@jbrowse/plugin-sequence 2.2.0 → 2.2.2

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

@@ -1,8 +1,8 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`adapter can fetch features from volvox.2bit 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 20000,
     "refName": "ctgA",
     "seq": 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c",
@@ -12,16 +12,16 @@ Array [
 ]
 `;
 
-exports[`adapter can fetch features from volvox.2bit 2`] = `Array []`;
+exports[`adapter can fetch features from volvox.2bit 2`] = `[]`;
 
 exports[`adapter can fetch regions from with chrom.sizes 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 50001,
     "refName": "ctgA",
     "start": 0,
   },
-  Object {
+  {
     "end": 6079,
     "refName": "ctgB",
     "start": 0,

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

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

package/src/index.ts

@@ -6,7 +6,6 @@ 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'
@@ -21,7 +20,6 @@ export default class SequencePlugin extends Plugin {
     BgzipFastaAdapterF(pluginManager)
     ChromSizesAdapterF(pluginManager)
     IndexedFastaAdapterF(pluginManager)
-    GCContentAdapterF(pluginManager)
     SequenceSearchAdapterF(pluginManager)
     ReferenceSequenceTrackF(pluginManager)
     LinearReferenceSequenceDisplayF(pluginManager)

package/dist/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,17 +0,0 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
-export default class extends BaseFeatureDataAdapter {
-    private windowSize;
-    private windowDelta;
-    private gcMode;
-    static capabilities: string[];
-    configure(): Promise<BaseFeatureDataAdapter>;
-    getRefNames(): Promise<string[]>;
-    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources(): void;
-}

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -1,89 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const util_1 = require("@jbrowse/core/util");
-const operators_1 = require("rxjs/operators");
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.windowSize = 1000;
-        this.windowDelta = 1000;
-        this.gcMode = 'content';
-    }
-    async configure() {
-        var _a;
-        const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
-        if (!adapter) {
-            throw new Error('Error getting subadapter');
-        }
-        return adapter.dataAdapter;
-    }
-    async getRefNames() {
-        const adapter = await this.configure();
-        return adapter.getRefNames();
-    }
-    getFeatures(query, opts) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a;
-            const sequenceAdapter = await this.configure();
-            const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
-            const f = this.windowSize === 1;
-            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((0, operators_1.toArray)()).toPromise();
-            const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
-            for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
-                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                let nc = 0;
-                let ng = 0;
-                let len = 0;
-                for (let j = 0; j < r.length; j++) {
-                    if (r[j] === 'c' || r[j] === 'C') {
-                        nc++;
-                    }
-                    else if (r[j] === 'g' || r[j] === 'G') {
-                        ng++;
-                    }
-                    if (r[j] !== 'N') {
-                        len++;
-                    }
-                }
-                const pos = queryStart;
-                let score;
-                if (this.gcMode === 'content') {
-                    score = (ng + nc) / (len || 1);
-                }
-                else if (this.gcMode === 'skew') {
-                    score = (ng - nc) / (ng + nc || 1);
-                }
-                observer.next(new util_1.SimpleFeature({
-                    uniqueId: `${this.id}_${pos + i}`,
-                    start: pos + i,
-                    end: pos + i + this.windowDelta,
-                    score,
-                }));
-            }
-            observer.complete();
-        });
-    }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
-}
-exports.default = default_1;
-default_1.capabilities = ['hasLocalStats'];
-//# sourceMappingURL=GCContentAdapter.js.map

package/dist/GCContentAdapter/GCContentAdapter.js.map

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package/dist/GCContentAdapter/configSchema.d.ts

@@ -1,3 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const GCContentAdapterF: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default GCContentAdapterF;

package/dist/GCContentAdapter/configSchema.js

@@ -1,17 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config GCContentAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const GCContentAdapterF = (pluginManager) => {
-    return (0, configuration_1.ConfigurationSchema)('GCContentAdapter', {
-        /**
-         * #slot
-         */
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true });
-};
-exports.default = GCContentAdapterF;
-//# sourceMappingURL=configSchema.js.map

package/dist/GCContentAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/GCContentAdapter/index.d.ts

@@ -1,3 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;

package/dist/GCContentAdapter/index.js

@@ -1,44 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'GCContentAdapter',
-        adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-        },
-        configSchema: (0, configSchema_1.default)(pluginManager),
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GCContentAdapter'))).then(r => r.default),
-    }));
-};
-//# sourceMappingURL=index.js.map

package/dist/GCContentAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,17 +0,0 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
-export default class extends BaseFeatureDataAdapter {
-    private windowSize;
-    private windowDelta;
-    private gcMode;
-    static capabilities: string[];
-    configure(): Promise<BaseFeatureDataAdapter>;
-    getRefNames(): Promise<string[]>;
-    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources(): void;
-}

package/esm/GCContentAdapter/GCContentAdapter.js

@@ -1,86 +0,0 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature } from '@jbrowse/core/util';
-import { toArray } from 'rxjs/operators';
-export default class default_1 extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.windowSize = 1000;
-        this.windowDelta = 1000;
-        this.gcMode = 'content';
-    }
-    async configure() {
-        var _a;
-        const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
-        if (!adapter) {
-            throw new Error('Error getting subadapter');
-        }
-        return adapter.dataAdapter;
-    }
-    async getRefNames() {
-        const adapter = await this.configure();
-        return adapter.getRefNames();
-    }
-    getFeatures(query, opts) {
-        return ObservableCreate(async (observer) => {
-            var _a;
-            const sequenceAdapter = await this.configure();
-            const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
-            const f = this.windowSize === 1;
-            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 = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
-            for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
-                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                let nc = 0;
-                let ng = 0;
-                let len = 0;
-                for (let j = 0; j < r.length; j++) {
-                    if (r[j] === 'c' || r[j] === 'C') {
-                        nc++;
-                    }
-                    else if (r[j] === 'g' || r[j] === 'G') {
-                        ng++;
-                    }
-                    if (r[j] !== 'N') {
-                        len++;
-                    }
-                }
-                const pos = queryStart;
-                let score;
-                if (this.gcMode === 'content') {
-                    score = (ng + nc) / (len || 1);
-                }
-                else if (this.gcMode === 'skew') {
-                    score = (ng - nc) / (ng + nc || 1);
-                }
-                observer.next(new SimpleFeature({
-                    uniqueId: `${this.id}_${pos + i}`,
-                    start: pos + i,
-                    end: pos + i + this.windowDelta,
-                    score,
-                }));
-            }
-            observer.complete();
-        });
-    }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
-}
-default_1.capabilities = ['hasLocalStats'];
-//# sourceMappingURL=GCContentAdapter.js.map

package/esm/GCContentAdapter/GCContentAdapter.js.map

@@ -1 +0,0 @@
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package/esm/GCContentAdapter/configSchema.d.ts

@@ -1,3 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const GCContentAdapterF: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default GCContentAdapterF;

package/esm/GCContentAdapter/configSchema.js

@@ -1,15 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config GCContentAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const GCContentAdapterF = (pluginManager) => {
-    return ConfigurationSchema('GCContentAdapter', {
-        /**
-         * #slot
-         */
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true });
-};
-export default GCContentAdapterF;
-//# sourceMappingURL=configSchema.js.map

package/esm/GCContentAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/GCContentAdapter/index.d.ts

@@ -1,3 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;

package/esm/GCContentAdapter/index.js

@@ -1,16 +0,0 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchemaF from './configSchema';
-export default (pluginManager) => {
-    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),
-    }));
-};
-//# sourceMappingURL=index.js.map

package/esm/GCContentAdapter/index.js.map

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package/src/GCContentAdapter/GCContentAdapter.ts

@@ -1,99 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { SimpleFeature, Feature, Region } from '@jbrowse/core/util'
-import { toArray } from 'rxjs/operators'
-
-export default class extends BaseFeatureDataAdapter {
-  private windowSize = 1000
-
-  private windowDelta = 1000
-
-  private gcMode = 'content'
-
-  public static capabilities = ['hasLocalStats']
-
-  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 = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
-      const f = this.windowSize === 1
-
-      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 = feats[0]?.get('seq') || ''
-
-      for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
-        const r = f ? residues[i] : residues.slice(i - hw, i + hw)
-        let nc = 0
-        let ng = 0
-        let len = 0
-        for (let j = 0; j < r.length; j++) {
-          if (r[j] === 'c' || r[j] === 'C') {
-            nc++
-          } else if (r[j] === 'g' || r[j] === 'G') {
-            ng++
-          }
-          if (r[j] !== 'N') {
-            len++
-          }
-        }
-        const pos = queryStart
-        let score
-        if (this.gcMode === 'content') {
-          score = (ng + nc) / (len || 1)
-        } else if (this.gcMode === 'skew') {
-          score = (ng - nc) / (ng + nc || 1)
-        }
-
-        observer.next(
-          new SimpleFeature({
-            uniqueId: `${this.id}_${pos + i}`,
-            start: pos + i,
-            end: pos + i + this.windowDelta,
-            score,
-          }),
-        )
-      }
-      observer.complete()
-    })
-  }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the forseeable future and can be purged
-   * from caches, etc
-   */
-  public freeResources(/* { region } */) {}
-}

package/src/GCContentAdapter/configSchema.ts

@@ -1,22 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config GCContentAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const GCContentAdapterF = (pluginManager: PluginManager) => {
-  return ConfigurationSchema(
-    'GCContentAdapter',
-    {
-      /**
-       * #slot
-       */
-      sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    },
-    { explicitlyTyped: true },
-  )
-}
-
-export default GCContentAdapterF

package/src/GCContentAdapter/index.ts

@@ -1,22 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchemaF from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  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),
-      }),
-  )
-}