@jbrowse/plugin-sequence 2.5.0 → 2.6.2

package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts

@@ -1,104 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import {
-  SimpleFeature,
-  Feature,
-  Region,
-  revcom,
-  doesIntersect2,
-} from '@jbrowse/core/util'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-
-export default class extends BaseFeatureDataAdapter {
-  public async configure() {
-    const adapter = await this.getSubAdapter?.(this.getConf('sequenceAdapter'))
-    if (!adapter) {
-      throw new Error('Error getting subadapter')
-    }
-    return adapter.dataAdapter as BaseFeatureDataAdapter
-  }
-
-  public async getRefNames() {
-    const adapter = await this.configure()
-    return adapter.getRefNames()
-  }
-
-  public getFeatures(query: Region, opts: BaseOptions) {
-    return ObservableCreate<Feature>(async observer => {
-      const sequenceAdapter = await this.configure()
-      const hw = 1000
-      let { start: queryStart, end: queryEnd } = query
-      queryStart = Math.max(0, queryStart - hw)
-      queryEnd += hw
-
-      if (queryEnd < 0 || queryStart > queryEnd) {
-        observer.complete()
-        return
-      }
-
-      const ret = sequenceAdapter.getFeatures(
-        {
-          ...query,
-          start: queryStart,
-          end: queryEnd,
-        },
-        opts,
-      )
-      const feats = await firstValueFrom(ret.pipe(toArray()))
-      const residues: string = feats[0]?.get('seq') || ''
-      const search = this.getConf('search') as string
-      const searchForward = this.getConf('searchForward')
-      const searchReverse = this.getConf('searchReverse')
-      const caseInsensitive = this.getConf('caseInsensitive')
-      const re = new RegExp(search, 'g' + (caseInsensitive ? 'i' : ''))
-
-      if (search) {
-        if (searchForward) {
-          const matches = residues.matchAll(re)
-          for (const match of matches) {
-            const s = queryStart + (match.index || 0)
-
-            if (doesIntersect2(s, s + search.length, query.start, query.end)) {
-              observer.next(
-                new SimpleFeature({
-                  uniqueId: `${this.id}-match-${s}-p`,
-                  refName: query.refName,
-                  start: s,
-                  end: s + match[0].length,
-                  name: match[0],
-                  strand: 1,
-                }),
-              )
-            }
-          }
-        }
-        if (searchReverse) {
-          const matches = revcom(residues).matchAll(re)
-          for (const match of matches) {
-            const s = queryEnd - (match.index || 0)
-            if (doesIntersect2(s, s + search.length, query.start, query.end)) {
-              observer.next(
-                new SimpleFeature({
-                  uniqueId: `${this.id}-match-${s}-n`,
-                  refName: query.refName,
-                  start: s - match[0].length,
-                  name: match[0],
-                  end: s,
-                  strand: -1,
-                }),
-              )
-            }
-          }
-        }
-      }
-
-      observer.complete()
-    })
-  }
-
-  public freeResources() {}
-}

package/src/SequenceSearchAdapter/configSchema.ts

@@ -1,51 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config SequenceSearchAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'SequenceSearchAdapter',
-  {
-    /**
-     * #slot
-     */
-    search: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Search string or regex to search for',
-    },
-    /**
-     * #slot
-     */
-    sequenceAdapter: {
-      type: 'frozen',
-      defaultValue: null,
-    },
-    /**
-     * #slot
-     */
-    searchForward: {
-      type: 'boolean',
-      defaultValue: true,
-    },
-    /**
-     * #slot
-     */
-    searchReverse: {
-      type: 'boolean',
-      defaultValue: true,
-    },
-    /**
-     * #slot
-     */
-    caseInsensitive: {
-      type: 'boolean',
-      defaultValue: true,
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default configSchema

package/src/SequenceSearchAdapter/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: 'SequenceSearchAdapter',
-        displayName: 'Sequence search adapter',
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        configSchema,
-        getAdapterClass: () =>
-          import('./SequenceSearchAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/TwoBitAdapter/TwoBitAdapter.test.ts

@@ -1,55 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './TwoBitAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch features from volvox.2bit', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      twoBitLocation: {
-        localPath: require.resolve('../../test_data/volvox.2bit'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  expect(featuresArray).toMatchSnapshot()
-
-  const features2 = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 45000,
-    end: 55000,
-  })
-
-  const featuresArray2 = await firstValueFrom(features2.pipe(toArray()))
-  expect(featuresArray2[0].get('end')).toBe(50001)
-
-  const features3 = adapter.getFeatures({
-    refName: 'ctgC',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray3 = await firstValueFrom(features3.pipe(toArray()))
-  expect(featuresArray3).toMatchSnapshot()
-})
-
-test('adapter can fetch regions from with chrom.sizes', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      chromSizesLocation: {
-        localPath: require.resolve('../../test_data/volvox.chrom.sizes'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  expect(await adapter.getRegions()).toMatchSnapshot()
-})

package/src/TwoBitAdapter/TwoBitAdapter.ts

@@ -1,108 +0,0 @@
-import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } from '@jbrowse/core/util/types'
-import { openLocation } from '@jbrowse/core/util/io'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { TwoBitFile } from '@gmod/twobit'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-export default class TwoBitAdapter extends BaseSequenceAdapter {
-  private twobit: TwoBitFile
-
-  // the chromSizesData can be used to speed up loading since TwoBit has to do
-  // many range requests at startup to perform the getRegions request
-  protected chromSizesData: Promise<Record<string, number> | undefined>
-
-  private async initChromSizes() {
-    const conf = readConfObject(this.config, 'chromSizesLocation')
-    // check against default and empty in case someone makes the field blank in
-    // config editor, may want better way to check "optional config slots" in
-    // future
-    if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
-      const file = openLocation(conf, this.pluginManager)
-      const data = await file.readFile('utf8')
-      return Object.fromEntries(
-        data
-          ?.split(/\n|\r\n|\r/)
-          .filter(line => !!line.trim())
-          .map(line => {
-            const [name, length] = line.split('\t')
-            return [name, +length]
-          }),
-      )
-    }
-    return undefined
-  }
-
-  constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    this.chromSizesData = this.initChromSizes()
-    this.twobit = new TwoBitFile({
-      filehandle: openLocation(
-        readConfObject(config, 'twoBitLocation'),
-        this.pluginManager,
-      ),
-    })
-  }
-
-  public async getRefNames() {
-    const chromSizesData = await this.chromSizesData
-    if (chromSizesData) {
-      return Object.keys(chromSizesData)
-    }
-    return this.twobit.getSequenceNames()
-  }
-
-  public async getRegions(): Promise<NoAssemblyRegion[]> {
-    const chromSizesData = await this.chromSizesData
-    if (chromSizesData) {
-      return Object.keys(chromSizesData).map(refName => ({
-        refName,
-        start: 0,
-        end: chromSizesData[refName],
-      }))
-    }
-    const refSizes = await this.twobit.getSequenceSizes()
-    return Object.keys(refSizes).map(refName => ({
-      refName,
-      start: 0,
-      end: refSizes[refName],
-    }))
-  }
-
-  /**
-   * Fetch features for a certain region
-   * @param param -
-   * @returns Observable of Feature objects in the region
-   */
-  public getFeatures({ refName, start, end }: NoAssemblyRegion) {
-    return ObservableCreate<Feature>(async observer => {
-      const size = await this.twobit.getSequenceSize(refName)
-      const regionEnd = size !== undefined ? Math.min(size, end) : end
-      const seq = await this.twobit.getSequence(refName, start, regionEnd)
-      if (seq) {
-        observer.next(
-          new SimpleFeature({
-            id: `${refName} ${start}-${regionEnd}`,
-            data: { refName, start, end: regionEnd, seq },
-          }),
-        )
-      }
-      observer.complete()
-    })
-  }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the foreseeable future and can be purged
-   * from caches, etc
-   */
-  public freeResources(/* { region } */): void {}
-}

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

@@ -1,30 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch features from volvox.2bit 1`] = `
-[
-  {
-    "end": 20000,
-    "refName": "ctgA",
-    "seq": 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c",
-    "start": 0,
-    "uniqueId": "ctgA 0-20000",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox.2bit 2`] = `[]`;
-
-exports[`adapter can fetch regions from with chrom.sizes 1`] = `
-[
-  {
-    "end": 50001,
-    "refName": "ctgA",
-    "start": 0,
-  },
-  {
-    "end": 6079,
-    "refName": "ctgB",
-    "start": 0,
-  },
-]
-`;

package/src/TwoBitAdapter/configSchema.ts

@@ -1,34 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config TwoBitAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const TwoBitAdapter = ConfigurationSchema(
-  'TwoBitAdapter',
-  {
-    /**
-     * #slot
-     */
-    twoBitLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
-    },
-    /**
-     * #slot
-     */
-    chromSizesLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/default.chrom.sizes',
-        locationType: 'UriLocation',
-      },
-      description:
-        'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default TwoBitAdapter

package/src/TwoBitAdapter/index.ts

@@ -1,19 +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: 'TwoBitAdapter',
-        displayName: 'TwoBit adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
-      }),
-  )
-}

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

@@ -1,5 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`plugin in a stock JBrowse 1`] = `{}`;
-
-exports[`plugin in a stock JBrowse 2`] = `{}`;

package/src/createExtensionPoints.ts

@@ -1,122 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.2bit$/i
-        const adapterName = 'TwoBitAdapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          twoBitLocation: file,
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-  pluginManager.addToExtensionPoint(
-    'Core-guessTrackTypeForLocation',
-    (trackTypeGuesser: TrackTypeGuesser) => {
-      return (adapterName: string) => {
-        if (adapterName === 'TwoBitAdapter') {
-          return 'ReferenceSequenceTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i
-        const adapterName = 'IndexedFastaAdapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          fastaLocation: file,
-          faiLocation: index || makeIndex(file, '.fai'),
-        }
-
-        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 === 'IndexedFastaAdapter') {
-          return 'ReferenceSequenceTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i
-        const adapterName = 'BgzipFastaAdapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          faiLocation: makeIndex(file, '.fai'),
-          gziLocation: makeIndex(file, '.gzi'),
-        }
-
-        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 === 'BgzipFastaAdapter') {
-          return 'ReferenceSequenceTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-}

package/src/index.test.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-test('plugin in a stock JBrowse', () => {
-  const pluginManager = new PluginManager([new ThisPlugin()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-
-  const TwoBitAdapter = pluginManager.getAdapterType('TwoBitAdapter')
-  const cfg = TwoBitAdapter.configSchema.create({ type: 'TwoBitAdapter' })
-  expect(getSnapshot(cfg)).toMatchSnapshot()
-
-  const FastaAdapter = pluginManager.getAdapterType('IndexedFastaAdapter')
-  const cfg2 = FastaAdapter.configSchema.create({ type: 'IndexedFastaAdapter' })
-  expect(getSnapshot(cfg2)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,28 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import TwoBitAdapterF from './TwoBitAdapter'
-import DivSequenceRendererF from './DivSequenceRenderer'
-import BgzipFastaAdapterF from './BgzipFastaAdapter'
-import ChromSizesAdapterF from './ChromSizesAdapter'
-import IndexedFastaAdapterF from './IndexedFastaAdapter'
-import SequenceSearchAdapterF from './SequenceSearchAdapter'
-import ReferenceSequenceTrackF from './ReferenceSequenceTrack'
-import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay'
-import createExtensionPoints from './createExtensionPoints'
-
-export default class SequencePlugin extends Plugin {
-  name = 'SequencePlugin'
-
-  install(pluginManager: PluginManager) {
-    DivSequenceRendererF(pluginManager)
-    TwoBitAdapterF(pluginManager)
-    BgzipFastaAdapterF(pluginManager)
-    ChromSizesAdapterF(pluginManager)
-    IndexedFastaAdapterF(pluginManager)
-    SequenceSearchAdapterF(pluginManager)
-    ReferenceSequenceTrackF(pluginManager)
-    LinearReferenceSequenceDisplayF(pluginManager)
-    createExtensionPoints(pluginManager)
-  }
-}