@jbrowse/plugin-wiggle 2.6.1 → 2.6.3

package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map

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

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package/esm/MultiWiggleRendering.js.map

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package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map

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package/esm/MultiXYPlotRenderer/configSchema.js.map

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package/esm/MultiXYPlotRenderer/index.js.map

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package/esm/QuantitativeTrack/configSchema.js.map

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package/esm/QuantitativeTrack/index.js.map

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package/esm/Tooltip.js.map

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package/esm/WiggleRPC/MultiWiggleGetSources.js.map

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package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map

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package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js.map

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package/esm/WiggleRPC/rpcMethods.js.map

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package/esm/XYPlotRenderer/XYPlotRenderer.js.map

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package/esm/index.js.map

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package/esm/shared/SetMinMaxDialog.js.map

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package/esm/shared/YScaleBar.js.map

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package/esm/shared/configShared.js.map

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package/esm/shared/modelShared.js.map

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package/esm/util.js.map

@@ -1 +0,0 @@
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package/src/BigWigAdapter/BigWigAdapter.test.ts

@@ -1,66 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import BigWigAdapter from './BigWigAdapter'
-import configSchema from './configSchema'
-
-describe('adapter can fetch features from volvox.bw', () => {
-  let adapter: BigWigAdapter
-  beforeEach(() => {
-    adapter = new BigWigAdapter(
-      configSchema.create({
-        bigWigLocation: {
-          localPath: require.resolve('./test_data/volvox.bw'),
-          locationType: 'LocalPathLocation',
-        },
-      }),
-    )
-  })
-  it('test basic aspects of getfeatures', async () => {
-    const features = adapter.getFeatures({
-      refName: 'ctgA',
-      start: 0,
-      end: 20000,
-      assemblyName: 'volvox',
-    })
-    expect(await adapter.refIdToName(0)).toBe('ctgA')
-    expect(await adapter.refIdToName(1)).toBe(undefined)
-    expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-    expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-    const featuresArray = await firstValueFrom(features.pipe(toArray()))
-    const featuresJsonArray = featuresArray.map(f => f.toJSON())
-    expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-  })
-  it('adapter can fetch stats from volvox.bw', async () => {
-    expect(await adapter.getGlobalStats()).toMatchSnapshot()
-  })
-  it('get region stats', async () => {
-    expect(
-      await adapter.getRegionQuantitativeStats({
-        refName: 'ctgA',
-        start: 10000,
-        end: 40000,
-        assemblyName: 'volvox',
-      }),
-    ).toMatchSnapshot()
-  })
-
-  it('get local stats', async () => {
-    expect(
-      await adapter.getMultiRegionQuantitativeStats([
-        {
-          refName: 'ctgA',
-          start: 10000,
-          end: 39999,
-          assemblyName: 'volvox',
-        },
-        {
-          refName: 'ctgB',
-          start: 0,
-          end: 99,
-          assemblyName: 'volvox',
-        },
-      ]),
-    ).toMatchSnapshot()
-  })
-})

package/src/BigWigAdapter/BigWigAdapter.ts

@@ -1,112 +0,0 @@
-import { BigWig } from '@gmod/bbi'
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
-import { openLocation } from '@jbrowse/core/util/io'
-import { updateStatus, Feature } from '@jbrowse/core/util'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import {
-  rectifyStats,
-  UnrectifiedQuantitativeStats,
-} from '@jbrowse/core/util/stats'
-
-interface WiggleOptions extends BaseOptions {
-  resolution?: number
-}
-
-export default class BigWigAdapter extends BaseFeatureDataAdapter {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private setupP?: Promise<{ bigwig: BigWig; header: any }>
-
-  public static capabilities = [
-    'hasResolution',
-    'hasLocalStats',
-    'hasGlobalStats',
-  ]
-
-  private async setupPre(opts?: BaseOptions) {
-    const { statusCallback = () => {} } = opts || {}
-    const pm = this.pluginManager
-    const bigwig = new BigWig({
-      filehandle: openLocation(this.getConf('bigWigLocation'), pm),
-    })
-    const header = await updateStatus(
-      'Downloading bigwig header',
-      statusCallback,
-      () => bigwig.getHeader(opts),
-    )
-    return { bigwig, header }
-  }
-
-  async setup(opts?: BaseOptions) {
-    if (!this.setupP) {
-      this.setupP = this.setupPre(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  public async getRefNames(opts?: BaseOptions) {
-    const { header } = await this.setup(opts)
-    return Object.keys(header.refsByName)
-  }
-
-  public async refIdToName(refId: number) {
-    const { header } = await this.setup()
-    return header.refsByNumber[refId]?.name
-  }
-
-  public async getGlobalStats(opts?: BaseOptions) {
-    const { header } = await this.setup(opts)
-    return rectifyStats(header.totalSummary as UnrectifiedQuantitativeStats)
-  }
-
-  public getFeatures(region: Region, opts: WiggleOptions = {}) {
-    const { refName, start, end } = region
-    const {
-      bpPerPx = 0,
-      signal,
-      resolution = 1,
-      statusCallback = () => {},
-    } = opts
-    return ObservableCreate<Feature>(async observer => {
-      statusCallback('Downloading bigwig data')
-      const source = this.getConf('source')
-      const { bigwig } = await this.setup(opts)
-      const feats = await bigwig.getFeatures(refName, start, end, {
-        ...opts,
-        basesPerSpan: bpPerPx / resolution,
-      })
-
-      for (const data of feats) {
-        if (source) {
-          // @ts-expect-error
-          data.source = source
-        }
-        const uniqueId = `${source}:${region.refName}:${data.start}-${data.end}`
-        // @ts-expect-error
-        data.refName = refName
-        data.uniqueId = uniqueId
-        observer.next({
-          // @ts-expect-error
-          get: (str: string) => (data as Record<string, unknown>)[str],
-          id: () => uniqueId,
-          // @ts-expect-error
-          toJSON: () => data,
-        })
-      }
-      observer.complete()
-    }, signal)
-  }
-
-  // always render bigwig instead of calculating a feature density for it
-  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
-    return { featureDensity: 0 }
-  }
-
-  public freeResources(): void {}
-}

package/src/BigWigAdapter/__snapshots__/BigWigAdapter.test.ts.snap

@@ -1,117 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch features from volvox.bw adapter can fetch stats from volvox.bw 1`] = `
-{
-  "basesCovered": 49984,
-  "featureDensity": 0.00002000640204865557,
-  "scoreMax": 38,
-  "scoreMean": 19.197983354673497,
-  "scoreMin": 1,
-  "scoreStdDev": 4.55961443138808,
-  "scoreSum": 959592,
-  "scoreSumSquares": 19461382,
-}
-`;
-
-exports[`adapter can fetch features from volvox.bw get local stats 1`] = `
-{
-  "basesCovered": 30000,
-  "featureCount": 30000,
-  "featureDensity": 1,
-  "scoreMax": 38,
-  "scoreMean": 19.297233333333335,
-  "scoreMin": 0,
-  "scoreStdDev": 4.380942680236127,
-  "scoreSum": 578917,
-  "scoreSumSquares": 11747257,
-}
-`;
-
-exports[`adapter can fetch features from volvox.bw get region stats 1`] = `
-{
-  "basesCovered": 30001,
-  "featureCount": 30001,
-  "featureDensity": 1,
-  "scoreMax": 38,
-  "scoreMean": 19.297356754774842,
-  "scoreMin": 5,
-  "scoreStdDev": 4.380921822290578,
-  "scoreSum": 578940,
-  "scoreSumSquares": 11747786,
-}
-`;
-
-exports[`adapter can fetch features from volvox.bw test basic aspects of getfeatures 1`] = `
-[
-  {
-    "end": 1003,
-    "refName": "ctgA",
-    "score": 18,
-    "start": 1002,
-    "uniqueId": ":ctgA:1002-1003",
-  },
-  {
-    "end": 1004,
-    "refName": "ctgA",
-    "score": 18,
-    "start": 1003,
-    "uniqueId": ":ctgA:1003-1004",
-  },
-  {
-    "end": 1005,
-    "refName": "ctgA",
-    "score": 18,
-    "start": 1004,
-    "uniqueId": ":ctgA:1004-1005",
-  },
-  {
-    "end": 1006,
-    "refName": "ctgA",
-    "score": 19,
-    "start": 1005,
-    "uniqueId": ":ctgA:1005-1006",
-  },
-  {
-    "end": 1007,
-    "refName": "ctgA",
-    "score": 20,
-    "start": 1006,
-    "uniqueId": ":ctgA:1006-1007",
-  },
-  {
-    "end": 1008,
-    "refName": "ctgA",
-    "score": 20,
-    "start": 1007,
-    "uniqueId": ":ctgA:1007-1008",
-  },
-  {
-    "end": 1009,
-    "refName": "ctgA",
-    "score": 20,
-    "start": 1008,
-    "uniqueId": ":ctgA:1008-1009",
-  },
-  {
-    "end": 1010,
-    "refName": "ctgA",
-    "score": 20,
-    "start": 1009,
-    "uniqueId": ":ctgA:1009-1010",
-  },
-  {
-    "end": 1011,
-    "refName": "ctgA",
-    "score": 20,
-    "start": 1010,
-    "uniqueId": ":ctgA:1010-1011",
-  },
-  {
-    "end": 1012,
-    "refName": "ctgA",
-    "score": 19,
-    "start": 1011,
-    "uniqueId": ":ctgA:1011-1012",
-  },
-]
-`;

package/src/BigWigAdapter/configSchema.ts

@@ -1,34 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config BigWigAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const BigWigAdapter = ConfigurationSchema(
-  'BigWigAdapter',
-  {
-    /**
-     * #slot
-     */
-    bigWigLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/my.bw',
-        locationType: 'UriLocation',
-      },
-    },
-
-    /**
-     * #slot
-     */
-    source: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Used for multiwiggle',
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default BigWigAdapter

package/src/BigWigAdapter/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'BigWigAdapter',
-        displayName: 'BigWig adapter',
-        configSchema,
-        adapterCapabilities: [
-          'hasResolution',
-          'hasLocalStats',
-          'hasGlobalStats',
-        ],
-        getAdapterClass: () => import('./BigWigAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/CreateMultiWiggleExtension/ConfirmDialog.tsx

@@ -1,68 +0,0 @@
-import React, { useState } from 'react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  Typography,
-} from '@mui/material'
-import Dialog from '@jbrowse/core/ui/Dialog'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-
-const ConfirmDialog = ({
-  tracks,
-  onClose,
-}: {
-  tracks: AnyConfigurationModel[]
-  onClose: (arg: boolean, arg1?: { name: string }) => void
-}) => {
-  const [val, setVal] = useState(`MultiWiggle ${Date.now()}`)
-  const allQuant = tracks.every(t => t.type === 'QuantitativeTrack')
-  return (
-    <Dialog
-      open
-      onClose={() => onClose(false)}
-      title="Confirm multi-wiggle track create"
-    >
-      <DialogContent>
-        <Typography>
-          {!allQuant
-            ? 'Not every track looks like a QuantitativeTrack. This could have unexpected behavior, confirm if it looks ok.'
-            : null}
-          Listing:
-        </Typography>
-        <ul>
-          {tracks.map(track => (
-            <li key={track.trackId}>
-              {readConfObject(track, 'name')} - {track.type}
-            </li>
-          ))}
-        </ul>
-        <TextField
-          value={val}
-          onChange={event => setVal(event.target.value)}
-          helperText="Track name"
-        />
-        <Typography>Confirm creation of track?</Typography>
-      </DialogContent>
-      <DialogActions>
-        <Button onClick={() => onClose(false)} color="primary">
-          Cancel
-        </Button>
-        <Button
-          onClick={() => onClose(true, { name: val })}
-          color="primary"
-          variant="contained"
-          autoFocus
-        >
-          Submit
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-}
-
-export default ConfirmDialog