@jbrowse/plugin-hic 2.6.1 → 2.6.2

package/dist/HicAdapter/HicAdapter.js

@@ -82,4 +82,3 @@ class HicAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources( /* { region } */) { }
 }
 exports.default = HicAdapter;
-//# sourceMappingURL=HicAdapter.js.map

package/dist/HicAdapter/configSchema.js

@@ -19,4 +19,3 @@ const HicAdapter = (0, configuration_1.ConfigurationSchema)('HicAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = HicAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/HicAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HicAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/HicRenderer/HicRenderer.js

@@ -123,4 +123,3 @@ class HicRenderer extends ServerSideRendererType_1.default {
     }
 }
 exports.default = HicRenderer;
-//# sourceMappingURL=HicRenderer.js.map

package/dist/HicRenderer/components/HicRendering.js

@@ -13,4 +13,3 @@ exports.default = (0, mobx_react_1.observer)(function HicRendering(props) {
     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 } })));
 });
-//# sourceMappingURL=HicRendering.js.map

package/dist/HicRenderer/configSchema.js

@@ -34,4 +34,3 @@ const HicRenderer = (0, configuration_1.ConfigurationSchema)('HicRenderer', {
     },
 }, { explicitlyTyped: true });
 exports.default = HicRenderer;
-//# sourceMappingURL=configSchema.js.map

package/dist/HicRenderer/index.js

@@ -14,4 +14,3 @@ exports.default = (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/HicTrack/configSchema.js

@@ -14,4 +14,3 @@ const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)
     baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
 });
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/HicTrack/index.js

@@ -17,4 +17,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearHicDisplay/configSchema.js

@@ -22,4 +22,3 @@ const HicTrackConfigFactory = (pluginManager) => {
     });
 };
 exports.default = HicTrackConfigFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearHicDisplay/index.js

@@ -21,4 +21,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearHicDisplay/model.js

@@ -92,4 +92,3 @@ exports.default = (configSchema) => mobx_state_tree_1.types
         },
     };
 });
-//# sourceMappingURL=model.js.map

package/dist/index.js

@@ -53,4 +53,3 @@ class HicPlugin extends Plugin_1.default {
     }
 }
 exports.default = HicPlugin;
-//# sourceMappingURL=index.js.map

package/esm/HicAdapter/HicAdapter.js

@@ -74,4 +74,3 @@ export default class HicAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-//# sourceMappingURL=HicAdapter.js.map

package/esm/HicAdapter/configSchema.js

@@ -17,4 +17,3 @@ const HicAdapter = ConfigurationSchema('HicAdapter', {
     },
 }, { explicitlyTyped: true });
 export default HicAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/HicAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./HicAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/HicRenderer/HicRenderer.js

@@ -94,4 +94,3 @@ export default class HicRenderer extends ServerSideRendererType {
         return features;
     }
 }
-//# sourceMappingURL=HicRenderer.js.map

package/esm/HicRenderer/components/HicRendering.js

@@ -8,4 +8,3 @@ export default observer(function HicRendering(props) {
     return (React.createElement("div", { style: { position: 'relative', width: canvasWidth, height } },
         React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } })));
 });
-//# sourceMappingURL=HicRendering.js.map

package/esm/HicRenderer/configSchema.js

@@ -32,4 +32,3 @@ const HicRenderer = ConfigurationSchema('HicRenderer', {
     },
 }, { explicitlyTyped: true });
 export default HicRenderer;
-//# sourceMappingURL=configSchema.js.map

package/esm/HicRenderer/index.js

@@ -9,4 +9,3 @@ export default (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/HicTrack/configSchema.js

@@ -12,4 +12,3 @@ const configSchema = (pluginManager) => ConfigurationSchema('HicTrack', {}, {
     baseConfiguration: createBaseTrackConfig(pluginManager),
 });
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/HicTrack/index.js

@@ -12,4 +12,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearHicDisplay/configSchema.js

@@ -20,4 +20,3 @@ const HicTrackConfigFactory = (pluginManager) => {
     });
 };
 export default HicTrackConfigFactory;
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearHicDisplay/index.js

@@ -16,4 +16,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearHicDisplay/model.js

@@ -90,4 +90,3 @@ export default (configSchema) => types
         },
     };
 });
-//# sourceMappingURL=model.js.map

package/esm/index.js

@@ -47,4 +47,3 @@ export default class HicPlugin extends Plugin {
         pluginManager.jexl.addFunction('colorString', (color) => color.string());
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-hic",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "JBrowse 2 hic adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "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",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -56,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/HicAdapter/HicAdapter.js.map

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package/dist/HicAdapter/configSchema.js.map

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package/dist/HicAdapter/index.js.map

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package/dist/HicRenderer/HicRenderer.js.map

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package/dist/HicRenderer/components/HicRendering.js.map

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package/esm/HicRenderer/HicRenderer.js.map

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package/esm/HicRenderer/components/HicRendering.js.map

@@ -1 +0,0 @@
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package/esm/HicRenderer/configSchema.js.map

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package/esm/HicRenderer/index.js.map

@@ -1 +0,0 @@
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package/esm/HicTrack/configSchema.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HicTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,CAAC,aAA4B,EAAE,EAAE,CACpD,mBAAmB,CACjB,UAAU,EACV,EAAE,EACF;IACE;;OAEG;IACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;CACxD,CACF,CAAA;AAEH,eAAe,YAAY,CAAA"}

package/esm/HicTrack/index.js.map

@@ -1 +0,0 @@
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package/esm/LinearHicDisplay/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/LinearHicDisplay/index.js.map

@@ -1 +0,0 @@
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package/esm/LinearHicDisplay/model.js.map

@@ -1 +0,0 @@
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package/esm/index.js.map

@@ -1 +0,0 @@
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package/src/HicAdapter/HicAdapter.ts

@@ -1,150 +0,0 @@
-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

@@ -1,26 +0,0 @@
-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

@@ -1,15 +0,0 @@
-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

@@ -1,170 +0,0 @@
-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

@@ -1,21 +0,0 @@
-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

@@ -1,24 +0,0 @@
-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

@@ -1,14 +0,0 @@
-// 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

@@ -1,42 +0,0 @@
-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

@@ -1,17 +0,0 @@
-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

@@ -1,23 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,33 +0,0 @@
-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

package/src/LinearHicDisplay/index.ts

@@ -1,21 +0,0 @@
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-
-import configSchemaFactory from './configSchema'
-import stateModelFactory from './model'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearHicDisplay',
-      displayName: 'Hi-C contact matrix display',
-      configSchema,
-      stateModel: stateModelFactory(configSchema),
-      trackType: 'HicTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: BaseLinearDisplayComponent,
-    })
-  })
-}

package/src/LinearHicDisplay/model.ts

@@ -1,104 +0,0 @@
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view'
-import { types, getEnv } from 'mobx-state-tree'
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
-
-/**
- * #stateModel LinearHicDisplay
- * #category display
- * extends `BaseLinearDisplay`
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export default (configSchema: AnyConfigurationSchemaType) =>
-  types
-    .compose(
-      'LinearHicDisplay',
-      BaseLinearDisplay,
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LinearHicDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        resolution: types.optional(types.number, 1),
-      }),
-    )
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        /**
-         * #getter
-         */
-        get blockType() {
-          return 'dynamicBlocks'
-        },
-        /**
-         * #getter
-         */
-        get rendererTypeName() {
-          return 'HicRenderer'
-        },
-        /**
-         * #method
-         */
-        renderProps() {
-          const config = self.rendererType.configSchema.create(
-            getConf(self, 'renderer') || {},
-            getEnv(self),
-          )
-
-          return {
-            ...superRenderProps(),
-            config,
-            rpcDriverName: self.rpcDriverName,
-            displayModel: self,
-            resolution: self.resolution,
-          }
-        },
-      }
-    })
-    .actions(self => ({
-      /**
-       * #action
-       */
-      setResolution(n: number) {
-        self.resolution = n
-      },
-    }))
-    .views(self => {
-      const { trackMenuItems: superTrackMenuItems } = self
-      return {
-        /**
-         * #getter
-         */
-        trackMenuItems() {
-          return [
-            ...superTrackMenuItems(),
-            {
-              label: 'Resolution',
-              subMenu: [
-                {
-                  label: 'Finer resolution',
-                  onClick: () => {
-                    self.setResolution(self.resolution * 2)
-                  },
-                },
-                {
-                  label: 'Coarser resolution',
-                  onClick: () => {
-                    self.setResolution(self.resolution / 2)
-                  },
-                },
-              ],
-            },
-          ]
-        },
-      }
-    })

package/src/declare.d.ts

@@ -1,2 +0,0 @@
-declare module '@jbrowse/core/util/offscreenCanvasPonyfill'
-declare module 'hic-straw'

package/src/index.ts

@@ -1,71 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import Color from 'color'
-import HicRendererF from './HicRenderer'
-import HicTrackF from './HicTrack'
-import LinearHicDisplayF from './LinearHicDisplay'
-import HicAdapterF from './HicAdapter'
-import {
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default class HicPlugin extends Plugin {
-  name = 'HicPlugin'
-
-  install(pluginManager: PluginManager) {
-    HicAdapterF(pluginManager)
-    HicRendererF(pluginManager)
-    HicTrackF(pluginManager)
-    LinearHicDisplayF(pluginManager)
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          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: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'HicAdapter') {
-            return 'HicTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-  }
-
-  configure(pluginManager: PluginManager) {
-    pluginManager.jexl.addFunction('alpha', (color: Color, value: number) =>
-      color.alpha(value),
-    )
-    pluginManager.jexl.addFunction('hsl', (color: Color) => color.hsl())
-    pluginManager.jexl.addFunction('colorString', (color: Color) =>
-      color.string(),
-    )
-  }
-}