@jbrowse/plugin-legacy-jbrowse 2.1.6 → 2.2.0

package/dist/JBrowse1Connection/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const JBrowse1Connection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default JBrowse1Connection;

package/dist/JBrowse1Connection/configSchema.js

@@ -2,7 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1Connection', {
+/**
+ * #config JBrowse1Connection
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const JBrowse1Connection = (0, configuration_1.ConfigurationSchema)('JBrowse1Connection', {
+    /**
+     * #slot
+     */
     dataDirLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -11,10 +18,19 @@ exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1Connection',
         },
         description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         description: 'name of the assembly the connection belongs to, should be a single entry',
         type: 'stringArray',
         defaultValue: [],
     },
-}, { baseConfiguration: models_1.baseConnectionConfig });
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: models_1.baseConnectionConfig,
+});
+exports.default = JBrowse1Connection;
 //# sourceMappingURL=configSchema.js.map

package/dist/JBrowse1Connection/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/configSchema.ts"],"names":[],"mappings":";;AAAA,uEAAiF;AACjF,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,kBAAkB,GAAG,IAAA,mCAAmB,EAC5C,oBAAoB,EACpB;IACE;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,iCAAiC;YACtC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,oGAAoG;KACvG;IACD;;OAEG;IACH,aAAa,EAAE;QACb,WAAW,EACT,0EAA0E;QAC5E,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE;;OAEG;IACH,iBAAiB,EAAE,6BAAoB;CACxC,CACF,CAAA;AAED,kBAAe,kBAAkB,CAAA"}

package/dist/JBrowse1TextSeachAdapter/HttpMap.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/*
+/**
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */

package/dist/JBrowse1TextSeachAdapter/configSchema.js

@@ -1,22 +1,41 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config JBrowse1TextSearchAdapter
+ * note: metadata about tracks and assemblies covered by text search adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1TextSearchAdapter', {
-    // metadata about tracks and assemblies covered by text search adapter
+    /**
+     * #slot
+     */
     namesIndexLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
         description: 'the location of the JBrowse1 names index data directory',
     },
+    /**
+     * #slot
+     */
     tracks: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of tracks covered by text search adapter',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of assemblies covered by text search adapter',
     },
-}, { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' });
+}, {
+    explicitlyTyped: true,
+    /**
+     * #identifier
+     */
+    explicitIdentifier: 'textSearchAdapterId',
+});
 //# sourceMappingURL=configSchema.js.map

package/dist/JBrowse1TextSeachAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,kBAAe,IAAA,mCAAmB,EAChC,2BAA2B,EAC3B;IACE;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,eAAe,EAAE,YAAY,EAAE,aAAa,EAAE;QACnE,WAAW,EAAE,yDAAyD;KACvE;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB;;OAEG;IACH,kBAAkB,EAAE,qBAAqB;CAC1C,CACF,CAAA"}

package/dist/NCListAdapter/NCListAdapter.d.ts

@@ -1,15 +1,14 @@
 import { Region } from '@jbrowse/core/util/types';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Instance } from 'mobx-state-tree';
 import NCListFeature from './NCListFeature';
-import MyConfigSchema from './configSchema';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     /**
      * Fetch features for a certain region. Use getFeaturesInRegion() if you also
      * want to verify that the store has features for the given reference sequence
@@ -21,6 +20,9 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     wrapFeature(ncFeature: any): NCListFeature;
     hasDataForRefName(refName: string): Promise<boolean>;
+    /**
+     * NCList is unable to get list of ref names so returns empty
+     */
     getRefNames(): Promise<string[]>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/NCListAdapter/NCListAdapter.js

@@ -8,13 +8,12 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_1 = require("@jbrowse/core/util");
 const generic_filehandle_1 = require("generic-filehandle");
-const configuration_1 = require("@jbrowse/core/configuration");
 const NCListFeature_1 = __importDefault(require("./NCListFeature"));
 class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const refNames = (0, configuration_1.readConfObject)(config, 'refNames');
-        const rootUrlTemplate = (0, configuration_1.readConfObject)(config, 'rootUrlTemplate');
+        const refNames = this.getConf('refNames');
+        const rootUrlTemplate = this.getConf('rootUrlTemplate');
         this.configRefNames = refNames;
         this.nclist = new nclist_1.default({
             baseUrl: '',
@@ -50,12 +49,11 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const root = await this.nclist.getDataRoot(refName);
         return !!(root && root.stats && root.stats.featureCount);
     }
-    /*
+    /**
      * NCList is unable to get list of ref names so returns empty
-     * @return Promise<string[]> of empty list
      */
-    getRefNames() {
-        return Promise.resolve(this.configRefNames || []);
+    async getRefNames() {
+        return this.configRefNames || [];
     }
     /**
      * called to provide a hint that data tied to a certain region

package/dist/NCListAdapter/NCListAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"NCListAdapter.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListAdapter.ts"],"names":[],"mappings":";;;;;AAAA,0DAAsC;AAEtC,yEAGgD;AAEhD,kDAA0D;AAC1D,6CAAqD;AACrD,2DAA+C;AAC/C,oEAA2C;AAK3C,MAAqB,aAAc,SAAQ,oCAAsB;IAM/D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACvD,IAAI,CAAC,cAAc,GAAG,QAAQ,CAAA;QAE9B,IAAI,CAAC,MAAM,GAAG,IAAI,gBAAW,CAAC;YAC5B,OAAO,EAAE,EAAE;YACX,WAAW,EAAE,eAAe,CAAC,GAAG;YAChC,QAAQ,EAAE,CAAC,GAAW,EAAE,EAAE,CACxB,IAAI,+BAAU,CACZ,MAAM,CACJ,eAAe,CAAC,OAAO;gBACrB,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE;gBAClD,CAAC,CAAC,GAAG,CACR,CACF,CAAC,QAAQ,EAAE;SACf,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;OAOG;IACH,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YACvB,IAAI,KAAK,EAAE,MAAM,OAAO,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;gBACjE,IAAA,uBAAgB,EAAC,MAAM,CAAC,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;aACzC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,8DAA8D;IAC9D,WAAW,CAAC,SAAc;QACxB,OAAO,IAAI,uBAAa,CACtB,SAAS,EACT,SAAS,EACT,GAAG,IAAI,CAAC,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,EAAE,CAC/B,CAAA;IACH,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,OAAe;QACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACnD,OAAO,CAAC,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,cAAc,IAAI,EAAE,CAAA;IAClC,CAAC;IAED;;;;OAIG;IACH,aAAa,KAAI,CAAC;CACnB;AA5ED,gCA4EC"}

package/dist/NCListAdapter/configSchema.d.ts

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

package/dist/NCListAdapter/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)('NCListAdapter', {
+/**
+ * #config NCListAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const NCListAdapter = (0, configuration_1.ConfigurationSchema)('NCListAdapter', {
+    /**
+     * #slot
+     */
     rootUrlTemplate: {
         type: 'fileLocation',
         defaultValue: {
@@ -9,10 +16,14 @@ exports.default = (0, configuration_1.ConfigurationSchema)('NCListAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     refNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of refNames used by the NCList used for aliasing',
     },
 }, { explicitlyTyped: true });
+exports.default = NCListAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/NCListAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/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,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,aAAa,CAAA"}

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const JBrowse1Connection: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default JBrowse1Connection;

package/esm/JBrowse1Connection/configSchema.js

@@ -1,6 +1,13 @@
 import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('JBrowse1Connection', {
+/**
+ * #config JBrowse1Connection
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const JBrowse1Connection = ConfigurationSchema('JBrowse1Connection', {
+    /**
+     * #slot
+     */
     dataDirLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -9,10 +16,19 @@ export default ConfigurationSchema('JBrowse1Connection', {
         },
         description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         description: 'name of the assembly the connection belongs to, should be a single entry',
         type: 'stringArray',
         defaultValue: [],
     },
-}, { baseConfiguration: baseConnectionConfig });
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseConnectionConfig,
+});
+export default JBrowse1Connection;
 //# sourceMappingURL=configSchema.js.map

package/esm/JBrowse1Connection/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,kBAAkB,GAAG,mBAAmB,CAC5C,oBAAoB,EACpB;IACE;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,iCAAiC;YACtC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,oGAAoG;KACvG;IACD;;OAEG;IACH,aAAa,EAAE;QACb,WAAW,EACT,0EAA0E;QAC5E,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE;;OAEG;IACH,iBAAiB,EAAE,oBAAoB;CACxC,CACF,CAAA;AAED,eAAe,kBAAkB,CAAA"}

package/esm/JBrowse1TextSeachAdapter/HttpMap.js

@@ -1,4 +1,4 @@
-/*
+/**
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */

package/esm/JBrowse1TextSeachAdapter/configSchema.js

@@ -1,20 +1,39 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config JBrowse1TextSearchAdapter
+ * note: metadata about tracks and assemblies covered by text search adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 export default ConfigurationSchema('JBrowse1TextSearchAdapter', {
-    // metadata about tracks and assemblies covered by text search adapter
+    /**
+     * #slot
+     */
     namesIndexLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
         description: 'the location of the JBrowse1 names index data directory',
     },
+    /**
+     * #slot
+     */
     tracks: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of tracks covered by text search adapter',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of assemblies covered by text search adapter',
     },
-}, { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' });
+}, {
+    explicitlyTyped: true,
+    /**
+     * #identifier
+     */
+    explicitIdentifier: 'textSearchAdapterId',
+});
 //# sourceMappingURL=configSchema.js.map

package/esm/JBrowse1TextSeachAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,2BAA2B,EAC3B;IACE,sEAAsE;IACtE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,eAAe,EAAE,YAAY,EAAE,aAAa,EAAE;QACnE,WAAW,EAAE,yDAAyD;KACvE;IACD,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,CACrE,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,eAAe,mBAAmB,CAChC,2BAA2B,EAC3B;IACE;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,eAAe,EAAE,YAAY,EAAE,aAAa,EAAE;QACnE,WAAW,EAAE,yDAAyD;KACvE;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB;;OAEG;IACH,kBAAkB,EAAE,qBAAqB;CAC1C,CACF,CAAA"}

package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -1,15 +1,14 @@
 import { Region } from '@jbrowse/core/util/types';
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { Instance } from 'mobx-state-tree';
 import NCListFeature from './NCListFeature';
-import MyConfigSchema from './configSchema';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     /**
      * Fetch features for a certain region. Use getFeaturesInRegion() if you also
      * want to verify that the store has features for the given reference sequence
@@ -21,6 +20,9 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     wrapFeature(ncFeature: any): NCListFeature;
     hasDataForRefName(refName: string): Promise<boolean>;
+    /**
+     * NCList is unable to get list of ref names so returns empty
+     */
     getRefNames(): Promise<string[]>;
     /**
      * called to provide a hint that data tied to a certain region

package/esm/NCListAdapter/NCListAdapter.js

@@ -3,13 +3,12 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { checkAbortSignal } from '@jbrowse/core/util';
 import { RemoteFile } from 'generic-filehandle';
-import { readConfObject } from '@jbrowse/core/configuration';
 import NCListFeature from './NCListFeature';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const refNames = readConfObject(config, 'refNames');
-        const rootUrlTemplate = readConfObject(config, 'rootUrlTemplate');
+        const refNames = this.getConf('refNames');
+        const rootUrlTemplate = this.getConf('rootUrlTemplate');
         this.configRefNames = refNames;
         this.nclist = new NCListStore({
             baseUrl: '',
@@ -45,12 +44,11 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         const root = await this.nclist.getDataRoot(refName);
         return !!(root && root.stats && root.stats.featureCount);
     }
-    /*
+    /**
      * NCList is unable to get list of ref names so returns empty
-     * @return Promise<string[]> of empty list
      */
-    getRefNames() {
-        return Promise.resolve(this.configRefNames || []);
+    async getRefNames() {
+        return this.configRefNames || [];
     }
     /**
      * called to provide a hint that data tied to a certain region

package/esm/NCListAdapter/NCListAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"NCListAdapter.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAK3C,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAM/D,YACE,MAAuC,EACvC,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QACnD,MAAM,eAAe,GAAG,cAAc,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;QACjE,IAAI,CAAC,cAAc,GAAG,QAAQ,CAAA;QAE9B,IAAI,CAAC,MAAM,GAAG,IAAI,WAAW,CAAC;YAC5B,OAAO,EAAE,EAAE;YACX,WAAW,EAAE,eAAe,CAAC,GAAG;YAChC,QAAQ,EAAE,CAAC,GAAW,EAAE,EAAE,CACxB,IAAI,UAAU,CACZ,MAAM,CACJ,eAAe,CAAC,OAAO;gBACrB,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE;gBAClD,CAAC,CAAC,GAAG,CACR,CACF,CAAC,QAAQ,EAAE;SACf,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;OAOG;IACH,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YACvB,IAAI,KAAK,EAAE,MAAM,OAAO,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;gBACjE,gBAAgB,CAAC,MAAM,CAAC,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;aACzC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,8DAA8D;IAC9D,WAAW,CAAC,SAAc;QACxB,OAAO,IAAI,aAAa,CACtB,SAAS,EACT,SAAS,EACT,GAAG,IAAI,CAAC,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,EAAE,CAC/B,CAAA;IACH,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,OAAe;QACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACnD,OAAO,CAAC,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED;;;OAGG;IACH,WAAW;QACT,OAAO,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,cAAc,IAAI,EAAE,CAAC,CAAA;IACnD,CAAC;IAED;;;;OAIG;IACH,aAAa,KAAI,CAAC;CACnB"}
+{"version":3,"file":"NCListAdapter.js","sourceRoot":"","sources":["../../src/NCListAdapter/NCListAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,cAAc,CAAA;AAEtC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAK3C,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IAM/D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACvD,IAAI,CAAC,cAAc,GAAG,QAAQ,CAAA;QAE9B,IAAI,CAAC,MAAM,GAAG,IAAI,WAAW,CAAC;YAC5B,OAAO,EAAE,EAAE;YACX,WAAW,EAAE,eAAe,CAAC,GAAG;YAChC,QAAQ,EAAE,CAAC,GAAW,EAAE,EAAE,CACxB,IAAI,UAAU,CACZ,MAAM,CACJ,eAAe,CAAC,OAAO;gBACrB,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,eAAe,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE;gBAClD,CAAC,CAAC,GAAG,CACR,CACF,CAAC,QAAQ,EAAE;SACf,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;OAOG;IACH,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YACvB,IAAI,KAAK,EAAE,MAAM,OAAO,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;gBACjE,gBAAgB,CAAC,MAAM,CAAC,CAAA;gBACxB,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAA;aACzC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,8DAA8D;IAC9D,WAAW,CAAC,SAAc;QACxB,OAAO,IAAI,aAAa,CACtB,SAAS,EACT,SAAS,EACT,GAAG,IAAI,CAAC,EAAE,IAAI,SAAS,CAAC,EAAE,EAAE,EAAE,CAC/B,CAAA;IACH,CAAC;IAED,KAAK,CAAC,iBAAiB,CAAC,OAAe;QACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACnD,OAAO,CAAC,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,cAAc,IAAI,EAAE,CAAA;IAClC,CAAC;IAED;;;;OAIG;IACH,aAAa,KAAI,CAAC;CACnB"}

package/esm/NCListAdapter/configSchema.d.ts

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

package/esm/NCListAdapter/configSchema.js

@@ -1,5 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export default ConfigurationSchema('NCListAdapter', {
+/**
+ * #config NCListAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const NCListAdapter = ConfigurationSchema('NCListAdapter', {
+    /**
+     * #slot
+     */
     rootUrlTemplate: {
         type: 'fileLocation',
         defaultValue: {
@@ -7,10 +14,14 @@ export default ConfigurationSchema('NCListAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
     refNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'List of refNames used by the NCList used for aliasing',
     },
 }, { explicitlyTyped: true });
+export default NCListAdapter;
 //# sourceMappingURL=configSchema.js.map

package/esm/NCListAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/NCListAdapter/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,eAAe,EAAE;QACf,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qCAAqC;YAC1C,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,uDAAuD;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,aAAa,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.1.6",
+  "version": "2.2.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
+  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
 }

package/src/JBrowse1Connection/configSchema.ts

@@ -1,9 +1,17 @@
 import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config JBrowse1Connection
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const JBrowse1Connection = ConfigurationSchema(
   'JBrowse1Connection',
   {
+    /**
+     * #slot
+     */
     dataDirLocation: {
       type: 'fileLocation',
       defaultValue: {
@@ -13,6 +21,9 @@ export default ConfigurationSchema(
       description:
         'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
       description:
         'name of the assembly the connection belongs to, should be a single entry',
@@ -20,5 +31,12 @@ export default ConfigurationSchema(
       defaultValue: [],
     },
   },
-  { baseConfiguration: baseConnectionConfig },
+  {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: baseConnectionConfig,
+  },
 )
+
+export default JBrowse1Connection

package/src/JBrowse1TextSeachAdapter/HttpMap.ts

@@ -1,4 +1,4 @@
-/*
+/**
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */

package/src/JBrowse1TextSeachAdapter/configSchema.ts

@@ -1,24 +1,44 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
+/**
+ * #config JBrowse1TextSearchAdapter
+ * note: metadata about tracks and assemblies covered by text search adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 export default ConfigurationSchema(
   'JBrowse1TextSearchAdapter',
   {
-    // metadata about tracks and assemblies covered by text search adapter
+    /**
+     * #slot
+     */
     namesIndexLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
       description: 'the location of the JBrowse1 names index data directory',
     },
+    /**
+     * #slot
+     */
     tracks: {
       type: 'stringArray',
       defaultValue: [],
       description: 'List of tracks covered by text search adapter',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
       type: 'stringArray',
       defaultValue: [],
       description: 'List of assemblies covered by text search adapter',
     },
   },
-  { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' },
+  {
+    explicitlyTyped: true,
+    /**
+     * #identifier
+     */
+    explicitIdentifier: 'textSearchAdapterId',
+  },
 )

package/src/NCListAdapter/NCListAdapter.ts

@@ -8,12 +8,10 @@ import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { checkAbortSignal } from '@jbrowse/core/util'
 import { RemoteFile } from 'generic-filehandle'
-import { Instance } from 'mobx-state-tree'
-import { readConfObject } from '@jbrowse/core/configuration'
 import NCListFeature from './NCListFeature'
-import MyConfigSchema from './configSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
 export default class NCListAdapter extends BaseFeatureDataAdapter {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -22,13 +20,13 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
   private configRefNames?: string[]
 
   constructor(
-    config: Instance<typeof MyConfigSchema>,
+    config: AnyConfigurationModel,
     getSubAdapter?: getSubAdapterType,
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const refNames = readConfObject(config, 'refNames')
-    const rootUrlTemplate = readConfObject(config, 'rootUrlTemplate')
+    const refNames = this.getConf('refNames')
+    const rootUrlTemplate = this.getConf('rootUrlTemplate')
     this.configRefNames = refNames
 
     this.nclist = new NCListStore({
@@ -78,12 +76,11 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
     return !!(root && root.stats && root.stats.featureCount)
   }
 
-  /*
+  /**
    * NCList is unable to get list of ref names so returns empty
-   * @return Promise<string[]> of empty list
    */
-  getRefNames() {
-    return Promise.resolve(this.configRefNames || [])
+  async getRefNames() {
+    return this.configRefNames || []
   }
 
   /**

package/src/NCListAdapter/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config NCListAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const NCListAdapter = ConfigurationSchema(
   'NCListAdapter',
   {
+    /**
+     * #slot
+     */
     rootUrlTemplate: {
       type: 'fileLocation',
       defaultValue: {
@@ -10,6 +18,9 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     */
     refNames: {
       type: 'stringArray',
       defaultValue: [],
@@ -18,3 +29,4 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+export default NCListAdapter