@jbrowse/plugin-sequence 2.0.0 → 2.1.2

package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts

@@ -0,0 +1,103 @@
+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'
+
+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 ret.pipe(toArray()).toPromise()
+      const residues: string = feats[0]?.get('seq') || ''
+      const search = this.getConf('search')
+      const searchFoward = this.getConf('searchForward')
+      const searchReverse = this.getConf('searchReverse')
+      const caseInsensitive = this.getConf('caseInsensitive')
+      const re = new RegExp(search, 'g' + (caseInsensitive ? 'i' : ''))
+
+      if (search) {
+        if (searchFoward) {
+          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

@@ -0,0 +1,31 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+const configSchema = ConfigurationSchema(
+  'SequenceSearchAdapter',
+  {
+    search: {
+      type: 'string',
+      defaultValue: '',
+      description: 'Search string or regex to search for',
+    },
+    sequenceAdapter: {
+      type: 'frozen',
+      defaultValue: null,
+    },
+    searchForward: {
+      type: 'boolean',
+      defaultValue: true,
+    },
+    searchReverse: {
+      type: 'boolean',
+      defaultValue: true,
+    },
+    caseInsensitive: {
+      type: 'boolean',
+      defaultValue: true,
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

package/src/SequenceSearchAdapter/index.ts

@@ -0,0 +1,22 @@
+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',
+        adapterMetadata: {
+          category: null,
+          hiddenFromGUI: true,
+          displayName: null,
+          description: null,
+        },
+        configSchema,
+        getAdapterClass: () =>
+          import('./SequenceSearchAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/TwoBitAdapter/index.ts

@@ -1 +1,21 @@
-export { default as configSchema } from './configSchema'
+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',
+        configSchema,
+        adapterMetadata: {
+          category: null,
+          hiddenFromGUI: true,
+          displayName: null,
+          description: null,
+        },
+        getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/createExtensionPoints.ts

@@ -0,0 +1,122 @@
+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.ts

@@ -1,278 +1,30 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import { Region, FileLocation } from '@jbrowse/core/util/types'
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-import {
-  makeIndex,
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-import { configSchema as bgzipFastaAdapterConfigSchema } from './BgzipFastaAdapter'
-import { configSchema as chromSizesAdapterConfigSchema } from './ChromSizesAdapter'
-import {
-  configSchema as divSequenceRendererConfigSchema,
-  ReactComponent as DivSequenceRendererReactComponent,
-} from './DivSequenceRenderer'
-import { configSchema as indexedFastaAdapterConfigSchema } from './IndexedFastaAdapter'
-import {
-  configSchema as linearReferenceSequenceDisplayConfigSchema,
-  modelFactory as linearReferenceSequenceDisplayModelFactory,
-} from './LinearReferenceSequenceDisplay'
-import { configSchema as twoBitAdapterConfigSchema } from './TwoBitAdapter'
-import GCContentAdapterF from './GCContentAdapter'
-import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig'
-
-/* 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,
-    }
-  }
-}
+import TwoBitAdapterF from './TwoBitAdapter'
+import DivSequenceRendererF from './DivSequenceRenderer'
+import BgzipFastaAdapterF from './BgzipFastaAdapter'
+import ChromSizesAdapterF from './ChromSizesAdapter'
+import IndexedFastaAdapterF from './IndexedFastaAdapter'
+import GCContentAdapterF from './GCContentAdapter'
+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) {
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'TwoBitAdapter',
-          configSchema: twoBitAdapterConfigSchema,
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          getAdapterClass: () =>
-            import('./TwoBitAdapter/TwoBitAdapter').then(r => r.default),
-        }),
-    )
-    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.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'ChromSizesAdapter',
-          configSchema: chromSizesAdapterConfigSchema,
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          getAdapterClass: () =>
-            import('./ChromSizesAdapter/ChromSizesAdapter').then(
-              r => r.default,
-            ),
-        }),
-    )
-
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'IndexedFastaAdapter',
-          configSchema: indexedFastaAdapterConfigSchema,
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          getAdapterClass: () =>
-            import('./IndexedFastaAdapter/IndexedFastaAdapter').then(
-              r => r.default,
-            ),
-        }),
-    )
-    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.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BgzipFastaAdapter',
-          configSchema: bgzipFastaAdapterConfigSchema,
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          getAdapterClass: () =>
-            import('./BgzipFastaAdapter/BgzipFastaAdapter').then(
-              r => r.default,
-            ),
-        }),
-    )
-
-    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)
-        }
-      },
-    )
-
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'GCContentAdapter',
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          ...pluginManager.load(GCContentAdapterF),
-        }),
-    )
-    pluginManager.addTrackType(() => {
-      const configSchema = createReferenceSeqTrackConfig(pluginManager)
-
-      return new TrackType({
-        name: 'ReferenceSequenceTrack',
-        configSchema,
-        stateModel: createBaseTrackModel(
-          pluginManager,
-          'ReferenceSequenceTrack',
-          configSchema,
-        ),
-      })
-    })
-
-    pluginManager.addDisplayType(() => {
-      const stateModel = linearReferenceSequenceDisplayModelFactory(
-        linearReferenceSequenceDisplayConfigSchema,
-      )
-      return {
-        name: 'LinearReferenceSequenceDisplay',
-        configSchema: linearReferenceSequenceDisplayConfigSchema,
-        stateModel,
-        trackType: 'ReferenceSequenceTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      }
-    })
-
-    pluginManager.addRendererType(
-      () =>
-        new DivSequenceRenderer({
-          name: 'DivSequenceRenderer',
-          ReactComponent: DivSequenceRendererReactComponent,
-          configSchema: divSequenceRendererConfigSchema,
-          pluginManager,
-        }),
-    )
+    DivSequenceRendererF(pluginManager)
+    TwoBitAdapterF(pluginManager)
+    BgzipFastaAdapterF(pluginManager)
+    ChromSizesAdapterF(pluginManager)
+    IndexedFastaAdapterF(pluginManager)
+    GCContentAdapterF(pluginManager)
+    SequenceSearchAdapterF(pluginManager)
+    ReferenceSequenceTrackF(pluginManager)
+    LinearReferenceSequenceDisplayF(pluginManager)
+    createExtensionPoints(pluginManager)
   }
 }

package/dist/referenceSeqTrackConfig.js.map

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

@@ -1 +0,0 @@
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