@jbrowse/plugin-sequence 2.1.7 → 2.2.1

package/dist/BgzipFastaAdapter/configSchema.d.ts

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

package/dist/BgzipFastaAdapter/configSchema.js

@@ -1,11 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter', {
+/**
+ * #config BgzipFastaAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const BgzipFastaAdapter = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter', {
+    /**
+     * #slot
+     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -13,6 +23,9 @@ exports.default = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter',
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',
@@ -21,6 +34,9 @@ exports.default = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter',
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     gziLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -29,4 +45,5 @@ exports.default = (0, configuration_1.ConfigurationSchema)('BgzipFastaAdapter',
         },
     },
 }, { explicitlyTyped: true });
+exports.default = BgzipFastaAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/BgzipFastaAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iBAAiB,GAAG,IAAA,mCAAmB,EAC3C,mBAAmB,EACnB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;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;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,iBAAiB,CAAA"}

package/dist/ChromSizesAdapter/configSchema.d.ts

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

package/dist/ChromSizesAdapter/configSchema.js

@@ -1,7 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter', {
+/**
+ * #config ChromSizesAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const ChromSizesAdapter = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter', {
+    /**
+     * #slot
+     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -10,4 +17,5 @@ exports.default = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter',
         },
     },
 }, { explicitlyTyped: true });
+exports.default = ChromSizesAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/ChromSizesAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iBAAiB,GAAG,IAAA,mCAAmB,EAC3C,mBAAmB,EACnB;IACE;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,iBAAiB,CAAA"}

package/dist/DivSequenceRenderer/configSchema.d.ts

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

package/dist/DivSequenceRenderer/configSchema.js

@@ -1,11 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('DivSequenceRenderer', {
+/**
+ * #config DivSequenceRenderer
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const DivSequenceRenderer = (0, configuration_1.ConfigurationSchema)('DivSequenceRenderer', {
+    /**
+     * #slot
+     */
     height: {
         type: 'number',
         description: 'height in pixels of each line of sequence',
         defaultValue: 16,
     },
 }, { explicitlyTyped: true });
+exports.default = DivSequenceRenderer;
 //# sourceMappingURL=configSchema.js.map

package/dist/DivSequenceRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,2CAA2C;QACxD,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,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,kBAAe,mBAAmB,CAAA"}

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;

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) => {

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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package/dist/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/dist/IndexedFastaAdapter/configSchema.js

@@ -1,15 +1,28 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('IndexedFastaAdapter', {
+/**
+ * #config IndexedFastaAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const IndexedFastaAdapter = (0, configuration_1.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',
@@ -19,4 +32,5 @@ exports.default = (0, configuration_1.ConfigurationSchema)('IndexedFastaAdapter'
         },
     },
 }, { explicitlyTyped: true });
+exports.default = IndexedFastaAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/IndexedFastaAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,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,kBAAe,mBAAmB,CAAA"}

package/dist/LinearReferenceSequenceDisplay/configSchema.js

@@ -6,5 +6,14 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = void 0;
 const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema_1 = __importDefault(require("../DivSequenceRenderer/configSchema"));
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', { renderer: configSchema_1.default }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
+/**
+ * #config LinearReferenceSequenceDisplay
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', {
+    /**
+     * #slot
+     */
+    renderer: configSchema_1.default,
+}, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":";;;;;;AAAA,+DAAiE;AACjE,uFAAgG;AAEnF,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,sBAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":";;;;;;AAAA,+DAAiE;AACjE,uFAAgG;AAEhG;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAE3D,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,gCAAgC,EAChC;IACE;;OAEG;IACH,QAAQ,EAAE,sBAA+B;CAC1C,EACD,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/dist/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/dist/ReferenceSequenceTrack/configSchema.js

@@ -4,32 +4,55 @@ exports.createReferenceSeqTrackConfig = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@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
 function createReferenceSeqTrackConfig(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('ReferenceSequenceTrack', {
+        /**
+         * #slot
+         * configuration for track adapter
+         */
         adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+        /**
+         * #slot
+         * configuration for the displays e.g. LinearReferenceSequenceDisplay
+         */
         displays: mobx_state_tree_1.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: (0, configuration_1.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,
@@ -57,6 +80,10 @@ function createReferenceSeqTrackConfig(pluginManager) {
             }
             return { ...snap, displays };
         },
+        /**
+         * #identifier
+         * all tracks have a globally unique 'trackId'
+         */
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,
         actions: (self) => ({

package/dist/ReferenceSequenceTrack/configSchema.js.map

@@ -1 +1 @@
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package/dist/SequenceSearchAdapter/configSchema.js

@@ -1,24 +1,43 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config SequenceSearchAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = (0, configuration_1.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/dist/SequenceSearchAdapter/configSchema.js.map

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

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) {

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/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/dist/TwoBitAdapter/configSchema.js

@@ -1,11 +1,21 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
+/**
+ * #config TwoBitAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const TwoBitAdapter = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
+    /**
+     * #slot
+     */
     twoBitLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -15,4 +25,5 @@ exports.default = (0, configuration_1.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 });
+exports.default = TwoBitAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/TwoBitAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,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,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,aAAa,GAAG,IAAA,mCAAmB,EACvC,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,kBAAe,aAAa,CAAA"}

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/BgzipFastaAdapter/configSchema.d.ts

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

package/esm/BgzipFastaAdapter/configSchema.js

@@ -1,9 +1,19 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('BgzipFastaAdapter', {
+/**
+ * #config BgzipFastaAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const BgzipFastaAdapter = ConfigurationSchema('BgzipFastaAdapter', {
+    /**
+     * #slot
+     */
     fastaLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/seq.fa.gz', locationType: 'UriLocation' },
     },
+    /**
+     * #slot
+     */
     faiLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -11,6 +21,9 @@ export default ConfigurationSchema('BgzipFastaAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     metadataLocation: {
         description: 'Optional metadata file',
         type: 'fileLocation',
@@ -19,6 +32,9 @@ export default ConfigurationSchema('BgzipFastaAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     gziLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -27,4 +43,5 @@ export default ConfigurationSchema('BgzipFastaAdapter', {
         },
     },
 }, { explicitlyTyped: true });
+export default BgzipFastaAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/BgzipFastaAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,mBAAmB,EACnB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iBAAiB,GAAG,mBAAmB,CAC3C,mBAAmB,EACnB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;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;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,iBAAiB,CAAA"}

package/esm/ChromSizesAdapter/configSchema.d.ts

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

package/esm/ChromSizesAdapter/configSchema.js

@@ -1,5 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('ChromSizesAdapter', {
+/**
+ * #config ChromSizesAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const ChromSizesAdapter = ConfigurationSchema('ChromSizesAdapter', {
+    /**
+     * #slot
+     */
     chromSizesLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -8,4 +15,5 @@ export default ConfigurationSchema('ChromSizesAdapter', {
         },
     },
 }, { explicitlyTyped: true });
+export default ChromSizesAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/ChromSizesAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,iBAAiB,GAAG,mBAAmB,CAC3C,mBAAmB,EACnB;IACE;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,iBAAiB,CAAA"}

package/esm/DivSequenceRenderer/configSchema.d.ts

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