@jbrowse/plugin-sequence 2.5.0 → 2.6.2

package/src/DivSequenceRenderer/configSchema.ts

@@ -1,23 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config DivSequenceRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const DivSequenceRenderer = ConfigurationSchema(
-  'DivSequenceRenderer',
-  {
-    /**
-     * #slot
-     */
-    height: {
-      type: 'number',
-      description: 'height in pixels of each line of sequence',
-      defaultValue: 16,
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default DivSequenceRenderer

package/src/DivSequenceRenderer/index.ts

@@ -1,31 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import { Region } from '@jbrowse/core/util/types'
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
-import ReactComponent from './components/DivSequenceRendering'
-import configSchema from './configSchema'
-
-/* adjust in both directions */
-class DivSequenceRenderer extends FeatureRendererType {
-  supportsSVG = true
-
-  getExpandedRegion(region: Region) {
-    return {
-      ...region,
-      start: Math.max(region.start - 3, 0),
-      end: region.end + 3,
-    }
-  }
-}
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addRendererType(
-    () =>
-      new DivSequenceRenderer({
-        name: 'DivSequenceRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
-}

package/src/IndexedFastaAdapter/IndexedFastaAdapter.test.ts

@@ -1,53 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './IndexedFastaAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch sequence from volvox.fa', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      fastaLocation: {
-        localPath: require.resolve('../../test_data/volvox.fa'),
-        locationType: 'LocalPathLocation',
-      },
-      faiLocation: {
-        localPath: require.resolve('../../test_data/volvox.fa.fai'),
-        locationType: 'LocalPathLocation',
-      },
-      metadataLocation: {
-        localPath: require.resolve('../../test_data/hello.txt'),
-        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 data = await adapter.getHeader()
-  expect(data?.trim()).toBe('hello world')
-
-  const featuresArray3 = await firstValueFrom(features3.pipe(toArray()))
-  expect(featuresArray3).toMatchSnapshot()
-})

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -1,113 +0,0 @@
-import { IndexedFasta } from '@gmod/indexedfasta'
-import {
-  BaseSequenceAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation, 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'
-import AbortablePromiseCache from 'abortable-promise-cache'
-import QuickLRU from '@jbrowse/core/util/QuickLRU'
-
-type T = { refName: string; start: number; end: number; fasta: IndexedFasta }
-
-export default class extends BaseSequenceAdapter {
-  protected setupP?: Promise<{ fasta: IndexedFasta }>
-
-  private seqCache = new AbortablePromiseCache<T, string | undefined>({
-    cache: new QuickLRU({ maxSize: 200 }),
-    fill: async (args: T, signal?: AbortSignal) => {
-      const { refName, start, end, fasta } = args
-      return fasta.getSequence(refName, start, end, { ...args, signal })
-    },
-  })
-
-  public async getRefNames(opts?: BaseOptions) {
-    const { fasta } = await this.setup()
-    return fasta.getSequenceNames(opts)
-  }
-
-  public async getRegions(opts?: BaseOptions) {
-    const { fasta } = await this.setup()
-    const seqSizes = await fasta.getSequenceSizes(opts)
-    return Object.keys(seqSizes).map(refName => ({
-      refName,
-      start: 0,
-      end: seqSizes[refName],
-    }))
-  }
-
-  public async setupPre() {
-    const fastaLocation = this.getConf('fastaLocation') as FileLocation
-    const faiLocation = this.getConf('faiLocation') as FileLocation
-
-    return {
-      fasta: new IndexedFasta({
-        fasta: openLocation(fastaLocation, this.pluginManager),
-        fai: openLocation(faiLocation, this.pluginManager),
-      }),
-    }
-  }
-
-  public async getHeader() {
-    const loc = this.getConf('metadataLocation')
-    return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
-      ? null
-      : openLocation(loc, this.pluginManager).readFile('utf8')
-  }
-
-  public async setup() {
-    if (!this.setupP) {
-      this.setupP = this.setupPre().catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {
-    const { refName, start, end } = region
-    return ObservableCreate<Feature>(async observer => {
-      const { fasta } = await this.setup()
-      const size = await fasta.getSequenceSize(refName, opts)
-      const regionEnd = size !== undefined ? Math.min(size, end) : end
-      const chunks = []
-      const chunkSize = 128000
-
-      const s = start - (start % chunkSize)
-      const e = end + (chunkSize - (end % chunkSize))
-      for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
-        const r = {
-          refName,
-          start: chunkStart,
-          end: chunkStart + chunkSize,
-        }
-        chunks.push(
-          this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts?.signal),
-        )
-      }
-      const seq = (await Promise.all(chunks))
-        .join('')
-        .slice(start - s)
-        .slice(0, end - start)
-      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/IndexedFastaAdapter/__snapshots__/IndexedFastaAdapter.test.ts.snap

@@ -1,15 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch sequence from volvox.fa 1`] = `
-[
-  {
-    "end": 20000,
-    "refName": "ctgA",
-    "seq": "cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgattatgattggttctttagccttggtttagattggtagtagtagcggcgctaatgctacctgaattgagaactcgagcgggggctaggcaaattctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgaccaccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctccttggtcgctccgttgtacccaggctactttgaaagagcgcagaatacttagacggtatcgatcatggtagcatagcattctgataacatgtatggagttcgaacatccgtctggggccggacggtccgtttgaggttggttgatctgggtgatagtcagcaagatagacgttagataacaaattaaaggattttaccttagattgcgactagtacaacggtacatcggtgattcgcgctctactagatcacgctatgggtaccataaacaaacggtggaccttctcaagctggttgacgcctcagcaacataggcttcctcctccacgcatctcagcataaaaggcttataaactgcttctttgtgccagagcaactcaattaagcccttggtaccgtgggcacgcattctgtcacggtgaccaactgttcatcctgaatcgccgaatgggactatttggtacaggaatcaagcggatggcactactgcagcttatttacgacggtattcttaaagtttttaagacaatgtatttcatgggtagttcggtttgttttattgctacacaggctcttgtagacgacctacttagcactacggccgagcgcaataacccccggaaagcacttgctactgggaggcgggtttatccatcggcaataggggttatcagtactaccaagaagattgtgaagatattaacagcattgaaaaaagttcggactgggcatgaaacgtgtgtcagagttagagtccttgagggactgaatgggtttgtcccaggcccaagcttgaggtggatgtcacctcgggtactgcctctattacagaggtatcttaatggcgcatccagccttgtggctgggtctacgtacgcgtgggcaccatacgtatgttggcaggaaaggtcaatcatgcttgtttcctcgtcgcagaaacgttcacactattggctcgcgggatcgaacgggcctgattatttttccagctcctgcgttcctatcacgccaactgtcgctaataaaatgttatatagagataacccattgctatgcaaggatggagaaaccgcttcacaacaccctagaattacttcagcactaacatctaagataccgggaaaaccgtaggtgccacttggttttgagggcaatgcctcttgcactggcgattcgtggagtaaccttgctaccgatttccaccttttctaggtatgattacatgcgatcgccattgtcagtcgtcgtacgaaatccaggaaggaattcgaatacatgaccgaaagctatggcatcataagcgtggctctttactaaggacacgtgtagtcggctgatttcgcgcagaacttcgctcaccggacagtgactgctgtccgaacttgggggcagcgtagattctagctagagaccgcagcgaaaatgccactcgctaggtggctatggacgtccagctataggcccccacattcgtatgtatactccggtaattgagtctacctttcgaaagatcaaagttcacaaaccttctctcacgttaacatagatgctcgcacatagctagtccggtgataaagcggccgtgcatgcgagtatttagcgcacggaacagatattaggctgcgaaataccctcatatgctacagcgcaggtaacagacggttgatctccccgtagaattccctcaaggccggatcgttctcatgagtagcctttgtctgacatttcctctcaatagattgcagactcctgtgtcgtgggaaaacttcgcggaatcgctgtcgttacataaatctaaacagtgcagtccaagctatttactaccacgtatcataatgaacatctctttgtgaaatacgccggtacgccgagagatcgcccacattgcgtgtcaccaagacccagtgtctattgggcgcgctggttatagtatgcggaggcacccgatgtgctgctaatcactacaaactcgacaccaagaggcgaccgcgtgcgggagggctagaacgcgagagccacgtcaacgtggtggtaccgctcctgatgatacgagcactgtgctggcaccgctgccctatgtccagctaacaggtgtcacataatatcgcatctatagttgagtatcttatcgctagcgttacttgtgagttctcgggtagaatcgtcgtagcattctagtccttagcgtaagcaacgatatcgccgatattataggggcaataggtctcacccaccacgggtgtatatttaacgccctaagtagttaacggagactattaaacaattatgcacgtgaaagattagggtactgcacacgtgtcacgttgacgatgtaaacaccataaaggttgttctgtgatgcgatgcccatacctgcggtgcaacgtcctaaacttatgcggatcaccttctaattcagccgacgttgagaacgccagctatactctgtgagtacaaggtgaaagccccagatcaaaatattggagtcttgtccgtagctcttgggtggagagtgtgaccacgtttatcccttaatactgagactcttctcgttccacgccccggacattcgcgatacagcctagtttgataggtggctacaagggctctatccgaatagcacaaaactcagtcctagtgcgtataggtcgtgctctgcggttatacgctccacagaagaaagtacccactgcagtttgtcggtgggacttagcaaaacctgtaaccaaaaccgcacatggactctgttttggtggcgtggagtgtgcccgccgcctttatgctgggtcaaaatactatatgatttgttgtggtcgggcgcgacattggctcttatggtttataactattattcggtgcacagaaccgacttatgccccgattttgcacctcccgagagaaatggtactagtcattgtctcggggttttacaactcaaggataatctgccagcggtaccccgaaaaatcccatcccgaacggctggtacctatgctggagaccgaaatggagccagtgctatgcaaaccctcgctctttctatttggcccgaccagctgcgagagtcattcgacatacattgcgatggctggttcatctctctgcttcggattccgatcctgctgcctatggccacaacacgaaagagatcttggatacgtcctcaccatagtccaacggacaaatatggaggtgtacgcgcacggatacgagtacgacgggccgcccaatgctggtccttcgtgttatactgtttacttgcctccggtaagagtgtacagcttgtacccacgcggtggaggaccttacgcgtcgtccgcaggtgtggagatttcgctacctgttgcattggggcctcgccttacgtttttttcgacggaggcccgacccgccaggccagaccctcatcattgggatttttactgccttggacggcagattctgatgctggtaacgcgcttggcacacaccctggtcgtaattacgtactatcacctctattttaccaggggcgggccccgcctcaacgatcggtagtctcgttagaacagttgcttatactccgttagcactcacaactcggagaatgagcttacacagtccgtaatagtctccacagcttcccctggaaggttcgtacaggggccctggggtctaatgtgctaccgcctaacttcgttagtgtaaggtctcgtgtgcacctccaataacgctgcatttttgtatagaactcctttataggcctgactcttcggaacagcccactaattgacgtgcacgatgctgcatatacccttctcaatgacgcataccggtgactaaatcctgtggctggttgacactttgcataacccaccacgaaaacgcggtttgcacgtggttggaagcgagtaccggttaagggaagttacgtaaacccaacatagtgagcgatgcttaaaacactgcatgcgaacaacgaccggaacgagagcctaatagaaccaaatggataggtggttacgaaatccgcgcacaagtgtcgtgccactctcgtaaagaatgattgcttgcttatctatgagaaacctaataggcacgcacgtgtcgccagggaaaaaccaccatccgacaagacgctgaaaatcgagatagatgcagcccgcgcgtactttaagcacgatagccatcttgagcgcgacgattcagcttacggagattacttctcaaagcggacacctcgacgctgaagctctctatcgatgcacttgcatgtccatctacggcttgagcgaaccatgcttaacgcttggatgacgttgttagtcggattcgatcgtaccatactgtcctatccatcataacttcccgaattaaaactcattttctaccctcatttgtttcattggcgcatatgagcgccccatgggcgctgatcgacacaggcttgtagcgcacggctcgtcttgcagtagataaccatagtctttacgtcgcatatattaatatatcctcagacttccactgcggtattttggatcgtggcgtctgggacagtcacactctttaacgggagcgcgttcaatgtctgagtccatccgtgcagttcggtgcgatttta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c",
-    "start": 0,
-    "uniqueId": "ctgA 0-20000",
-  },
-]
-`;
-
-exports[`adapter can fetch sequence from volvox.fa 2`] = `[]`;

package/src/IndexedFastaAdapter/configSchema.ts

@@ -1,39 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config IndexedFastaAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const IndexedFastaAdapter = ConfigurationSchema(
-  'IndexedFastaAdapter',
-  {
-    /**
-     * #slot
-     */
-    fastaLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
-    },
-    /**
-     * #slot
-     */
-    faiLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
-    },
-    /**
-     * #slot
-     */
-    metadataLocation: {
-      description: 'Optional metadata file',
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/fa.metadata.yaml',
-        locationType: 'UriLocation',
-      },
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default IndexedFastaAdapter

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

package/src/LinearReferenceSequenceDisplay/configSchema.ts

@@ -1,18 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema'
-
-/**
- * #config LinearReferenceSequenceDisplay
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export const configSchema = ConfigurationSchema(
-  'LinearReferenceSequenceDisplay',
-  {
-    /**
-     * #slot
-     */
-    renderer: divSequenceRendererConfigSchema,
-  },
-  { explicitIdentifier: 'displayId', explicitlyTyped: true },
-)

package/src/LinearReferenceSequenceDisplay/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 { configSchema } from './configSchema'
-import { modelFactory } from './model'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const stateModel = modelFactory(configSchema)
-    return new DisplayType({
-      name: 'LinearReferenceSequenceDisplay',
-      configSchema,
-      stateModel,
-      displayName: 'Reference sequence display',
-      trackType: 'ReferenceSequenceTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: BaseLinearDisplayComponent,
-    })
-  })
-}

package/src/LinearReferenceSequenceDisplay/model.ts

@@ -1,148 +0,0 @@
-import { addDisposer, types } from 'mobx-state-tree'
-import {
-  BaseLinearDisplay,
-  LinearGenomeViewModel,
-} from '@jbrowse/plugin-linear-genome-view'
-import {
-  AnyConfigurationSchemaType,
-  ConfigurationReference,
-} from '@jbrowse/core/configuration'
-import { getContainingView } from '@jbrowse/core/util'
-import { autorun } from 'mobx'
-
-type LGV = LinearGenomeViewModel
-
-/**
- * #stateModel LinearReferenceSequenceDisplay
- * base model `BaseLinearDisplay`
- */
-export function modelFactory(configSchema: AnyConfigurationSchemaType) {
-  return types
-    .compose(
-      'LinearReferenceSequenceDisplay',
-      BaseLinearDisplay,
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LinearReferenceSequenceDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(configSchema),
-        /**
-         * #property
-         */
-        showForward: true,
-        /**
-         * #property
-         */
-        showReverse: true,
-        /**
-         * #property
-         */
-        showTranslation: true,
-      }),
-    )
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        /**
-         * #method
-         */
-        renderProps() {
-          const { showForward, rpcDriverName, showReverse, showTranslation } =
-            self
-          return {
-            ...superRenderProps(),
-            config: self.configuration.renderer,
-            rpcDriverName,
-            showForward,
-            showReverse,
-            showTranslation,
-          }
-        },
-      }
-    })
-    .views(self => ({
-      /**
-       * #method
-       */
-      regionCannotBeRendered(/* region */) {
-        const view = getContainingView(self) as LGV
-        return view?.bpPerPx >= 1 ? 'Zoom in to see sequence' : undefined
-      },
-      /**
-       * #getter
-       */
-      get rendererTypeName() {
-        return self.configuration.renderer.type
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      toggleShowForward() {
-        self.showForward = !self.showForward
-      },
-      /**
-       * #action
-       */
-      toggleShowReverse() {
-        self.showReverse = !self.showReverse
-      },
-      /**
-       * #action
-       */
-      toggleShowTranslation() {
-        self.showTranslation = !self.showTranslation
-      },
-      afterAttach() {
-        addDisposer(
-          self,
-          autorun(() => {
-            const view = getContainingView(self) as LGV
-            if (view?.bpPerPx >= 1) {
-              self.setHeight(50)
-            } else {
-              const { showTranslation, showReverse, showForward } = self
-              const r1 = showReverse && showTranslation ? 60 : 0
-              const r2 = showForward && showTranslation ? 60 : 0
-              const t = r1 + r2
-              const r = showReverse ? 20 : 0
-              const s = showForward ? 20 : 0
-              self.setHeight(t + r + s)
-            }
-          }),
-        )
-      },
-    }))
-    .views(self => ({
-      /**
-       * #method
-       */
-      trackMenuItems() {
-        return [
-          {
-            label: 'Show forward',
-            type: 'checkbox',
-            checked: self.showForward,
-            onClick: () => self.toggleShowForward(),
-          },
-          {
-            label: 'Show reverse',
-            type: 'checkbox',
-            checked: self.showReverse,
-            onClick: () => self.toggleShowReverse(),
-          },
-          {
-            label: 'Show translation',
-            type: 'checkbox',
-            checked: self.showTranslation,
-            onClick: () => self.toggleShowTranslation(),
-          },
-        ]
-      },
-    }))
-}

package/src/ReferenceSequenceTrack/configSchema.ts

@@ -1,117 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-// Note: this is primarily a copy of createBaseTrackConfig, except with a
-// subset of the config slots, to avoid including fields that don't make sense
-// for the ReferenceSequenceTrack
-
-/**
- * #config ReferenceSequenceTrack
- * used to display base level DNA sequence tracks
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'ReferenceSequenceTrack',
-    {
-      /**
-       * #slot
-       * configuration for track adapter
-       */
-      adapter: pluginManager.pluggableConfigSchemaType('adapter'),
-
-      /**
-       * #slot
-       * configuration for the displays e.g. LinearReferenceSequenceDisplay
-       */
-      displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
-
-      /**
-       * #slot
-       */
-      name: {
-        type: 'string',
-        description:
-          'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
-        defaultValue: '',
-      },
-
-      /**
-       * #slot
-       */
-      metadata: {
-        type: 'frozen',
-        description: 'anything to add about this track',
-        defaultValue: {},
-      },
-
-      formatAbout: ConfigurationSchema('FormatAbout', {
-        /**
-         * #slot formatAbout.config
-         */
-        config: {
-          type: 'frozen',
-          description: 'formats configuration in about dialog',
-          defaultValue: {},
-          contextVariable: ['config'],
-        },
-
-        /**
-         * #slot formatAbout.hideUris
-         */
-        hideUris: {
-          type: 'boolean',
-          defaultValue: false,
-        },
-      }),
-    },
-    {
-      preProcessSnapshot: s => {
-        const snap = JSON.parse(JSON.stringify(s))
-        const displayTypes = new Set()
-        const { displays = [] } = snap
-        if (snap.trackId !== 'placeholderId') {
-          // Gets the displays on the track snapshot and the possible displays
-          // from the track type and adds any missing possible displays to the
-          // snapshot
-          displays.forEach((d: any) => d && displayTypes.add(d.type))
-          const trackType = pluginManager.getTrackType(snap.type)
-          trackType.displayTypes.forEach(displayType => {
-            if (!displayTypes.has(displayType.name)) {
-              displays.push({
-                displayId: `${snap.trackId}-${displayType.name}`,
-                type: displayType.name,
-              })
-            }
-          })
-        }
-        return { ...snap, displays }
-      },
-      /**
-       * #identifier
-       * all tracks have a globally unique 'trackId'
-       */
-      explicitIdentifier: 'trackId',
-      explicitlyTyped: true,
-      actions: (self: any) => ({
-        addDisplayConf(displayConf: { type: string; displayId: string }) {
-          const { type } = displayConf
-          if (!type) {
-            throw new Error(`unknown display type ${type}`)
-          }
-          const display = self.displays.find(
-            (d: any) => d && d.displayId === displayConf.displayId,
-          )
-          if (display) {
-            return display
-          }
-          const length = self.displays.push(displayConf)
-          return self.displays[length - 1]
-        },
-      }),
-    },
-  )
-}

package/src/ReferenceSequenceTrack/index.ts

@@ -1,22 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
-import { createReferenceSeqTrackConfig } from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addTrackType(() => {
-    const configSchema = createReferenceSeqTrackConfig(pluginManager)
-
-    return new TrackType({
-      name: 'ReferenceSequenceTrack',
-      displayName: 'Reference sequence track',
-      configSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'ReferenceSequenceTrack',
-        configSchema,
-      ),
-    })
-  })
-}