@jbrowse/plugin-sequence 2.2.0 → 2.2.2

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -2,15 +2,11 @@ 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';
-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 setupP?: Promise<{
         fasta: IndexedFasta;
     }>;
     private seqCache;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getRegions(opts?: BaseOptions): Promise<{
         refName: string;
@@ -27,7 +23,7 @@ export default class extends BaseSequenceAdapter {
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -11,8 +11,8 @@ 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 {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
+    constructor() {
+        super(...arguments);
         this.seqCache = new abortable_promise_cache_1.default({
             cache: new QuickLRU_1.default({ maxSize: 200 }),
             fill: async (args, signal) => {
@@ -92,7 +92,7 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAiD;AACjD,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAA2D;AAC3D,sFAA2D;AAC3D,2EAAkD;AAIlD,eAAqB,SAAQ,iCAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,iCAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,kBAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAyFJ,CAAC;IAvFQ,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,2BAAY,CAAC;gBACtB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAlGD,4BAkGC"}

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -37,12 +37,12 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
             const feats = await ret.pipe((0, operators_1.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 searchForward = 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) {
+                if (searchForward) {
                     const matches = residues.matchAll(re);
                     for (const match of matches) {
                         const s = queryStart + (match.index || 0);

package/dist/SequenceSearchAdapter/SequenceSearchAdapter.js.map

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package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -19,7 +19,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
     getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/dist/TwoBitAdapter/TwoBitAdapter.js

@@ -10,13 +10,6 @@ const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeatur
 const twobit_1 = require("@gmod/twobit");
 const configuration_1 = require("@jbrowse/core/configuration");
 class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        this.chromSizesData = this.initChromSizes();
-        this.twobit = new twobit_1.TwoBitFile({
-            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
-        });
-    }
     async initChromSizes() {
         const conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
         // check against default and empty in case someone makes the field blank in
@@ -32,6 +25,13 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
         }
         return undefined;
     }
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.chromSizesData = this.initChromSizes();
+        this.twobit = new twobit_1.TwoBitFile({
+            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), this.pluginManager),
+        });
+    }
     async getRefNames() {
         const chromSizesData = await this.chromSizesData;
         if (chromSizesData) {
@@ -76,7 +76,7 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/dist/TwoBitAdapter/TwoBitAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IAOpD,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAhGD,gCAgGC"}

package/dist/index.js

@@ -9,7 +9,6 @@ const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
 const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
 const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
 const IndexedFastaAdapter_1 = __importDefault(require("./IndexedFastaAdapter"));
-const GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
 const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
 const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
 const LinearReferenceSequenceDisplay_1 = __importDefault(require("./LinearReferenceSequenceDisplay"));
@@ -25,7 +24,6 @@ class SequencePlugin extends Plugin_1.default {
         (0, BgzipFastaAdapter_1.default)(pluginManager);
         (0, ChromSizesAdapter_1.default)(pluginManager);
         (0, IndexedFastaAdapter_1.default)(pluginManager);
-        (0, GCContentAdapter_1.default)(pluginManager);
         (0, SequenceSearchAdapter_1.default)(pluginManager);
         (0, ReferenceSequenceTrack_1.default)(pluginManager);
         (0, LinearReferenceSequenceDisplay_1.default)(pluginManager);

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAGzC,oEAA4C;AAC5C,gFAAwD;AACxD,4EAAoD;AACpD,4EAAoD;AACpD,gFAAwD;AACxD,0EAAkD;AAClD,oFAA4D;AAC5D,sFAA8D;AAC9D,sGAA8E;AAC9E,oFAA2D;AAE3D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAczB,CAAC;IAZC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;QACtC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,+BAAqB,EAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF;AAfD,iCAeC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAGzC,oEAA4C;AAC5C,gFAAwD;AACxD,4EAAoD;AACpD,4EAAoD;AACpD,gFAAwD;AACxD,oFAA4D;AAC5D,sFAA8D;AAC9D,sGAA8E;AAC9E,oFAA2D;AAE3D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAazB,CAAC;IAXC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;QACtC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,+BAAqB,EAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF;AAdD,iCAcC"}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -2,15 +2,11 @@ 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';
-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 setupP?: Promise<{
         fasta: IndexedFasta;
     }>;
     private seqCache;
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getRegions(opts?: BaseOptions): Promise<{
         refName: string;
@@ -27,7 +23,7 @@ export default class extends BaseSequenceAdapter {
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -6,8 +6,8 @@ import { SimpleFeature } from '@jbrowse/core/util';
 import AbortablePromiseCache from 'abortable-promise-cache';
 import QuickLRU from '@jbrowse/core/util/QuickLRU';
 export default class extends BaseSequenceAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
+    constructor() {
+        super(...arguments);
         this.seqCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 200 }),
             fill: async (args, signal) => {
@@ -87,7 +87,7 @@ export default class extends BaseSequenceAdapter {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js

@@ -35,12 +35,12 @@ export default class extends BaseFeatureDataAdapter {
             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 searchForward = 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) {
+                if (searchForward) {
                     const matches = residues.matchAll(re);
                     for (const match of matches) {
                         const s = queryStart + (match.index || 0);

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.js.map

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package/esm/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -19,7 +19,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
     getFeatures({ refName, start, end }: NoAssemblyRegion): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources(): void;

package/esm/TwoBitAdapter/TwoBitAdapter.js

@@ -5,13 +5,6 @@ import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { TwoBitFile } from '@gmod/twobit';
 import { readConfObject } from '@jbrowse/core/configuration';
 export default class TwoBitAdapter extends BaseSequenceAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        this.chromSizesData = this.initChromSizes();
-        this.twobit = new TwoBitFile({
-            filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
-        });
-    }
     async initChromSizes() {
         const conf = readConfObject(this.config, 'chromSizesLocation');
         // check against default and empty in case someone makes the field blank in
@@ -27,6 +20,13 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
         }
         return undefined;
     }
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.chromSizesData = this.initChromSizes();
+        this.twobit = new TwoBitFile({
+            filehandle: openLocation(readConfObject(config, 'twoBitLocation'), this.pluginManager),
+        });
+    }
     async getRefNames() {
         const chromSizesData = await this.chromSizesData;
         if (chromSizesData) {
@@ -71,7 +71,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
     }
     /**
      * called to provide a hint that data tied to a certain region
-     * will not be needed for the forseeable future and can be purged
+     * will not be needed for the foreseeable future and can be purged
      * from caches, etc
      */
     freeResources( /* { region } */) { }

package/esm/TwoBitAdapter/TwoBitAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAK5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,mBAAmB;IAOpD,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,UAAU,CAAC;YAC3B,UAAU,EAAE,YAAY,CACtB,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}

package/esm/index.js

@@ -4,7 +4,6 @@ import DivSequenceRendererF from './DivSequenceRenderer';
 import BgzipFastaAdapterF from './BgzipFastaAdapter';
 import ChromSizesAdapterF from './ChromSizesAdapter';
 import IndexedFastaAdapterF from './IndexedFastaAdapter';
-import GCContentAdapterF from './GCContentAdapter';
 import SequenceSearchAdapterF from './SequenceSearchAdapter';
 import ReferenceSequenceTrackF from './ReferenceSequenceTrack';
 import LinearReferenceSequenceDisplayF from './LinearReferenceSequenceDisplay';
@@ -20,7 +19,6 @@ export default class SequencePlugin extends Plugin {
         BgzipFastaAdapterF(pluginManager);
         ChromSizesAdapterF(pluginManager);
         IndexedFastaAdapterF(pluginManager);
-        GCContentAdapterF(pluginManager);
         SequenceSearchAdapterF(pluginManager);
         ReferenceSequenceTrackF(pluginManager);
         LinearReferenceSequenceDisplayF(pluginManager);

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAE3D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAczB,CAAC;IAZC,OAAO,CAAC,aAA4B;QAClC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,sBAAsB,CAAC,aAAa,CAAC,CAAA;QACrC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,qBAAqB,CAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,+BAA+B,MAAM,kCAAkC,CAAA;AAC9E,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAE3D,MAAM,CAAC,OAAO,OAAO,cAAe,SAAQ,MAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAazB,CAAC;IAXC,OAAO,CAAC,aAA4B;QAClC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,sBAAsB,CAAC,aAAa,CAAC,CAAA;QACrC,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,+BAA+B,CAAC,aAAa,CAAC,CAAA;QAC9C,qBAAqB,CAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.2.0",
+  "version": "2.2.2",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -27,7 +27,7 @@
     "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/sequence",
     "prepublishOnly": "yarn test",
-    "prepack": "yarn build; yarn useDist",
+    "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
@@ -59,5 +59,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
 }

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

@@ -1,8 +1,8 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`can use a indexed fasta with gzi 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 20000,
     "refName": "ctgA",
     "seq": 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c",
@@ -12,4 +12,4 @@ Array [
 ]
 `;
 
-exports[`can use a indexed fasta with gzi 2`] = `Array []`;
+exports[`can use a indexed fasta with gzi 2`] = `[]`;

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -7,11 +7,8 @@ import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { SimpleFeature, Feature } from '@jbrowse/core/util'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import AbortablePromiseCache from 'abortable-promise-cache'
 import QuickLRU from '@jbrowse/core/util/QuickLRU'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 type T = { refName: string; start: number; end: number; fasta: IndexedFasta }
 
@@ -26,14 +23,6 @@ export default class extends BaseSequenceAdapter {
     },
   })
 
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-  }
-
   public async getRefNames(opts?: BaseOptions) {
     const { fasta } = await this.setup()
     return fasta.getSequenceNames(opts)
@@ -117,7 +106,7 @@ export default class extends BaseSequenceAdapter {
 
   /**
    * called to provide a hint that data tied to a certain region
-   * will not be needed for the forseeable future and can be purged
+   * will not be needed for the foreseeable future and can be purged
    * from caches, etc
    */
   public freeResources(/* { region } */): void {}

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

@@ -1,8 +1,8 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`adapter can fetch sequence from volvox.fa 1`] = `
-Array [
-  Object {
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c",
@@ -12,4 +12,4 @@ Array [
 ]
 `;
 
-exports[`adapter can fetch sequence from volvox.fa 2`] = `Array []`;
+exports[`adapter can fetch sequence from volvox.fa 2`] = `[]`;

package/src/SequenceSearchAdapter/SequenceSearchAdapter.ts

@@ -50,13 +50,13 @@ export default class extends BaseFeatureDataAdapter {
       const feats = await ret.pipe(toArray()).toPromise()
       const residues: string = feats[0]?.get('seq') || ''
       const search = this.getConf('search')
-      const searchFoward = this.getConf('searchForward')
+      const searchForward = 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) {
+        if (searchForward) {
           const matches = residues.matchAll(re)
           for (const match of matches) {
             const s = queryStart + (match.index || 0)

package/src/TwoBitAdapter/TwoBitAdapter.ts

@@ -101,7 +101,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
 
   /**
    * called to provide a hint that data tied to a certain region
-   * will not be needed for the forseeable future and can be purged
+   * will not be needed for the foreseeable future and can be purged
    * from caches, etc
    */
   public freeResources(/* { region } */): void {}