@jbrowse/plugin-sequence 2.11.0 → 2.11.2

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,6 +1,6 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class extends IndexedFasta {
+export default class BgzipFastaAdapter extends IndexedFasta {
     setupPre(): Promise<{
         fasta: BgzipIndexedFasta;
     }>;

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const indexedfasta_1 = require("@gmod/indexedfasta");
 const io_1 = require("@jbrowse/core/util/io");
 const IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
-class default_1 extends IndexedFastaAdapter_1.default {
+class BgzipFastaAdapter extends IndexedFastaAdapter_1.default {
     async setupPre() {
         const fastaLocation = this.getConf('fastaLocation');
         const faiLocation = this.getConf('faiLocation');
@@ -19,4 +19,4 @@ class default_1 extends IndexedFastaAdapter_1.default {
         return { fasta: new indexedfasta_1.BgzipIndexedFasta(fastaOpts) };
     }
 }
-exports.default = default_1;
+exports.default = BgzipFastaAdapter;

package/dist/BgzipFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BgzipFastaAdapterF(pluginManager: PluginManager): void;

package/dist/BgzipFastaAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (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) => {
+function BgzipFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'BgzipFastaAdapter',
         displayName: 'Bgzip-indexed FASTA adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = BgzipFastaAdapterF;

package/dist/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,5 +1,5 @@
 import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class extends BaseAdapter implements RegionsAdapter {
+export default class ChromSizesAdapter extends BaseAdapter implements RegionsAdapter {
     protected setupP?: Promise<Record<string, number>>;
     setupPre(): Promise<{
         [k: string]: number;

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
-class default_1 extends BaseAdapter_1.BaseAdapter {
+class ChromSizesAdapter extends BaseAdapter_1.BaseAdapter {
     async setupPre() {
         const pm = this.pluginManager;
         const file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
@@ -38,4 +38,4 @@ class default_1 extends BaseAdapter_1.BaseAdapter {
     }
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = ChromSizesAdapter;

package/dist/ChromSizesAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChromSizesAdapterF(pluginManager: PluginManager): void;

package/dist/ChromSizesAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (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) => {
+function ChromSizesAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'ChromSizesAdapter',
         displayName: 'Chrom sizes adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = ChromSizesAdapterF;

package/dist/DivSequenceRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function DivSequenceRendererF(pluginManager: PluginManager): void;

package/dist/DivSequenceRenderer/index.js

@@ -20,11 +20,12 @@ class DivSequenceRenderer extends FeatureRendererType_1.default {
         };
     }
 }
-exports.default = (pluginManager) => {
+function DivSequenceRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DivSequenceRenderer({
         name: 'DivSequenceRenderer',
         ReactComponent: DivSequenceRendering_1.default,
         configSchema: configSchema_1.default,
         pluginManager,
     }));
-};
+}
+exports.default = DivSequenceRendererF;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -2,7 +2,7 @@ import { IndexedFasta } from '@gmod/indexedfasta';
 import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
-export default class extends BaseSequenceAdapter {
+export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     protected setupP?: Promise<{
         fasta: IndexedFasta;
     }>;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -10,7 +10,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
+class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new abortable_promise_cache_1.default({
@@ -97,4 +97,4 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
      */
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = IndexedFastaAdapter;

package/dist/IndexedFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function IndexedFastaAdapterF(pluginManager: PluginManager): void;

package/dist/IndexedFastaAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (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) => {
+function IndexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'IndexedFastaAdapter',
         displayName: 'Indexed FASTA adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = IndexedFastaAdapterF;

package/dist/LinearReferenceSequenceDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearReferenceSequenceDisplayF(pluginManager: PluginManager): void;

package/dist/LinearReferenceSequenceDisplay/index.js

@@ -4,7 +4,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configSchema_1 = require("./configSchema");
 const model_1 = require("./model");
-exports.default = (pluginManager) => {
+function LinearReferenceSequenceDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const stateModel = (0, model_1.modelFactory)(configSchema_1.configSchema);
         return new pluggableElementTypes_1.DisplayType({
@@ -17,4 +17,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearReferenceSequenceDisplayF;

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -70,34 +70,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string; /**
-             * #property
-             */
+            type: string;
             defaultValue: number;
             description: string;
-        };
+        }; /**
+         * #property
+         */
         height: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         mouseover: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
@@ -227,6 +225,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -355,34 +354,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string; /**
-             * #property
-             */
+            type: string;
             defaultValue: number;
             description: string;
-        };
+        }; /**
+         * #property
+         */
         height: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         mouseover: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;

package/dist/ReferenceSequenceTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ReferenceSequenceTrackF(pluginManager: PluginManager): void;

package/dist/ReferenceSequenceTrack/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = require("./configSchema");
-exports.default = (pluginManager) => {
+function ReferenceSequenceTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = (0, configSchema_1.createReferenceSeqTrackConfig)(pluginManager);
         return new TrackType_1.default({
@@ -16,4 +16,5 @@ exports.default = (pluginManager) => {
             stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });
     });
-};
+}
+exports.default = ReferenceSequenceTrackF;

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

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

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -5,7 +5,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const operators_1 = require("rxjs/operators");
 const rxjs_2 = require("rxjs");
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+class SequenceSearchAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configure() {
         var _a;
         const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
@@ -22,10 +22,9 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
         return (0, rxjs_1.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;
+            const hw = 10000;
+            const queryEnd = query.end + hw;
+            const queryStart = Math.max(0, query.start - hw);
             if (queryEnd < 0 || queryStart > queryEnd) {
                 observer.complete();
                 return;
@@ -46,13 +45,14 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (searchForward) {
                     const matches = residues.matchAll(re);
                     for (const match of matches) {
-                        const s = queryStart + (match.index || 0);
-                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                        const s = queryStart + match.index;
+                        const e = queryStart + match.index + match[0].length;
+                        if ((0, util_1.doesIntersect2)(s, e, query.start, query.end)) {
                             observer.next(new util_1.SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-p`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-pos`,
                                 refName: query.refName,
                                 start: s,
-                                end: s + match[0].length,
+                                end: e,
                                 name: match[0],
                                 strand: 1,
                             }));
@@ -62,14 +62,15 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (searchReverse) {
                     const matches = (0, util_1.revcom)(residues).matchAll(re);
                     for (const match of matches) {
-                        const s = queryEnd - (match.index || 0);
-                        if ((0, util_1.doesIntersect2)(s, s + search.length, query.start, query.end)) {
+                        const e = queryEnd - match.index;
+                        const s = queryEnd - match.index - match[0].length;
+                        if ((0, util_1.doesIntersect2)(s, e, query.start, query.end)) {
                             observer.next(new util_1.SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-n`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-neg`,
                                 refName: query.refName,
-                                start: s - match[0].length,
+                                start: s,
+                                end: e,
                                 name: match[0],
-                                end: s,
                                 strand: -1,
                             }));
                         }
@@ -81,4 +82,4 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-exports.default = default_1;
+exports.default = SequenceSearchAdapter;

package/dist/SequenceSearchAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function SequenceSearchAdapterF(pluginManager: PluginManager): void;

package/dist/SequenceSearchAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (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) => {
+function SequenceSearchAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'SequenceSearchAdapter',
         displayName: 'Sequence search adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = SequenceSearchAdapterF;

package/dist/TwoBitAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function TwoBitAdapterF(pluginManager: PluginManager): void;

package/dist/TwoBitAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (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) => {
+function TwoBitAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'TwoBitAdapter',
         displayName: 'TwoBit adapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./TwoBitAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = TwoBitAdapterF;

package/dist/createExtensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/createExtensionPoints.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.2bit$/i;
@@ -82,4 +82,5 @@ exports.default = (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}
+exports.default = ExtensionPointsF;

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.d.ts

@@ -1,6 +1,6 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class extends IndexedFasta {
+export default class BgzipFastaAdapter extends IndexedFasta {
     setupPre(): Promise<{
         fasta: BgzipIndexedFasta;
     }>;

package/esm/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,7 +1,7 @@
 import { BgzipIndexedFasta } from '@gmod/indexedfasta';
 import { openLocation } from '@jbrowse/core/util/io';
 import IndexedFasta from '../IndexedFastaAdapter/IndexedFastaAdapter';
-export default class extends IndexedFasta {
+export default class BgzipFastaAdapter extends IndexedFasta {
     async setupPre() {
         const fastaLocation = this.getConf('fastaLocation');
         const faiLocation = this.getConf('faiLocation');

package/esm/BgzipFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BgzipFastaAdapterF(pluginManager: PluginManager): void;

package/esm/BgzipFastaAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function BgzipFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'BgzipFastaAdapter',
         displayName: 'Bgzip-indexed FASTA adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
     }));
-};
+}

package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,5 +1,5 @@
 import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export default class extends BaseAdapter implements RegionsAdapter {
+export default class ChromSizesAdapter extends BaseAdapter implements RegionsAdapter {
     protected setupP?: Promise<Record<string, number>>;
     setupPre(): Promise<{
         [k: string]: number;

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,6 +1,6 @@
 import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
-export default class extends BaseAdapter {
+export default class ChromSizesAdapter extends BaseAdapter {
     async setupPre() {
         const pm = this.pluginManager;
         const file = openLocation(this.getConf('chromSizesLocation'), pm);

package/esm/ChromSizesAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChromSizesAdapterF(pluginManager: PluginManager): void;

package/esm/ChromSizesAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function ChromSizesAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ChromSizesAdapter',
         displayName: 'Chrom sizes adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
     }));
-};
+}

package/esm/DivSequenceRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function DivSequenceRendererF(pluginManager: PluginManager): void;

package/esm/DivSequenceRenderer/index.js

@@ -15,11 +15,11 @@ class DivSequenceRenderer extends FeatureRendererType {
         };
     }
 }
-export default (pluginManager) => {
+export default function DivSequenceRendererF(pluginManager) {
     pluginManager.addRendererType(() => new DivSequenceRenderer({
         name: 'DivSequenceRenderer',
         ReactComponent,
         configSchema,
         pluginManager,
     }));
-};
+}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -2,7 +2,7 @@ import { IndexedFasta } from '@gmod/indexedfasta';
 import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
-export default class extends BaseSequenceAdapter {
+export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     protected setupP?: Promise<{
         fasta: IndexedFasta;
     }>;

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -5,7 +5,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature } from '@jbrowse/core/util';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from '@jbrowse/core/util/QuickLRU';
-export default class extends BaseSequenceAdapter {
+export default class IndexedFastaAdapter extends BaseSequenceAdapter {
     constructor() {
         super(...arguments);
         this.seqCache = new AbortablePromiseCache({

package/esm/IndexedFastaAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function IndexedFastaAdapterF(pluginManager: PluginManager): void;

package/esm/IndexedFastaAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function IndexedFastaAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'IndexedFastaAdapter',
         displayName: 'Indexed FASTA adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
     }));
-};
+}

package/esm/LinearReferenceSequenceDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearReferenceSequenceDisplayF(pluginManager: PluginManager): void;

package/esm/LinearReferenceSequenceDisplay/index.js

@@ -2,7 +2,7 @@ import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { configSchema } from './configSchema';
 import { modelFactory } from './model';
-export default (pluginManager) => {
+export default function LinearReferenceSequenceDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const stateModel = modelFactory(configSchema);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -70,34 +70,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string; /**
-             * #property
-             */
+            type: string;
             defaultValue: number;
             description: string;
-        };
+        }; /**
+         * #property
+         */
         height: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         mouseover: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
@@ -227,6 +225,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
@@ -355,34 +354,32 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
-            description: string; /**
-             * #property
-             */
+            description: string;
             defaultValue: number;
         };
         fetchSizeLimit: {
-            type: string; /**
-             * #property
-             */
+            type: string;
             defaultValue: number;
             description: string;
-        };
+        }; /**
+         * #property
+         */
         height: {
             type: string;
-            defaultValue: number; /**
-             * #property
-             */
+            defaultValue: number;
             description: string;
         };
         mouseover: {
             type: string;
             description: string;
-            /**
-             * #getter
-             */
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;

package/esm/ReferenceSequenceTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ReferenceSequenceTrackF(pluginManager: PluginManager): void;

package/esm/ReferenceSequenceTrack/index.js

@@ -1,7 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { createReferenceSeqTrackConfig } from './configSchema';
-export default (pluginManager) => {
+export default function ReferenceSequenceTrackF(pluginManager) {
     pluginManager.addTrackType(() => {
         const configSchema = createReferenceSeqTrackConfig(pluginManager);
         return new TrackType({
@@ -11,4 +11,4 @@ export default (pluginManager) => {
             stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });
     });
-};
+}

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.d.ts

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

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -3,7 +3,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { SimpleFeature, revcom, doesIntersect2, } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
-export default class extends BaseFeatureDataAdapter {
+export default class SequenceSearchAdapter extends BaseFeatureDataAdapter {
     async configure() {
         var _a;
         const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
@@ -20,10 +20,9 @@ export default class extends BaseFeatureDataAdapter {
         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;
+            const hw = 10000;
+            const queryEnd = query.end + hw;
+            const queryStart = Math.max(0, query.start - hw);
             if (queryEnd < 0 || queryStart > queryEnd) {
                 observer.complete();
                 return;
@@ -44,13 +43,14 @@ export default class extends BaseFeatureDataAdapter {
                 if (searchForward) {
                     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)) {
+                        const s = queryStart + match.index;
+                        const e = queryStart + match.index + match[0].length;
+                        if (doesIntersect2(s, e, query.start, query.end)) {
                             observer.next(new SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-p`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-pos`,
                                 refName: query.refName,
                                 start: s,
-                                end: s + match[0].length,
+                                end: e,
                                 name: match[0],
                                 strand: 1,
                             }));
@@ -60,14 +60,15 @@ export default class extends BaseFeatureDataAdapter {
                 if (searchReverse) {
                     const matches = revcom(residues).matchAll(re);
                     for (const match of matches) {
-                        const s = queryEnd - (match.index || 0);
-                        if (doesIntersect2(s, s + search.length, query.start, query.end)) {
+                        const e = queryEnd - match.index;
+                        const s = queryEnd - match.index - match[0].length;
+                        if (doesIntersect2(s, e, query.start, query.end)) {
                             observer.next(new SimpleFeature({
-                                uniqueId: `${this.id}-match-${s}-n`,
+                                uniqueId: `${this.id}-${s}-${match[0]}-neg`,
                                 refName: query.refName,
-                                start: s - match[0].length,
+                                start: s,
+                                end: e,
                                 name: match[0],
-                                end: s,
                                 strand: -1,
                             }));
                         }

package/esm/SequenceSearchAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function SequenceSearchAdapterF(pluginManager: PluginManager): void;

package/esm/SequenceSearchAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function SequenceSearchAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'SequenceSearchAdapter',
         displayName: 'Sequence search adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         configSchema,
         getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),
     }));
-};
+}

package/esm/TwoBitAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function TwoBitAdapterF(pluginManager: PluginManager): void;

package/esm/TwoBitAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function TwoBitAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'TwoBitAdapter',
         displayName: 'TwoBit adapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         },
         getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
     }));
-};
+}

package/esm/createExtensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/esm/createExtensionPoints.js

@@ -1,5 +1,5 @@
 import { makeIndex, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.2bit$/i;
@@ -80,4 +80,4 @@ export default (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "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": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }