@jbrowse/plugin-hic 2.6.1

package/esm/index.js

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+import Plugin from '@jbrowse/core/Plugin';
+import HicRendererF from './HicRenderer';
+import HicTrackF from './HicTrack';
+import LinearHicDisplayF from './LinearHicDisplay';
+import HicAdapterF from './HicAdapter';
+import { getFileName, } from '@jbrowse/core/util/tracks';
+export default class HicPlugin extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'HicPlugin';
+    }
+    install(pluginManager) {
+        HicAdapterF(pluginManager);
+        HicRendererF(pluginManager);
+        HicTrackF(pluginManager);
+        LinearHicDisplayF(pluginManager);
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.hic/i;
+                const adapterName = 'HicAdapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    hicLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+            return (adapterName) => {
+                if (adapterName === 'HicAdapter') {
+                    return 'HicTrack';
+                }
+                return trackTypeGuesser(adapterName);
+            };
+        });
+    }
+    configure(pluginManager) {
+        pluginManager.jexl.addFunction('alpha', (color, value) => color.alpha(value));
+        pluginManager.jexl.addFunction('hsl', (color) => color.hsl());
+        pluginManager.jexl.addFunction('colorString', (color) => color.string());
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,60 @@
+{
+  "name": "@jbrowse/plugin-hic",
+  "version": "2.6.1",
+  "description": "JBrowse 2 hic adapters, tracks, etc.",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/hic"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "dist/index.js",
+  "files": [
+    "dist",
+    "src",
+    "esm"
+  ],
+  "scripts": {
+    "build": "npm-run-all build:*",
+    "test": "cd ../..; jest plugins/hic",
+    "prepublishOnly": "yarn test",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
+  },
+  "dependencies": {
+    "color": "^3.1.3",
+    "hic-straw": "^2.0.3"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "react": ">=16.8.0",
+    "rxjs": "^7.0.0"
+  },
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}

package/src/HicAdapter/HicAdapter.ts

@@ -0,0 +1,150 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { Region, FileLocation } from '@jbrowse/core/util/types'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { openLocation } from '@jbrowse/core/util/io'
+import type { GenericFilehandle } from 'generic-filehandle'
+import HicStraw from 'hic-straw'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+interface ContactRecord {
+  bin1: number
+  bin2: number
+  counts: number
+}
+
+interface HicMetadata {
+  chromosomes: {
+    name: string
+    length: number
+    id: number
+  }[]
+  resolutions: number[]
+}
+interface Ref {
+  chr: string
+  start: number
+  end: number
+}
+
+interface HicOptions extends BaseOptions {
+  resolution?: number
+  bpPerPx?: number
+}
+
+// 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
+class GenericFilehandleWrapper {
+  constructor(private filehandle: GenericFilehandle) {}
+
+  async read(position: number, length: number) {
+    const { buffer: b, bytesRead } = await this.filehandle.read(
+      Buffer.allocUnsafe(length),
+      0,
+      length,
+      position,
+    )
+    // xref https://stackoverflow.com/a/31394257/2129219
+    return b.buffer.slice(b.byteOffset, b.byteOffset + bytesRead)
+  }
+}
+export function openFilehandleWrapper(
+  location: FileLocation,
+  pluginManager?: PluginManager,
+) {
+  return new GenericFilehandleWrapper(openLocation(location, pluginManager))
+}
+
+interface HicParser {
+  getContactRecords: (
+    normalize: string,
+    ref: Ref,
+    ref2: Ref,
+    units: string,
+    binsize: number,
+  ) => Promise<ContactRecord[]>
+  getMetaData: () => Promise<HicMetadata>
+}
+
+export default class HicAdapter extends BaseFeatureDataAdapter {
+  private hic: HicParser
+
+  public constructor(
+    config: AnyConfigurationModel,
+    getSubAdapter?: getSubAdapterType,
+    pluginManager?: PluginManager,
+  ) {
+    super(config, getSubAdapter, pluginManager)
+    const hicLocation = this.getConf('hicLocation')
+    this.hic = new HicStraw({
+      file: openFilehandleWrapper(hicLocation, this.pluginManager),
+    })
+  }
+
+  private async setup(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
+    statusCallback('Downloading .hic header')
+    const result = await this.hic.getMetaData()
+    statusCallback('')
+    return result
+  }
+
+  public async getHeader(opts?: BaseOptions) {
+    const ret = await this.setup(opts)
+    const { chromosomes, ...rest } = ret
+    return rest
+  }
+
+  async getRefNames(opts?: BaseOptions) {
+    const metadata = await this.setup(opts)
+    return metadata.chromosomes.map(chr => chr.name)
+  }
+
+  async getResolution(bpPerPx: number, opts?: BaseOptions) {
+    const { resolutions } = await this.setup(opts)
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    let chosenResolution = resolutions.at(-1)!
+
+    for (let i = resolutions.length - 1; i >= 0; i -= 1) {
+      const r = resolutions[i]
+      if (r <= 2 * bpPerPx) {
+        chosenResolution = r
+      }
+    }
+    return chosenResolution
+  }
+
+  getFeatures(region: Region, opts: HicOptions = {}) {
+    return ObservableCreate<ContactRecord>(async observer => {
+      const { refName: chr, start, end } = region
+      const { resolution, bpPerPx = 1, statusCallback = () => {} } = opts
+      const res = await this.getResolution(bpPerPx / (resolution || 1000), opts)
+      statusCallback('Downloading .hic data')
+
+      const records = await this.hic.getContactRecords(
+        'KR',
+        { start, chr, end },
+        { start, chr, end },
+        'BP',
+        res,
+      )
+      records.forEach(record => {
+        observer.next(record)
+      })
+      statusCallback('')
+      observer.complete()
+    }, opts.signal) as any // eslint-disable-line @typescript-eslint/no-explicit-any
+  }
+
+  // don't do feature stats estimation, similar to bigwigadapter
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
+    return { featureDensity: 0 }
+  }
+
+  freeResources(/* { region } */): void {}
+}

package/src/HicAdapter/configSchema.ts

@@ -0,0 +1,26 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config HicAdapter
+ * #category adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const HicAdapter = ConfigurationSchema(
+  'HicAdapter',
+  {
+    /**
+     * #slot
+     */
+    hicLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.hic',
+        locationType: 'UriLocation',
+      },
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default HicAdapter

package/src/HicAdapter/index.ts

@@ -0,0 +1,15 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'HicAdapter',
+        displayName: 'Hi-C adapter',
+        configSchema,
+        getAdapterClass: () => import('./HicAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/HicRenderer/HicRenderer.tsx

@@ -0,0 +1,170 @@
+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 { abortBreakPoint } from '@jbrowse/core/util'
+import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'
+import { toArray } from 'rxjs/operators'
+import { readConfObject } from '@jbrowse/core/configuration'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+interface HicFeature {
+  bin1: number
+  bin2: number
+  counts: number
+}
+
+interface HicDataAdapter extends BaseFeatureDataAdapter {
+  getResolution: (bp: number) => Promise<number>
+}
+
+export interface RenderArgs extends ServerSideRenderArgs {
+  regions: Region[]
+}
+
+export interface RenderArgsDeserialized
+  extends ServerSideRenderArgsDeserialized {
+  regions: Region[]
+  dataAdapter: HicDataAdapter
+  bpPerPx: number
+  highResolutionScaling: number
+  resolution: number
+  adapterConfig: AnyConfigurationModel
+}
+
+export interface RenderArgsDeserializedWithFeatures
+  extends RenderArgsDeserialized {
+  features: HicFeature[]
+}
+
+export type ResultsSerialized = ServerSideResultsSerialized
+
+export type ResultsDeserialized = ServerSideResultsDeserialized
+
+export default class HicRenderer extends ServerSideRendererType {
+  supportsSVG = true
+
+  async makeImageData(
+    ctx: CanvasRenderingContext2D,
+    props: RenderArgsDeserializedWithFeatures,
+  ) {
+    const {
+      features,
+      config,
+      bpPerPx,
+      signal,
+      resolution,
+      sessionId,
+      adapterConfig,
+      regions,
+    } = props
+    const [region] = regions
+    const { dataAdapter } = await getAdapter(
+      this.pluginManager,
+      sessionId,
+      adapterConfig,
+    )
+    const res = await (dataAdapter as HicDataAdapter).getResolution(
+      bpPerPx / resolution,
+    )
+
+    const Color = await import('color').then(f => f.default)
+    const w = res / (bpPerPx * Math.sqrt(2))
+    const baseColor = Color(readConfObject(config, 'baseColor'))
+    if (features.length) {
+      const offset = features[0].bin1
+      let maxScore = 0
+      let minBin = 0
+      let maxBin = 0
+      await abortBreakPoint(signal)
+      for (let i = 0; i < features.length; i++) {
+        const { bin1, bin2, counts } = features[i]
+        maxScore = Math.max(counts, maxScore)
+        minBin = Math.min(Math.min(bin1, bin2), minBin)
+        maxBin = Math.max(Math.max(bin1, bin2), maxBin)
+      }
+      await abortBreakPoint(signal)
+      function horizontallyFlip() {
+        ctx.scale(-1, 1)
+        const width = (region.end - region.start) / bpPerPx
+        ctx.translate(-width, 0)
+      }
+      if (region.reversed === true) {
+        horizontallyFlip()
+      }
+      ctx.rotate(-Math.PI / 4)
+      let start = Date.now()
+      for (let i = 0; i < features.length; i++) {
+        const { bin1, bin2, counts } = features[i]
+        ctx.fillStyle = readConfObject(config, 'color', {
+          count: counts,
+          maxScore,
+          baseColor,
+        })
+        ctx.fillRect((bin1 - offset) * w, (bin2 - offset) * w, w, w)
+        if (+Date.now() - start > 400) {
+          await abortBreakPoint(signal)
+          start = +Date.now()
+        }
+      }
+    }
+  }
+
+  async render(renderProps: RenderArgsDeserialized) {
+    const { config, regions, bpPerPx } = renderProps
+    const [region] = regions
+    const width = (region.end - region.start) / bpPerPx
+    const height = readConfObject(config, 'maxHeight')
+    const features = await this.getFeatures(renderProps)
+
+    const res = await renderToAbstractCanvas(width, height, renderProps, ctx =>
+      this.makeImageData(ctx, {
+        ...renderProps,
+        features,
+      }),
+    )
+    const results = await super.render({
+      ...renderProps,
+      ...res,
+      features,
+      region: renderProps.regions[0],
+      height,
+      width,
+    })
+
+    return {
+      ...results,
+      ...res,
+      height,
+      width,
+    }
+  }
+
+  async getFeatures(args: RenderArgsDeserialized) {
+    const { regions, sessionId, adapterConfig } = args
+    const { dataAdapter } = await getAdapter(
+      this.pluginManager,
+      sessionId,
+      adapterConfig,
+    )
+    const features = await (dataAdapter as BaseFeatureDataAdapter)
+      .getFeatures(regions[0], args)
+      .pipe(toArray())
+      .toPromise()
+    // cast to any to avoid return-type conflict, because the
+    // types of features returned by our getFeatures are quite
+    // different from the base interface
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    return features as any
+  }
+}
+
+export {
+  type RenderArgsSerialized,
+  type RenderResults,
+} from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType'

package/src/HicRenderer/components/HicRendering.test.tsx

@@ -0,0 +1,21 @@
+import React from 'react'
+import { render } from '@testing-library/react'
+import HicRendering from './HicRendering'
+
+// these tests do very little, let's try to expand them at some point
+test('one', () => {
+  const { container } = render(
+    <HicRendering
+      width={500}
+      height={500}
+      regions={[{ assemblyName: 'volvox', refName: 'zonk', start: 1, end: 3 }]}
+      bpPerPx={3}
+      blockKey="test"
+      /*
+      // @ts-expect-error */
+      displayModel={{}}
+    />,
+  )
+
+  expect(container.firstChild).toMatchSnapshot()
+})

package/src/HicRenderer/components/HicRendering.tsx

@@ -0,0 +1,24 @@
+import React from 'react'
+import { Region } from '@jbrowse/core/util/types'
+import { PrerenderedCanvas } from '@jbrowse/core/ui'
+import { observer } from 'mobx-react'
+
+export default observer(function HicRendering(props: {
+  blockKey: string
+  width: number
+  height: number
+  regions: Region[]
+  bpPerPx: number
+}) {
+  const { width, height } = props
+  const canvasWidth = Math.ceil(width)
+  // need to call this in render so we get the right observer behavior
+  return (
+    <div style={{ position: 'relative', width: canvasWidth, height }}>
+      <PrerenderedCanvas
+        {...props}
+        style={{ position: 'absolute', left: 0, top: 0 }}
+      />
+    </div>
+  )
+})

package/src/HicRenderer/components/__snapshots__/HicRendering.test.tsx.snap

@@ -0,0 +1,14 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`one 1`] = `
+<div
+  style="position: relative; width: 500px; height: 500px;"
+>
+  <canvas
+    data-testid="prerendered_canvas_test"
+    height="500"
+    style="width: 500px; height: 500px; position: absolute; left: 0px; top: 0px;"
+    width="500"
+  />
+</div>
+`;

package/src/HicRenderer/configSchema.ts

@@ -0,0 +1,42 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config HicRenderer
+ * #category renderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const HicRenderer = 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:colorString(hsl(alpha(baseColor,min(1,count/(maxScore/20)))))`,
+      contextVariable: ['count', 'maxScore', 'baseColor'],
+    },
+
+    /**
+     * #slot
+     */
+    maxHeight: {
+      type: 'integer',
+      description: 'the maximum height to be used in a hic rendering',
+      defaultValue: 600,
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default HicRenderer

package/src/HicRenderer/index.ts

@@ -0,0 +1,17 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import ReactComponent from './components/HicRendering'
+import configSchema from './configSchema'
+import HicRenderer from './HicRenderer'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addRendererType(
+    () =>
+      new HicRenderer({
+        name: 'HicRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
+  )
+}

package/src/HicTrack/configSchema.ts

@@ -0,0 +1,23 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config HicTrack
+ * #category track
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = (pluginManager: PluginManager) =>
+  ConfigurationSchema(
+    'HicTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
+  )
+
+export default configSchema

package/src/HicTrack/index.ts

@@ -0,0 +1,16 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
+import configSchemaF from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addTrackType(() => {
+    const configSchema = configSchemaF(pluginManager)
+    return new TrackType({
+      name: 'HicTrack',
+      displayName: 'Hi-C track',
+      configSchema,
+      stateModel: createBaseTrackModel(pluginManager, 'HicTrack', configSchema),
+    })
+  })
+}

package/src/LinearHicDisplay/configSchema.ts

@@ -0,0 +1,33 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
+import { Instance } from 'mobx-state-tree'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config LinearHicDisplay
+ * #category display
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const HicTrackConfigFactory = (pluginManager: PluginManager) => {
+  return ConfigurationSchema(
+    'LinearHicDisplay',
+    {
+      /**
+       * #slot
+       */
+      renderer: pluginManager.getRendererType('HicRenderer').configSchema,
+    },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
+  )
+}
+
+export type HicTrackConfigModel = ReturnType<typeof HicTrackConfigFactory>
+export type HicTrackConfig = Instance<HicTrackConfigModel>
+export default HicTrackConfigFactory