@jbrowse/plugin-sequence 2.2.1 → 2.3.0

package/dist/BgzipFastaAdapter/index.js

@@ -31,12 +31,10 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'BgzipFastaAdapter',
+        displayName: 'Bgzip-indexed FASTA adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
     }));

package/dist/BgzipFastaAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,YAAY,EAAZ,sBAAY;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,kDAAO,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,WAAW,EAAE,6BAA6B;QAC1C,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/ChromSizesAdapter/index.js

@@ -31,12 +31,10 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'ChromSizesAdapter',
+        displayName: 'Chrom sizes adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
     }));

package/dist/ChromSizesAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,YAAY,EAAZ,sBAAY;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,kDAAO,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,WAAW,EAAE,qBAAqB;QAClC,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -23,7 +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

@@ -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/index.js

@@ -31,12 +31,10 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'IndexedFastaAdapter',
+        displayName: 'Indexed FASTA adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
     }));

package/dist/IndexedFastaAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,qBAAqB;QAC3B,YAAY,EAAZ,sBAAY;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,kDAAO,uBAAuB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACvD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,qBAAqB;QAC3B,WAAW,EAAE,uBAAuB;QACpC,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,uBAAuB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACvD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/LinearReferenceSequenceDisplay/index.js

@@ -1,19 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+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) => {
     pluginManager.addDisplayType(() => {
         const stateModel = (0, model_1.modelFactory)(configSchema_1.configSchema);
-        return {
+        return new pluggableElementTypes_1.DisplayType({
             name: 'LinearReferenceSequenceDisplay',
             configSchema: configSchema_1.configSchema,
             stateModel,
+            displayName: 'Reference sequence display',
             trackType: 'ReferenceSequenceTrack',
             viewType: 'LinearGenomeView',
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
-        };
+        });
     });
 };
 //# sourceMappingURL=index.js.map

package/dist/LinearReferenceSequenceDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":";;AACA,kFAA+E;AAE/E,iDAA6C;AAC7C,mCAAsC;AAEtC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,UAAU,GAAG,IAAA,oBAAY,EAAC,2BAAY,CAAC,CAAA;QAC7C,OAAO;YACL,IAAI,EAAE,gCAAgC;YACtC,YAAY,EAAZ,2BAAY;YACZ,UAAU;YACV,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":";;AAAA,+EAAiE;AAEjE,kFAA+E;AAE/E,iDAA6C;AAC7C,mCAAsC;AAEtC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,UAAU,GAAG,IAAA,oBAAY,EAAC,2BAAY,CAAC,CAAA;QAC7C,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,gCAAgC;YACtC,YAAY,EAAZ,2BAAY;YACZ,UAAU;YACV,WAAW,EAAE,4BAA4B;YACzC,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -115,10 +115,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/dist/ReferenceSequenceTrack/index.js

@@ -11,6 +11,7 @@ exports.default = (pluginManager) => {
         const configSchema = (0, configSchema_1.createReferenceSeqTrackConfig)(pluginManager);
         return new TrackType_1.default({
             name: 'ReferenceSequenceTrack',
+            displayName: 'Reference sequence track',
             configSchema,
             stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });

package/dist/ReferenceSequenceTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/index.ts"],"names":[],"mappings":";;;;;AAEA,8FAAqE;AACrE,uEAAiF;AACjF,iDAA8D;AAE9D,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,IAAA,4CAA6B,EAAC,aAAa,CAAC,CAAA;QAEjE,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,wBAAwB;YAC9B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/index.ts"],"names":[],"mappings":";;;;;AAEA,8FAAqE;AACrE,uEAAiF;AACjF,iDAA8D;AAE9D,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,IAAA,4CAA6B,EAAC,aAAa,CAAC,CAAA;QAEjE,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,wBAAwB;YAC9B,WAAW,EAAE,0BAA0B;YACvC,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

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

@@ -1 +1 @@
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+{"version":3,"file":"SequenceSearchAdapter.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/SequenceSearchAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,kDAA0D;AAC1D,6CAM2B;AAC3B,8CAAwC;AAExC,eAAqB,SAAQ,oCAAsB;IAC1C,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,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,EAAE,GAAG,IAAI,CAAA;YACf,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,IAAA,mBAAO,GAAE,CAAC,CAAC,SAAS,EAAE,CAAA;YACnD,MAAM,QAAQ,GAAW,CAAA,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,KAAI,EAAE,CAAA;YACnD,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;YACrC,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;YACnD,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;YACnD,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;YACvD,MAAM,EAAE,GAAG,IAAI,MAAM,CAAC,MAAM,EAAE,GAAG,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;YAEjE,IAAI,MAAM,EAAE;gBACV,IAAI,aAAa,EAAE;oBACjB,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;oBACrC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE;wBAC3B,MAAM,CAAC,GAAG,UAAU,GAAG,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAA;wBAEzC,IAAI,IAAA,qBAAc,EAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;gCAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,UAAU,CAAC,IAAI;gCACnC,OAAO,EAAE,KAAK,CAAC,OAAO;gCACtB,KAAK,EAAE,CAAC;gCACR,GAAG,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;gCACxB,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC;gCACd,MAAM,EAAE,CAAC;6BACV,CAAC,CACH,CAAA;yBACF;qBACF;iBACF;gBACD,IAAI,aAAa,EAAE;oBACjB,MAAM,OAAO,GAAG,IAAA,aAAM,EAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;oBAC7C,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE;wBAC3B,MAAM,CAAC,GAAG,QAAQ,GAAG,CAAC,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAA;wBACvC,IAAI,IAAA,qBAAc,EAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE;4BAChE,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;gCAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,UAAU,CAAC,IAAI;gCACnC,OAAO,EAAE,KAAK,CAAC,OAAO;gCACtB,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM;gCAC1B,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC;gCACd,GAAG,EAAE,CAAC;gCACN,MAAM,EAAE,CAAC,CAAC;6BACX,CAAC,CACH,CAAA;yBACF;qBACF;iBACF;aACF;YAED,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,KAAI,CAAC;CAC1B;AAxFD,4BAwFC"}

package/dist/SequenceSearchAdapter/index.js

@@ -31,11 +31,9 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'SequenceSearchAdapter',
+        displayName: 'Sequence search adapter',
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SequenceSearchAdapter'))).then(r => r.default),

package/dist/SequenceSearchAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,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,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,yBAAyB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACzD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SequenceSearchAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,uBAAuB;QAC7B,WAAW,EAAE,yBAAyB;QACtC,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,yBAAyB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACzD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

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

@@ -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/index.js

@@ -31,12 +31,10 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'TwoBitAdapter',
+        displayName: 'TwoBit adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./TwoBitAdapter'))).then(r => r.default),
     }));

package/dist/TwoBitAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,YAAY,EAAZ,sBAAY;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,kDAAO,iBAAiB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,eAAe;QACrB,WAAW,EAAE,gBAAgB;QAC7B,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,iBAAiB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/BgzipFastaAdapter/index.js

@@ -3,12 +3,10 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'BgzipFastaAdapter',
+        displayName: 'Bgzip-indexed FASTA adapter',
         configSchema,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
     }));

package/esm/BgzipFastaAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/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,mBAAmB;QACzB,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,qBAAqB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/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,mBAAmB;QACzB,WAAW,EAAE,6BAA6B;QAC1C,YAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,qBAAqB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/ChromSizesAdapter/index.js

@@ -3,12 +3,10 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'ChromSizesAdapter',
+        displayName: 'Chrom sizes adapter',
         configSchema,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
     }));

package/esm/ChromSizesAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/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,mBAAmB;QACzB,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,qBAAqB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/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,mBAAmB;QACzB,WAAW,EAAE,qBAAqB;QAClC,YAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,qBAAqB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -23,7 +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

@@ -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/index.js

@@ -3,12 +3,10 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'IndexedFastaAdapter',
+        displayName: 'Indexed FASTA adapter',
         configSchema,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => import('./IndexedFastaAdapter').then(r => r.default),
     }));

package/esm/IndexedFastaAdapter/index.js.map

@@ -1 +1 @@
-{"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"}
+{"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,WAAW,EAAE,uBAAuB;QACpC,YAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;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/index.js

@@ -1,17 +1,19 @@
+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) => {
     pluginManager.addDisplayType(() => {
         const stateModel = modelFactory(configSchema);
-        return {
+        return new DisplayType({
             name: 'LinearReferenceSequenceDisplay',
             configSchema,
             stateModel,
+            displayName: 'Reference sequence display',
             trackType: 'ReferenceSequenceTrack',
             viewType: 'LinearGenomeView',
             ReactComponent: BaseLinearDisplayComponent,
-        };
+        });
     });
 };
 //# sourceMappingURL=index.js.map

package/esm/LinearReferenceSequenceDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,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,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,gCAAgC;YACtC,YAAY;YACZ,UAAU;YACV,WAAW,EAAE,4BAA4B;YACzC,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -115,10 +115,10 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/esm/ReferenceSequenceTrack/index.js

@@ -6,6 +6,7 @@ export default (pluginManager) => {
         const configSchema = createReferenceSeqTrackConfig(pluginManager);
         return new TrackType({
             name: 'ReferenceSequenceTrack',
+            displayName: 'Reference sequence track',
             configSchema,
             stateModel: createBaseTrackModel(pluginManager, 'ReferenceSequenceTrack', configSchema),
         });

package/esm/ReferenceSequenceTrack/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/index.ts"],"names":[],"mappings":"AAEA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,EAAE,6BAA6B,EAAE,MAAM,gBAAgB,CAAA;AAE9D,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,6BAA6B,CAAC,aAAa,CAAC,CAAA;QAEjE,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,wBAAwB;YAC9B,WAAW,EAAE,0BAA0B;YACvC,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,wBAAwB,EACxB,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/SequenceSearchAdapter/SequenceSearchAdapter.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

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

@@ -3,11 +3,9 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'SequenceSearchAdapter',
+        displayName: 'Sequence search adapter',
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         configSchema,
         getAdapterClass: () => import('./SequenceSearchAdapter').then(r => r.default),

package/esm/SequenceSearchAdapter/index.js.map

@@ -1 +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"}
+{"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,WAAW,EAAE,yBAAyB;QACtC,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;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/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

@@ -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/index.js

@@ -3,12 +3,10 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'TwoBitAdapter',
+        displayName: 'TwoBit adapter',
         configSchema,
         adapterMetadata: {
-            category: null,
             hiddenFromGUI: true,
-            displayName: null,
-            description: null,
         },
         getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
     }));

package/esm/TwoBitAdapter/index.js.map

@@ -1 +1 @@
-{"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"}
+{"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,WAAW,EAAE,gBAAgB;QAC7B,YAAY;QACZ,eAAe,EAAE;YACf,aAAa,EAAE,IAAI;SACpB;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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "2.2.1",
+  "version": "2.3.0",
   "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",
@@ -49,7 +49,6 @@
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
-    "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0"
   },
@@ -59,5 +58,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
+  "gitHead": "a85b280a8af4d1a11e81ab42913f5f6049e6e580"
 }

package/src/BgzipFastaAdapter/index.ts

@@ -8,12 +8,10 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'BgzipFastaAdapter',
+        displayName: 'Bgzip-indexed FASTA adapter',
         configSchema,
         adapterMetadata: {
-          category: null,
           hiddenFromGUI: true,
-          displayName: null,
-          description: null,
         },
         getAdapterClass: () =>
           import('./BgzipFastaAdapter').then(r => r.default),

package/src/ChromSizesAdapter/index.ts

@@ -8,12 +8,10 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'ChromSizesAdapter',
+        displayName: 'Chrom sizes adapter',
         configSchema,
         adapterMetadata: {
-          category: null,
           hiddenFromGUI: true,
-          displayName: null,
-          description: null,
         },
         getAdapterClass: () =>
           import('./ChromSizesAdapter').then(r => r.default),

package/src/DivSequenceRenderer/components/DivSequenceRendering.test.js

@@ -1,5 +1,4 @@
 import React from 'react'
-import ReactPropTypes from 'prop-types'
 import { render } from '@testing-library/react'
 import { createJBrowseTheme } from '@jbrowse/core/ui'
 import PrecomputedLayout from '@jbrowse/core/util/layouts/PrecomputedLayout'
@@ -37,7 +36,6 @@ class ErrorCatcher extends React.Component {
     return children
   }
 }
-ErrorCatcher.propTypes = { children: ReactPropTypes.node.isRequired }
 
 describe('<DivSequenceRendering />', () => {
   // This just keeps our testing logs clean by not displaying `console.error`s

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -106,7 +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/index.ts

@@ -8,12 +8,10 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'IndexedFastaAdapter',
+        displayName: 'Indexed FASTA adapter',
         configSchema,
         adapterMetadata: {
-          category: null,
           hiddenFromGUI: true,
-          displayName: null,
-          description: null,
         },
         getAdapterClass: () =>
           import('./IndexedFastaAdapter').then(r => r.default),

package/src/LinearReferenceSequenceDisplay/index.ts

@@ -1,3 +1,4 @@
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
 
@@ -7,13 +8,14 @@ import { modelFactory } from './model'
 export default (pluginManager: PluginManager) => {
   pluginManager.addDisplayType(() => {
     const stateModel = modelFactory(configSchema)
-    return {
+    return new DisplayType({
       name: 'LinearReferenceSequenceDisplay',
       configSchema,
       stateModel,
+      displayName: 'Reference sequence display',
       trackType: 'ReferenceSequenceTrack',
       viewType: 'LinearGenomeView',
       ReactComponent: BaseLinearDisplayComponent,
-    }
+    })
   })
 }

package/src/ReferenceSequenceTrack/index.ts

@@ -10,6 +10,7 @@ export default (pluginManager: PluginManager) => {
 
     return new TrackType({
       name: 'ReferenceSequenceTrack',
+      displayName: 'Reference sequence track',
       configSchema,
       stateModel: createBaseTrackModel(
         pluginManager,

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/SequenceSearchAdapter/index.ts

@@ -8,11 +8,9 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'SequenceSearchAdapter',
+        displayName: 'Sequence search adapter',
         adapterMetadata: {
-          category: null,
           hiddenFromGUI: true,
-          displayName: null,
-          description: null,
         },
         configSchema,
         getAdapterClass: () =>

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 {}

package/src/TwoBitAdapter/index.ts

@@ -8,12 +8,10 @@ export default (pluginManager: PluginManager) => {
     () =>
       new AdapterType({
         name: 'TwoBitAdapter',
+        displayName: 'TwoBit adapter',
         configSchema,
         adapterMetadata: {
-          category: null,
           hiddenFromGUI: true,
-          displayName: null,
-          description: null,
         },
         getAdapterClass: () => import('./TwoBitAdapter').then(r => r.default),
       }),