@jbrowse/plugin-sequence 2.1.7 → 2.2.1

package/esm/DivSequenceRenderer/configSchema.js

@@ -1,9 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('DivSequenceRenderer', {
+/**
+ * #config DivSequenceRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const DivSequenceRenderer = ConfigurationSchema('DivSequenceRenderer', {
+    /**
+     * #slot
+     */
     height: {
         type: 'number',
         description: 'height in pixels of each line of sequence',
         defaultValue: 16,
     },
 }, { explicitlyTyped: true });
+export default DivSequenceRenderer;
 //# sourceMappingURL=configSchema.js.map

package/esm/DivSequenceRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,2CAA2C;QACxD,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}

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;

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) => {

package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EACL,mBAAmB,GAEpB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAW,MAAM,oBAAoB,CAAA;AAC3D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAIlD,MAAM,CAAC,OAAO,MAAO,SAAQ,mBAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,qBAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,QAAQ,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,YAAY,CAAC;gBACtB,KAAK,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,YAAY,CAAC,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,YAAY,CAAC,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,gBAAgB,CAAU,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,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/IndexedFastaAdapter/configSchema.d.ts

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

package/esm/IndexedFastaAdapter/configSchema.js

@@ -1,13 +1,26 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('IndexedFastaAdapter', {
+/**
+ * #config IndexedFastaAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const IndexedFastaAdapter = ConfigurationSchema('IndexedFastaAdapter', {
+    /**
+     * #slot
+     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',
@@ -17,4 +30,5 @@ export default ConfigurationSchema('IndexedFastaAdapter', {
         },
     },
 }, { explicitlyTyped: true });
+export default IndexedFastaAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/IndexedFastaAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,qBAAqB,EAAE,YAAY,EAAE,aAAa,EAAE;KAC1E;IACD;;OAEG;IACH,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,mBAAmB,CAAA"}

package/esm/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,4 +1,13 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { default as divSequenceRendererConfigSchema } from '../DivSequenceRenderer/configSchema';
-export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', { renderer: divSequenceRendererConfigSchema }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
+/**
+ * #config LinearReferenceSequenceDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+export const configSchema = ConfigurationSchema('LinearReferenceSequenceDisplay', {
+    /**
+     * #slot
+     */
+    renderer: divSequenceRendererConfigSchema,
+}, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/esm/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,OAAO,IAAI,+BAA+B,EAAE,MAAM,qCAAqC,CAAA;AAEhG;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,gCAAgC,EAChC;IACE;;OAEG;IACH,QAAQ,EAAE,+BAA+B;CAC1C,EACD,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/esm/LinearReferenceSequenceDisplay/model.d.ts

@@ -182,7 +182,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
@@ -202,8 +202,8 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
 }, import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
+    height: number;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;

package/esm/ReferenceSequenceTrack/configSchema.js

@@ -1,32 +1,55 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import { types } from 'mobx-state-tree';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/*
-Note: this is primarily a copy of createBaseTrackConfig, except with a subset
-of the config slots, to avoid including fields that don't make sense for the
-ReferenceSequenceTrack
-*/
+// Note: this is primarily a copy of createBaseTrackConfig, except with a
+// subset of the config slots, to avoid including fields that don't make sense
+// for the ReferenceSequenceTrack
+/**
+ * #config ReferenceSequenceTrack
+ * used to display base level DNA sequence tracks
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export function createReferenceSeqTrackConfig(pluginManager) {
     return ConfigurationSchema('ReferenceSequenceTrack', {
+        /**
+         * #slot
+         * configuration for track adapter
+         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        /**
+         * #slot
+         * configuration for the displays e.g. LinearReferenceSequenceDisplay
+         */
         displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+        /**
+         * #slot
+         */
         name: {
             type: 'string',
-            description: 'optional track name',
+            description: 'optional track name, otherwise uses the "Reference sequence (assemblyName)"',
             defaultValue: '',
         },
+        /**
+         * #slot
+         */
         metadata: {
             type: 'frozen',
             description: 'anything to add about this track',
             defaultValue: {},
         },
         formatAbout: ConfigurationSchema('FormatAbout', {
+            /**
+             * #slot formatAbout.config
+             */
             config: {
                 type: 'frozen',
                 description: 'formats configuration in about dialog',
                 defaultValue: {},
                 contextVariable: ['config'],
             },
+            /**
+             * #slot formatAbout.hideUris
+             */
             hideUris: {
                 type: 'boolean',
                 defaultValue: false,
@@ -54,6 +77,10 @@ export function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
+        /**
+         * #identifier
+         * all tracks have a globally unique 'trackId'
+         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/esm/ReferenceSequenceTrack/configSchema.js.map

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package/esm/SequenceSearchAdapter/configSchema.js

@@ -1,22 +1,41 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config SequenceSearchAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = ConfigurationSchema('SequenceSearchAdapter', {
+    /**
+     * #slot
+     */
     search: {
         type: 'string',
         defaultValue: '',
         description: 'Search string or regex to search for',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
         type: 'frozen',
         defaultValue: null,
     },
+    /**
+     * #slot
+     */
     searchForward: {
         type: 'boolean',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     searchReverse: {
         type: 'boolean',
         defaultValue: true,
     },
+    /**
+     * #slot
+     */
     caseInsensitive: {
         type: 'boolean',
         defaultValue: true,

package/esm/SequenceSearchAdapter/configSchema.js.map

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

package/esm/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) {

package/esm/TwoBitAdapter/TwoBitAdapter.js.map

@@ -1 +1 @@
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package/esm/TwoBitAdapter/configSchema.d.ts

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

package/esm/TwoBitAdapter/configSchema.js

@@ -1,9 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('TwoBitAdapter', {
+/**
+ * #config TwoBitAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const TwoBitAdapter = ConfigurationSchema('TwoBitAdapter', {
+    /**
+     * #slot
+     */
     twoBitLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -13,4 +23,5 @@ export default ConfigurationSchema('TwoBitAdapter', {
         description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
     },
 }, { explicitlyTyped: true });
+export default TwoBitAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/TwoBitAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,aAAa,GAAG,mBAAmB,CACvC,eAAe,EACf;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,aAAa,CAAA"}

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 @@
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+{"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": "2.1.7",
+  "version": "2.2.1",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -59,5 +59,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
+  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
 }

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/BgzipFastaAdapter/configSchema.ts

@@ -1,12 +1,22 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+/**
+ * #config BgzipFastaAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-export default ConfigurationSchema(
+const BgzipFastaAdapter = ConfigurationSchema(
   'BgzipFastaAdapter',
   {
+    /**
+     * #slot
+     */
     fastaLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -14,6 +24,9 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
       description: 'Optional metadata file',
       type: 'fileLocation',
@@ -22,6 +35,9 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     */
     gziLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -32,3 +48,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default BgzipFastaAdapter

package/src/ChromSizesAdapter/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config ChromSizesAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const ChromSizesAdapter = ConfigurationSchema(
   'ChromSizesAdapter',
   {
+    /**
+     * #slot
+     */
     chromSizesLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -13,3 +21,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default ChromSizesAdapter

package/src/DivSequenceRenderer/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config DivSequenceRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const DivSequenceRenderer = ConfigurationSchema(
   'DivSequenceRenderer',
   {
+    /**
+     * #slot
+     */
     height: {
       type: 'number',
       description: 'height in pixels of each line of sequence',
@@ -11,3 +19,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default DivSequenceRenderer

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)