@jbrowse/plugin-sequence 2.17.0 → 2.18.0

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,70 +1,37 @@
-import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-// 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
+import { types } from 'mobx-state-tree';
+function x() { }
 export function createReferenceSeqTrackConfig(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
-         */
         sequenceType: {
             type: 'string',
             description: 'either dna or pep',
             defaultValue: 'dna',
         },
-        /**
-         * #slot
-         */
         description: {
             description: 'a description of the track',
             type: 'string',
             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,
@@ -76,9 +43,6 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             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) => d && displayTypes.add(d.type));
                 const trackType = pluginManager.getTrackType(snap.type);
                 trackType === null || trackType === void 0 ? void 0 : trackType.displayTypes.forEach(displayType => {
@@ -92,10 +56,6 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
-        /**
-         * #identifier
-         * all tracks have a globally unique 'trackId'
-         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/esm/ReferenceSequenceTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ReferenceSequenceTrackF(pluginManager: PluginManager): void;

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, doesIntersect2, revcom } from '@jbrowse/core/util';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
-import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
+import { toArray } from 'rxjs/operators';
 export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     async configure() {
         var _a;

package/esm/SequenceSearchAdapter/configSchema.d.ts

@@ -1,36 +1,21 @@
 declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     search: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     sequenceAdapter: {
         type: string;
         defaultValue: null;
     };
-    /**
-     * #slot
-     */
     searchForward: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     searchReverse: {
         type: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     caseInsensitive: {
         type: string;
         defaultValue: boolean;

package/esm/SequenceSearchAdapter/configSchema.js

@@ -1,41 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config SequenceSearchAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 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,

package/esm/SequenceSearchAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SequenceSearchAdapterF(pluginManager: PluginManager): void;

package/esm/SequenceSearchAdapter/index.js

@@ -1,13 +1,15 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default function SequenceSearchAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'SequenceSearchAdapter',
-        displayName: 'Sequence search adapter',
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        configSchema,
-        getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'SequenceSearchAdapter',
+            displayName: 'Sequence search adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema,
+            getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
+        });
+    });
 }

package/esm/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,26 +1,29 @@
+import { TwoBitFile } from '@gmod/twobit';
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class TwoBitAdapter extends BaseSequenceAdapter {
-    private twobit;
-    protected chromSizesData: Promise<Record<string, number> | undefined>;
+    protected setupP?: Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: Record<string, number> | undefined;
+    }>;
     private initChromSizes;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    setupPre(): Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: {
+            [k: string]: number;
+        } | undefined;
+    }>;
+    setup(): Promise<{
+        twobit: TwoBitFile;
+        chromSizesData: Record<string, number> | undefined;
+    }>;
     getRefNames(): Promise<string[]>;
-    getRegions(): Promise<NoAssemblyRegion[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
+    getRegions(): Promise<{
+        refName: string;
+        start: number;
+        end: number;
+    }[]>;
     getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
-    /**
-     * 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
-     */
     freeResources(): void;
 }

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -1,15 +1,12 @@
+import { TwoBitFile } from '@gmod/twobit';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { TwoBitFile } from '@gmod/twobit';
-import { readConfObject } from '@jbrowse/core/configuration';
 export default class TwoBitAdapter extends BaseSequenceAdapter {
     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');
@@ -23,23 +20,31 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
         }
         return undefined;
     }
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const pm = this.pluginManager;
-        this.chromSizesData = this.initChromSizes();
-        this.twobit = new TwoBitFile({
-            filehandle: openLocation(this.getConf('twoBitLocation'), pm),
-        });
+    async setupPre() {
+        return {
+            twobit: new TwoBitFile({
+                filehandle: openLocation(this.getConf('twoBitLocation'), this.pluginManager),
+            }),
+            chromSizesData: await this.initChromSizes(),
+        };
     }
-    async getRefNames() {
-        const chromSizesData = await this.chromSizesData;
-        if (chromSizesData) {
-            return Object.keys(chromSizesData);
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        return this.twobit.getSequenceNames();
+        return this.setupP;
+    }
+    async getRefNames() {
+        const { chromSizesData, twobit } = await this.setup();
+        return chromSizesData
+            ? Object.keys(chromSizesData)
+            : twobit.getSequenceNames();
     }
     async getRegions() {
-        const chromSizesData = await this.chromSizesData;
+        const { chromSizesData, twobit } = await this.setup();
         if (chromSizesData) {
             return Object.keys(chromSizesData).map(refName => ({
                 refName,
@@ -47,23 +52,21 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
                 end: chromSizesData[refName],
             }));
         }
-        const refSizes = await this.twobit.getSequenceSizes();
-        return Object.keys(refSizes).map(refName => ({
-            refName,
-            start: 0,
-            end: refSizes[refName],
-        }));
+        else {
+            const refSizes = await 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
-     */
     getFeatures({ refName, start, end }) {
         return ObservableCreate(async (observer) => {
-            const size = await this.twobit.getSequenceSize(refName);
+            const { twobit } = await this.setup();
+            const size = await twobit.getSequenceSize(refName);
             const regionEnd = size !== undefined ? Math.min(size, end) : end;
-            const seq = await this.twobit.getSequence(refName, start, regionEnd);
+            const seq = await twobit.getSequence(refName, start, regionEnd);
             if (seq) {
                 observer.next(new SimpleFeature({
                     id: `${refName} ${start}-${regionEnd}`,
@@ -73,10 +76,5 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
             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
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/TwoBitAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     twoBitLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const TwoBitAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: string;
         defaultValue: {

package/esm/TwoBitAdapter/configSchema.js

@@ -1,19 +1,10 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config TwoBitAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
-    /**
-     * #slot
-     */
     twoBitLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/TwoBitAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function TwoBitAdapterF(pluginManager: PluginManager): void;

package/esm/UnindexedFastaAdapter/UnindexedFastaAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 declare function parseSmallFasta(text: string): Map<string, {
     readonly description: string;
     readonly sequence: string;

package/esm/UnindexedFastaAdapter/UnindexedFastaAdapter.js

@@ -1,8 +1,8 @@
-import { BaseSequenceAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
-import { readConfObject } from '@jbrowse/core/configuration';
 function parseSmallFasta(text) {
     return new Map(text
         .split('>')
@@ -80,5 +80,5 @@ export default class UnindexedFastaAdapter extends BaseSequenceAdapter {
             observer.complete();
         });
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }

package/esm/UnindexedFastaAdapter/configSchema.d.ts

@@ -4,9 +4,6 @@ declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configu
         defaultValue: string;
         contextVariable: string[];
     };
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: string;
         defaultValue: {
@@ -14,9 +11,6 @@ declare const UnindexedFastaAdapter: import("@jbrowse/core/configuration/configu
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: string;
         type: string;

package/esm/UnindexedFastaAdapter/configSchema.js

@@ -1,17 +1,11 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config UnindexedFastaAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const UnindexedFastaAdapter = ConfigurationSchema('UnindexedFastaAdapter', {
     rewriteRefNames: {
         type: 'string',
         defaultValue: '',
         contextVariable: ['refName'],
     },
-    /**
-     * #slot
-     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -19,9 +13,6 @@ const UnindexedFastaAdapter = ConfigurationSchema('UnindexedFastaAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',

package/esm/UnindexedFastaAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function UnindexedFastaAdapterF(pluginManager: PluginManager): void;

package/esm/UnindexedFastaAdapter/index.js

@@ -1,13 +1,15 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export default function UnindexedFastaAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'UnindexedFastaAdapter',
-        displayName: 'Unindexed FASTA adapter',
-        configSchema,
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./UnindexedFastaAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'UnindexedFastaAdapter',
+            displayName: 'Unindexed FASTA adapter',
+            configSchema,
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            getAdapterClass: () => import('./UnindexedFastaAdapter').then(r => r.default),
+        });
+    });
 }

package/esm/createExtensionPoints.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/esm/createExtensionPoints.js

@@ -1,4 +1,4 @@
-import { makeIndex, getFileName, } from '@jbrowse/core/util/tracks';
+import { getFileName, makeIndex } from '@jbrowse/core/util/tracks';
 export default function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class SequencePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,13 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
-import TwoBitAdapterF from './TwoBitAdapter';
-import DivSequenceRendererF from './DivSequenceRenderer';
 import BgzipFastaAdapterF from './BgzipFastaAdapter';
 import ChromSizesAdapterF from './ChromSizesAdapter';
+import DivSequenceRendererF from './DivSequenceRenderer';
 import IndexedFastaAdapterF from './IndexedFastaAdapter';
-import UnindexedFastaAdapterF from './UnindexedFastaAdapter';
-import SequenceSearchAdapterF from './SequenceSearchAdapter';
-import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
 import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay';
+import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
+import SequenceSearchAdapterF from './SequenceSearchAdapter';
+import TwoBitAdapterF from './TwoBitAdapter';
+import UnindexedFastaAdapterF from './UnindexedFastaAdapter';
 import createExtensionPoints from './createExtensionPoints';
 export default class SequencePlugin extends Plugin {
     constructor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -57,5 +57,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }