@jbrowse/plugin-sequence 2.0.0 → 2.1.2

package/esm/DivSequenceRenderer/index.d.ts

@@ -1,2 +1,3 @@
-export { default as ReactComponent } from './components/DivSequenceRendering';
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/DivSequenceRenderer/index.js

@@ -1,3 +1,26 @@
-export { default as ReactComponent } from './components/DivSequenceRendering';
-export { default as configSchema } from './configSchema';
+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 {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    getExpandedRegion(region) {
+        return {
+            ...region,
+            start: Math.max(region.start - 3, 0),
+            end: region.end + 3,
+        };
+    }
+}
+export default (pluginManager) => {
+    pluginManager.addRendererType(() => new DivSequenceRenderer({
+        name: 'DivSequenceRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/DivSequenceRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/index.ts"],"names":[],"mappings":"AAGA,OAAO,mBAAmB,MAAM,mEAAmE,CAAA;AACnG,OAAO,cAAc,MAAM,mCAAmC,CAAA;AAC9D,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,+BAA+B;AAC/B,MAAM,mBAAoB,SAAQ,mBAAmB;IAArD;;QACE,gBAAW,GAAG,IAAI,CAAA;IASpB,CAAC;IAPC,iBAAiB,CAAC,MAAc;QAC9B,OAAO;YACL,GAAG,MAAM;YACT,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,CAAC,CAAC;YACpC,GAAG,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC;SACpB,CAAA;IACH,CAAC;CACF;AAED,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,mBAAmB,CAAC;QACtB,IAAI,EAAE,qBAAqB;QAC3B,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,6 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature, Region } from '@jbrowse/core/util';
 export default class extends BaseFeatureDataAdapter {
     private windowSize;
     private windowDelta;
@@ -8,11 +7,6 @@ export default class extends BaseFeatureDataAdapter {
     static capabilities: string[];
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/GCContentAdapter/GCContentAdapter.js

@@ -1,7 +1,6 @@
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { readConfObject } from '@jbrowse/core/configuration';
+import { SimpleFeature } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
 export default class default_1 extends BaseFeatureDataAdapter {
     constructor() {
@@ -12,27 +11,17 @@ export default class default_1 extends BaseFeatureDataAdapter {
     }
     async configure() {
         var _a;
-        // instantiate the sequence adapter
-        const sequenceAdapter = readConfObject(this.config, 'sequenceAdapter');
-        const dataAdapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, sequenceAdapter));
-        if (!dataAdapter) {
+        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 dataAdapter.dataAdapter;
+        return adapter.dataAdapter;
     }
     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
-     */
     getFeatures(query, opts) {
-        this.windowSize = 1000;
-        this.windowDelta = 1000;
-        this.gcMode = 'content';
         return ObservableCreate(async (observer) => {
             var _a;
             const sequenceAdapter = await this.configure();
@@ -49,7 +38,7 @@ export default class default_1 extends BaseFeatureDataAdapter {
                 ...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) {

package/esm/GCContentAdapter/GCContentAdapter.js.map

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

@@ -1,6 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./GCContentAdapter").default>;
-};
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/esm/GCContentAdapter/index.js

@@ -1,8 +1,16 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchemaF from './configSchema';
 export default (pluginManager) => {
-    return {
-        configSchema: pluginManager.load(configSchemaF),
+    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 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAE,aAAa,CAAC,aAAa,CAAC;QAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/IndexedFastaAdapter/index.d.ts

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

package/esm/IndexedFastaAdapter/index.js

@@ -1,2 +1,16 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'IndexedFastaAdapter',
+        configSchema,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/IndexedFastaAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,qBAAqB;QAC3B,YAAY;QACZ,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,uBAAuB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACvD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,4 +1,4 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { configSchema as divSequenceRendererConfigSchema } from '../DivSequenceRenderer';
+import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema';
 export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', { renderer: divSequenceRendererConfigSchema }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,YAAY,IAAI,+BAA+B,EAAE,MAAM,wBAAwB,CAAA;AAExF,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,+BAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,OAAO,IAAI,+BAA+B,EAAE,MAAM,qCAAqC,CAAA;AAEhG,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,+BAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/esm/LinearReferenceSequenceDisplay/index.d.ts

@@ -1,2 +1,3 @@
-export { configSchema } from './configSchema';
-export { modelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LinearReferenceSequenceDisplay/index.js

@@ -1,3 +1,17 @@
-export { configSchema } from './configSchema';
-export { modelFactory } from './model';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import { configSchema } from './configSchema';
+import { modelFactory } from './model';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const stateModel = modelFactory(configSchema);
+        return {
+            name: 'LinearReferenceSequenceDisplay',
+            configSchema,
+            stateModel,
+            trackType: 'ReferenceSequenceTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        };
+    });
+};
 //# sourceMappingURL=index.js.map

package/esm/LinearReferenceSequenceDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAA;AAEtC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,UAAU,GAAG,YAAY,CAAC,YAAY,CAAC,CAAA;QAC7C,OAAO;YACL,IAAI,EAAE,gCAAgC;YACtC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -182,7 +182,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {

package/esm/{referenceSeqTrackConfig.js → ReferenceSequenceTrack/configSchema.js}

@@ -60,4 +60,4 @@ export function createReferenceSeqTrackConfig(pluginManager) {
         }),
     });
 }
-//# sourceMappingURL=referenceSeqTrackConfig.js.map
+//# sourceMappingURL=configSchema.js.map

package/esm/ReferenceSequenceTrack/configSchema.js.map

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

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

package/esm/ReferenceSequenceTrack/index.js

@@ -0,0 +1,14 @@
+import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import { createReferenceSeqTrackConfig } from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addTrackType(() => {
+        const configSchema = createReferenceSeqTrackConfig(pluginManager);
+        return new TrackType({
+            name: 'ReferenceSequenceTrack',
+            configSchema,
+            stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/ReferenceSequenceTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/index.ts"],"names":[],"mappings":"AAEA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,EAAE,6BAA6B,EAAE,MAAM,gBAAgB,CAAA;AAE9D,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,6BAA6B,CAAC,aAAa,CAAC,CAAA;QAEjE,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,wBAAwB;YAC9B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

@@ -0,0 +1,8 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+export default class extends BaseFeatureDataAdapter {
+    configure(): Promise<BaseFeatureDataAdapter>;
+    getRefNames(): Promise<string[]>;
+    getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -0,0 +1,81 @@
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
+import { toArray } from 'rxjs/operators';
+export default class extends BaseFeatureDataAdapter {
+    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 = 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 = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.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();
+        });
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=SequenceSearchAdapter.js.map

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map

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

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/SequenceSearchAdapter/configSchema.js

@@ -0,0 +1,26 @@
+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;
+//# sourceMappingURL=configSchema.js.map

package/esm/SequenceSearchAdapter/configSchema.js.map

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

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

package/esm/SequenceSearchAdapter/index.js

@@ -0,0 +1,16 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'SequenceSearchAdapter',
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        configSchema,
+        getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
+    }));
+};
+//# sourceMappingURL=index.js.map

package/esm/SequenceSearchAdapter/index.js.map

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

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

package/esm/TwoBitAdapter/index.js

@@ -1,2 +1,16 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'TwoBitAdapter',
+        configSchema,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/TwoBitAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY;QACZ,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/createExtensionPoints.d.ts

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

package/esm/createExtensionPoints.js

@@ -0,0 +1,84 @@
+import { makeIndex, getFileName, } from '@jbrowse/core/util/tracks';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.2bit$/i;
+            const adapterName = 'TwoBitAdapter';
+            const fileName = getFileName(file);
+            const obj = {
+                type: adapterName,
+                twoBitLocation: file,
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'TwoBitAdapter') {
+                return 'ReferenceSequenceTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/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.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);
+        };
+    });
+};
+//# sourceMappingURL=createExtensionPoints.js.map

package/esm/createExtensionPoints.js.map

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