.ceil(width);
-    // need to call this in render so we get the right observer behavior
     return (react_1.default.createElement("div", { style: { position: 'relative', width: canvasWidth, height } },
         react_1.default.createElement(ui_1.PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } })));
 });

package/dist/HicRenderer/configSchema.d.ts

@@ -1,24 +1,15 @@
 declare const HicRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     baseColor: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     color: {
         type: string;
         description: string;
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     maxHeight: {
         type: string;
         description: string;

package/dist/HicRenderer/configSchema.js

@@ -1,32 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config HicRenderer
- * #category renderer
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HicRenderer = (0, configuration_1.ConfigurationSchema)('HicRenderer', {
-    /**
-     * #slot
-     */
     baseColor: {
         type: 'color',
         description: 'base color to be used in the hic alignment',
         defaultValue: '#f00',
     },
-    /**
-     * #slot
-     */
     color: {
         type: 'color',
         description: 'the color of each feature in a hic alignment',
         defaultValue: 'jexl:interpolate(count,scale)',
         contextVariable: ['count', 'maxScore', 'baseColor', 'scale'],
     },
-    /**
-     * #slot
-     */
     maxHeight: {
         type: 'integer',
         description: 'the maximum height to be used in a hic rendering',

package/dist/HicRenderer/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function HicRendererF(pluginManager: PluginManager): void;

package/dist/HicRenderer/index.js

@@ -4,9 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = HicRendererF;
+const HicRenderer_1 = __importDefault(require("./HicRenderer"));
 const HicRendering_1 = __importDefault(require("./components/HicRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-const HicRenderer_1 = __importDefault(require("./HicRenderer"));
 function HicRendererF(pluginManager) {
     pluginManager.addRendererType(() => new HicRenderer_1.default({
         name: 'HicRenderer',

package/dist/HicRenderer/makeImageData.d.ts

@@ -1,7 +1,7 @@
-import { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
-import { Region } from '@jbrowse/core/util/types';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { RenderArgsDeserializedWithFeatures } from './HicRenderer';
+import type { RenderArgsDeserializedWithFeatures } from './HicRenderer';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { RenderArgs as ServerSideRenderArgs } from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType';
+import type { Region } from '@jbrowse/core/util/types';
 export interface RenderArgs extends ServerSideRenderArgs {
     regions: Region[];
 }

package/dist/HicRenderer/makeImageData.js

@@ -4,15 +4,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeImageData = makeImageData;
-const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
 const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const colord_1 = require("@jbrowse/core/util/colord");
-const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const d3_interpolate_1 = require("@mui/x-charts-vendor/d3-interpolate");
+const d3_scale_1 = require("@mui/x-charts-vendor/d3-scale");
 const viridis_1 = __importDefault(require("./viridis"));
 async function makeImageData(ctx, props) {
-    const { features, config, bpPerPx, signal, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
+    const { features, config, bpPerPx, stopToken, resolution, sessionId, adapterConfig, useLogScale, colorScheme, regions, pluginManager, } = props;
     const region = regions[0];
     const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
     const res = await dataAdapter.getResolution(bpPerPx / resolution);
@@ -24,13 +24,13 @@ async function makeImageData(ctx, props) {
         let maxScore = 0;
         let minBin = 0;
         let maxBin = 0;
-        await (0, util_1.abortBreakPoint)(signal);
+        (0, stopToken_1.checkStopToken)(stopToken);
         for (const { bin1, bin2, counts } of features) {
             maxScore = Math.max(counts, maxScore);
             minBin = Math.min(Math.min(bin1, bin2), minBin);
             maxBin = Math.max(Math.max(bin1, bin2), maxBin);
         }
-        await (0, util_1.abortBreakPoint)(signal);
+        (0, stopToken_1.checkStopToken)(stopToken);
         const colorSchemes = {
             juicebox: ['rgba(0,0,0,0)', 'red'],
             fall: (0, d3_interpolate_1.interpolateRgbBasis)([
@@ -49,7 +49,6 @@ async function makeImageData(ctx, props) {
             viridis: viridis_1.default,
         };
         const m = useLogScale ? maxScore : maxScore / 20;
-        // @ts-expect-error
         const x1 = colorSchemes[colorScheme] || colorSchemes.juicebox;
         const scale = useLogScale
             ? (0, d3_scale_1.scaleSequentialLog)(x1).domain([1, m])
@@ -60,7 +59,7 @@ async function makeImageData(ctx, props) {
             ctx.translate(-width, 0);
         }
         ctx.rotate(-Math.PI / 4);
-        let start = Date.now();
+        let start = performance.now();
         for (const { bin1, bin2, counts } of features) {
             ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', {
                 count: counts,
@@ -70,9 +69,9 @@ async function makeImageData(ctx, props) {
                 useLogScale,
             });
             ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w);
-            if (+Date.now() - start > 400) {
-                await (0, util_1.abortBreakPoint)(signal);
-                start = +Date.now();
+            if (performance.now() - start > 400) {
+                (0, stopToken_1.checkStopToken)(stopToken);
+                start = performance.now();
             }
         }
         ctx.restore();

package/dist/HicRenderer/viridis.js

@@ -1,22 +1,5 @@
 "use strict";
-// @ts-nocheck
-// vendored from
-// https://github.com/d3/d3-scale-chromatic/blob/main/src/sequential-multi/viridis.js,
-// license reproduced below
-//
-// Copyright 2010-2024 Mike Bostock
 Object.defineProperty(exports, "__esModule", { value: true });
-// Permission to use, copy, modify, and/or distribute this software for any purpose
-// with or without fee is hereby granted, provided that the above copyright notice
-// and this permission notice appear in all copies.
-//
-// THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-// REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-// FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-// INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-// OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-// TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-// THIS SOFTWARE.
 function colors(specifier) {
     const n = (specifier.length / 6) | 0;
     const colors = new Array(n);

package/dist/HicTrack/configSchema.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;

package/dist/HicTrack/configSchema.js

@@ -2,15 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-/**
- * #config HicTrack
- * #category track
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('HicTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
 });
 exports.default = configSchema;

package/dist/HicTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function HicTrackF(pluginManager: PluginManager): void;

package/dist/LinearHicDisplay/configSchema.d.ts

@@ -1,9 +1,6 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 declare const HicTrackConfigFactory: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     renderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {

package/dist/LinearHicDisplay/configSchema.js

@@ -2,21 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-/**
- * #config LinearHicDisplay
- * #category display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const HicTrackConfigFactory = (pluginManager) => {
     return (0, configuration_1.ConfigurationSchema)('LinearHicDisplay', {
-        /**
-         * #slot
-         */
         renderer: pluginManager.getRendererType('HicRenderer').configSchema,
     }, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });

package/dist/LinearHicDisplay/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function LinearHicDisplayF(pluginManager: PluginManager): void;