@jbrowse/plugin-sequence 2.0.0 → 2.1.2

package/esm/index.js

@@ -1,197 +1,30 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-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 { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
-import { makeIndex, getFileName, } 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 TwoBitAdapterF from './TwoBitAdapter';
+import DivSequenceRendererF from './DivSequenceRenderer';
+import BgzipFastaAdapterF from './BgzipFastaAdapter';
+import ChromSizesAdapterF from './ChromSizesAdapter';
+import IndexedFastaAdapterF from './IndexedFastaAdapter';
 import GCContentAdapterF from './GCContentAdapter';
-import { createReferenceSeqTrackConfig } from './referenceSeqTrackConfig';
-/* adjust in both directions */
-class DivSequenceRenderer extends FeatureRendererType {
-    constructor() {
-        super(...arguments);
-        this.supportsSVG = true;
-    }
-    getExpandedRegion(region) {
-        return {
-            ...region,
-            start: Math.max(region.start - 3, 0),
-            end: region.end + 3,
-        };
-    }
-}
+import SequenceSearchAdapterF from './SequenceSearchAdapter';
+import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
+import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay';
+import createExtensionPoints from './createExtensionPoints';
 export default class SequencePlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'SequencePlugin';
     }
     install(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) => {
-            return (file, index, adapterHint) => {
-                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) => {
-            return (adapterName) => {
-                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) => {
-            return (file, index, adapterHint) => {
-                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) => {
-            return (adapterName) => {
-                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) => {
-            return (file, index, adapterHint) => {
-                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) => {
-            return (adapterName) => {
-                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);
     }
 }
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.0.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,16 +37,14 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@gmod/indexedfasta": "^2.0.2",
     "@gmod/twobit": "^1.1.12",
-    "abortable-promise-cache": "^1.5.0",
-    "generic-filehandle": "^2.2.2"
+    "abortable-promise-cache": "^1.5.0"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@jbrowse/plugin-wiggle": "^1.0.0",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@jbrowse/plugin-wiggle": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
@@ -61,5 +59,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/BgzipFastaAdapter/index.ts

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

package/src/ChromSizesAdapter/ChromSizesAdapter.ts

@@ -2,56 +2,40 @@ import {
   RegionsAdapter,
   BaseAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { GenericFilehandle } from 'generic-filehandle'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { Instance } from 'mobx-state-tree'
-import MyConfigSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class extends BaseAdapter implements RegionsAdapter {
   // the map of refSeq to length
-  protected refSeqs: Promise<Record<string, number>>
+  protected setupP?: Promise<{ [key: string]: number }>
 
-  protected source: string
-
-  public constructor(
-    config: Instance<typeof MyConfigSchema>,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const chromSizesLocation = readConfObject(config, 'chromSizesLocation')
-    if (!chromSizesLocation) {
-      throw new Error('must provide chromSizesLocation')
-    }
-    const file = openLocation(
-      chromSizesLocation as FileLocation,
-      this.pluginManager,
+  async setupPre() {
+    const pm = this.pluginManager
+    const file = openLocation(this.getConf('chromSizesLocation'), pm)
+    const data = await file.readFile('utf8')
+    return Object.fromEntries(
+      data
+        .split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f)
+        .map((line: string) => {
+          const [name, length] = line.split('\t')
+          return [name, +length]
+        }),
     )
-    this.source = file.toString()
-    this.refSeqs = this.init(file)
   }
 
-  private async init(file: GenericFilehandle) {
-    const data = await file.readFile('utf8')
-    const refSeqs: { [key: string]: number } = {}
-    if (!data.length) {
-      throw new Error(`Could not read file ${file.toString()}`)
+  async setup() {
+    if (!this.setupP) {
+      this.setupP = this.setupPre().catch(e => {
+        this.setupP = undefined
+        throw e
+      })
     }
-    data.split('\n').forEach((line: string) => {
-      if (line.length) {
-        const [name, length] = line.split('\t')
-        refSeqs[name] = +length
-      }
-    })
-    return refSeqs
+    return this.setupP
   }
 
   public async getRegions() {
-    const refSeqs = await this.refSeqs
+    const refSeqs = await this.setup()
     return Object.keys(refSeqs).map(refName => ({
       refName,
       start: 0,
@@ -59,10 +43,6 @@ export default class extends BaseAdapter implements RegionsAdapter {
     }))
   }
 
-  public getFeatures() {
-    throw new Error('sequence not available')
-  }
-
   public getHeader() {
     return {}
   }

package/src/ChromSizesAdapter/index.ts

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

package/src/DivSequenceRenderer/index.ts

@@ -1,2 +1,31 @@
-export { default as ReactComponent } from './components/DivSequenceRendering'
-export { default as configSchema } from './configSchema'
+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/GCContentAdapter/GCContentAdapter.ts

@@ -2,10 +2,8 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { readConfObject } from '@jbrowse/core/configuration'
+import { SimpleFeature, Feature, Region } from '@jbrowse/core/util'
 import { toArray } from 'rxjs/operators'
 
 export default class extends BaseFeatureDataAdapter {
@@ -18,30 +16,19 @@ export default class extends BaseFeatureDataAdapter {
   public static capabilities = ['hasLocalStats']
 
   public async configure() {
-    // instantiate the sequence adapter
-    const sequenceAdapter = readConfObject(this.config, 'sequenceAdapter')
-
-    const dataAdapter = await this.getSubAdapter?.(sequenceAdapter)
-    if (!dataAdapter) {
+    const adapter = await this.getSubAdapter?.(this.getConf('sequenceAdapter'))
+    if (!adapter) {
       throw new Error('Error getting subadapter')
     }
-    return dataAdapter.dataAdapter as BaseFeatureDataAdapter
+    return adapter.dataAdapter as BaseFeatureDataAdapter
   }
 
   public async getRefNames() {
-    const sequenceAdapter = await this.configure()
-    return sequenceAdapter.getRefNames()
+    const adapter = await this.configure()
+    return adapter.getRefNames()
   }
 
-  /**
-   * Fetch features for a certain region
-   * @param param -
-   * @returns Observable of Feature objects in the region
-   */
   public getFeatures(query: Region, opts: BaseOptions) {
-    this.windowSize = 1000
-    this.windowDelta = 1000
-    this.gcMode = 'content'
     return ObservableCreate<Feature>(async observer => {
       const sequenceAdapter = await this.configure()
       const hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
@@ -56,11 +43,14 @@ export default class extends BaseFeatureDataAdapter {
         return
       }
 
-      const ret = sequenceAdapter.getFeatures({
-        ...query,
-        start: queryStart,
-        end: queryEnd,
-      })
+      const ret = sequenceAdapter.getFeatures(
+        {
+          ...query,
+          start: queryStart,
+          end: queryEnd,
+        },
+        opts,
+      )
       const feats = await ret.pipe(toArray()).toPromise()
       const residues = feats[0]?.get('seq') || ''
 
@@ -105,5 +95,5 @@ export default class extends BaseFeatureDataAdapter {
    * will not be needed for the forseeable future and can be purged
    * from caches, etc
    */
-  public freeResources(/* { region } */): void {}
+  public freeResources(/* { region } */) {}
 }

package/src/GCContentAdapter/index.ts

@@ -1,9 +1,22 @@
 import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
 import configSchemaF from './configSchema'
 
 export default (pluginManager: PluginManager) => {
-  return {
-    configSchema: pluginManager.load(configSchemaF),
-    getAdapterClass: () => import('./GCContentAdapter').then(r => r.default),
-  }
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'GCContentAdapter',
+        adapterMetadata: {
+          category: null,
+          hiddenFromGUI: true,
+          displayName: null,
+          description: null,
+        },
+        configSchema: configSchemaF(pluginManager),
+        getAdapterClass: () =>
+          import('./GCContentAdapter').then(r => r.default),
+      }),
+  )
 }

package/src/IndexedFastaAdapter/index.ts

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

package/src/LinearReferenceSequenceDisplay/configSchema.ts

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { configSchema as divSequenceRendererConfigSchema } from '../DivSequenceRenderer'
+import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema'
 
 export const configSchema = ConfigurationSchema(
   'LinearReferenceSequenceDisplay',

package/src/LinearReferenceSequenceDisplay/index.ts

@@ -1,2 +1,19 @@
-export { configSchema } from './configSchema'
-export { modelFactory } from './model'
+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 {
+      name: 'LinearReferenceSequenceDisplay',
+      configSchema,
+      stateModel,
+      trackType: 'ReferenceSequenceTrack',
+      viewType: 'LinearGenomeView',
+      ReactComponent: BaseLinearDisplayComponent,
+    }
+  })
+}

package/src/ReferenceSequenceTrack/index.ts

@@ -0,0 +1,21 @@
+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',
+      configSchema,
+      stateModel: createBaseTrackModel(
+        pluginManager,
+        'ReferenceSequenceTrack',
+        configSchema,
+      ),
+    })
+  })
+}