@jbrowse/plugin-sequence 2.1.7 → 2.2.1

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 _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;

package/esm/GCContentAdapter/configSchema.js

@@ -1,7 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default (pluginManager) => {
-    return ConfigurationSchema('GCContentAdapter', {
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true });
-};
-//# 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

@@ -1 +0,0 @@
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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

@@ -1,12 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-export default (pluginManager: PluginManager) => {
-  return ConfigurationSchema(
-    'GCContentAdapter',
-    {
-      sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    },
-    { explicitlyTyped: true },
-  )
-}

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),
-      }),
-  )
-}