@jbrowse/plugin-sequence 2.1.0 → 2.1.3

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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+{"version":3,"file":"GCContentAdapter.js","sourceRoot":"","sources":["../../src/GCContentAdapter/GCContentAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAmB,MAAM,oBAAoB,CAAA;AACnE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,MAAM,CAAC,OAAO,gBAAO,SAAQ,sBAAsB;IAAnD;;QACU,eAAU,GAAG,IAAI,CAAA;QAEjB,gBAAW,GAAG,IAAI,CAAA;QAElB,WAAM,GAAG,SAAS,CAAA;IAqF5B,CAAC;IAjFQ,KAAK,CAAC,SAAS;;QACpB,MAAM,OAAO,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAC,CAAA,CAAA;QAC3E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,OAAO,OAAO,CAAC,WAAqC,CAAA;IACtD,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,IAAiB;QACjD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,EAAE,GAAG,IAAI,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA,CAAC,uBAAuB;YAClF,MAAM,CAAC,GAAG,IAAI,CAAC,UAAU,KAAK,CAAC,CAAA;YAE/B,IAAI,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;YAChD,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,UAAU,GAAG,EAAE,CAAC,CAAA;YACzC,QAAQ,IAAI,EAAE,CAAA;YAEd,IAAI,QAAQ,GAAG,CAAC,IAAI,UAAU,GAAG,QAAQ,EAAE;gBACzC,QAAQ,CAAC,QAAQ,EAAE,CAAA;gBACnB,OAAM;aACP;YAED,MAAM,GAAG,GAAG,eAAe,CAAC,WAAW,CACrC;gBACE,GAAG,KAAK;gBACR,KAAK,EAAE,UAAU;gBACjB,GAAG,EAAE,QAAQ;aACd,EACD,IAAI,CACL,CAAA;YACD,MAAM,KAAK,GAAG,MAAM,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,SAAS,EAAE,CAAA;YACnD,MAAM,QAAQ,GAAG,CAAA,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,KAAI,EAAE,CAAA;YAE3C,KAAK,IAAI,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE;gBAChE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;gBAC1D,IAAI,EAAE,GAAG,CAAC,CAAA;gBACV,IAAI,EAAE,GAAG,CAAC,CAAA;gBACV,IAAI,GAAG,GAAG,CAAC,CAAA;gBACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBACjC,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;wBAChC,EAAE,EAAE,CAAA;qBACL;yBAAM,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;wBACvC,EAAE,EAAE,CAAA;qBACL;oBACD,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;wBAChB,GAAG,EAAE,CAAA;qBACN;iBACF;gBACD,MAAM,GAAG,GAAG,UAAU,CAAA;gBACtB,IAAI,KAAK,CAAA;gBACT,IAAI,IAAI,CAAC,MAAM,KAAK,SAAS,EAAE;oBAC7B,KAAK,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,CAAC,CAAA;iBAC/B;qBAAM,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM,EAAE;oBACjC,KAAK,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,CAAA;iBACnC;gBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,GAAG,GAAG,CAAC,EAAE;oBACjC,KAAK,EAAE,GAAG,GAAG,CAAC;oBACd,GAAG,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,CAAC,WAAW;oBAC/B,KAAK;iBACN,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAG,CAAC;;AAlF3B,sBAAY,GAAG,CAAC,eAAe,CAAC,CAAA"}

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 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,OAAO;QACL,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,aAAa,CAAC;QAC/C,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACzE,CAAA;AACH,CAAC,CAAA"}
+{"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/IndexedFastaAdapter.d.ts

@@ -6,8 +6,9 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseSequenceAdapter {
-    protected fasta: IndexedFasta;
-    protected header?: Promise<string>;
+    protected setupP?: Promise<{
+        fasta: IndexedFasta;
+    }>;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -16,7 +17,13 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
+    setupPre(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getHeader(): Promise<string | null>;
+    setup(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -4,56 +4,61 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature } from '@jbrowse/core/util';
 import AbortablePromiseCache from 'abortable-promise-cache';
-import LRU from '@jbrowse/core/util/QuickLRU';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 export default class extends BaseSequenceAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         this.seqCache = new AbortablePromiseCache({
-            cache: new LRU({ maxSize: 200 }),
+            cache: new QuickLRU({ maxSize: 200 }),
             fill: async (args, signal) => {
-                const { refName, start, end } = args;
-                return this.fasta.getSequence(refName, start, end, { ...args, signal });
+                const { refName, start, end, fasta } = args;
+                return fasta.getSequence(refName, start, end, { ...args, signal });
             },
         });
-        const fastaLocation = this.getConf('fastaLocation');
-        const faiLocation = this.getConf('faiLocation');
-        const fastaOpts = {
-            fasta: openLocation(fastaLocation, this.pluginManager),
-            fai: openLocation(faiLocation, this.pluginManager),
-        };
-        this.fasta = new IndexedFasta(fastaOpts);
     }
-    getRefNames(opts) {
-        return this.fasta.getSequenceNames(opts);
+    async getRefNames(opts) {
+        const { fasta } = await this.setup();
+        return fasta.getSequenceNames(opts);
     }
     async getRegions(opts) {
-        const seqSizes = await this.fasta.getSequenceSizes(opts);
+        const { fasta } = await this.setup();
+        const seqSizes = await fasta.getSequenceSizes(opts);
         return Object.keys(seqSizes).map(refName => ({
             refName,
             start: 0,
             end: seqSizes[refName],
         }));
     }
+    async setupPre() {
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        return {
+            fasta: new IndexedFasta({
+                fasta: openLocation(fastaLocation, this.pluginManager),
+                fai: openLocation(faiLocation, this.pluginManager),
+            }),
+        };
+    }
     async getHeader() {
-        if (this.header) {
-            return this.header;
-        }
         const loc = this.getConf('metadataLocation');
-        if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
-            return null;
+        return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
+            ? null
+            : openLocation(loc).readFile('utf8');
+    }
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        this.header = openLocation(loc)
-            .readFile('utf8')
-            .catch(e => {
-            this.header = undefined;
-            throw e;
-        });
-        return this.header;
+        return this.setupP;
     }
     getFeatures(region, opts) {
         const { refName, start, end } = region;
         return ObservableCreate(async (observer) => {
-            const size = await this.fasta.getSequenceSize(refName, opts);
+            const { fasta } = await this.setup();
+            const size = await fasta.getSequenceSize(refName, opts);
             const regionEnd = size !== undefined ? Math.min(size, end) : end;
             const chunks = [];
             const chunkSize = 128000;
@@ -65,7 +70,7 @@ export default class extends BaseSequenceAdapter {
                     start: chunkStart,
                     end: chunkStart + chunkSize,
                 };
-                chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+                chunks.push(this.seqCache.get(JSON.stringify(r), { ...r, fasta }, opts === null || opts === void 0 ? void 0 : opts.signal));
             }
             const seq = (await Promise.all(chunks))
                 .join('')

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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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 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"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 @@
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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 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,YAAY,GAAG,mBAAmB,CACtC,uBAAuB,EACvB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,sCAAsC;KACpD;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

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 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/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,uBAAuB;QAC7B,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,yBAAyB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACzD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

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 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}
+{"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;