@jbrowse/plugin-legacy-jbrowse 2.16.1 → 2.18.0

package/dist/JBrowse1Connection/util.js

@@ -7,7 +7,7 @@ exports.isTrack = isTrack;
 exports.isSource = isSource;
 exports.deepUpdate = deepUpdate;
 exports.fillTemplate = fillTemplate;
-exports.clone = clone;
+exports.structuredClone = structuredClone;
 const get_value_1 = __importDefault(require("get-value"));
 function isTrack(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
@@ -28,16 +28,6 @@ function deepUpdate(a, b) {
     }
     return a;
 }
-/**
- * replace variables in a template string with values
- *
- * @param template - String with variable names in curly brackets
- * e.g., `http://foo/{bar}?arg={baz.foo}`
- * @param fillWith - object with attribute-value mappings
- * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`
- * @returns the template string with variables in fillWith replaced
- * e.g., 'htp://foo/someurl?arg=valueforbaz'
- */
 function fillTemplate(template, fillWith) {
     return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
         varName = varName.replaceAll(/\s+/g, '');
@@ -46,7 +36,6 @@ function fillTemplate(template, fillWith) {
             return typeof fill === 'function' ? fill(varName) : fill;
         }
         if (fillWith.callback) {
-            // @ts-expect-error
             const v = fillWith.callback.call(this, varName);
             if (v !== undefined) {
                 return v;
@@ -55,81 +44,43 @@ function fillTemplate(template, fillWith) {
         return match;
     });
 }
-/**
- * Clones objects (including DOM nodes) and all children.
- * Warning: do not clone cyclic structures
- * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
- * @param src - The object to clone
- */
-function clone(src) {
+function structuredClone(src) {
     if (!src ||
         typeof src !== 'object' ||
         Object.prototype.toString.call(src) === '[object Function]') {
-        // null, undefined, any non-object, or function
-        return src; // anything
+        return src;
     }
     if (src.nodeType && 'cloneNode' in src) {
-        // DOM Node
-        return src.cloneNode(true); // Node
+        return src.cloneNode(true);
     }
     if (src instanceof Date) {
-        // Date
-        return new Date(src.getTime()); // Date
+        return new Date(src.getTime());
     }
     if (src instanceof RegExp) {
-        // RegExp
-        return new RegExp(src); // RegExp
+        return new RegExp(src);
     }
     let r;
     if (Array.isArray(src)) {
-        // array
         r = [];
         for (let i = 0, l = src.length; i < l; ++i) {
             if (i in src) {
-                r[i] = clone(src[i]);
+                r[i] = structuredClone(src[i]);
             }
         }
-        // we don't clone functions for performance reasons
-        //    }else if(d.isFunction(src)){
-        //      // function
-        //      r = function(){ return src.apply(this, arguments); };
     }
     else {
-        // generic objects
         r = src.constructor ? new src.constructor() : {};
     }
-    return mixin(r, src, clone);
+    return mixin(r, src, a => structuredClone(a));
 }
-/**
- * Copies/adds all properties of source to dest; returns dest.
- * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
- *
- * All properties, including functions (sometimes termed "methods"), excluding
- * any non-standard extensions found in Object.prototype, are copied/added to
- * dest. Copying/adding each particular property is delegated to copyFunc
- * (if any); copyFunc defaults to the Javascript assignment operator if not
- * provided. Notice that by default, mixin executes a so-called "shallow copy"
- * and aggregate types are copied/added by reference.
- * @param dest - The object to which to copy/add all properties contained in
- * source.
- * @param source - The object from which to draw all properties to copy into dest.
- * @param copyFunc - The process used to copy/add a property in source; defaults
- * to the Javascript assignment operator.
- * @returns dest, as modified
- */
 function mixin(dest, source, copyFunc) {
     const empty = {};
     for (const name in source) {
-        // the (!(name in empty) || empty[name] !== s) condition avoids copying
-        // properties in "source" inherited from Object.prototype.	 For example,
-        // if dest has a custom toString() method, don't overwrite it with the
-        // toString() method that source inherited from Object.prototype
         const s = source[name];
         if (!(name in dest) ||
-            // @ts-expect-error
             (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {
             dest[name] = copyFunc ? copyFunc(s) : s;
         }
     }
-    return dest; // Object
+    return dest;
 }

package/dist/JBrowse1TextSearchAdapter/HttpMap.d.ts

@@ -3,9 +3,6 @@ export default class HttpMap {
     constructor(args: {
         url: string;
     });
-    /**
-     * loads meta.json file from names directory and reads number of hash_bits used
-     */
     readMeta(): Promise<{
         hashHexCharacters: number;
         compress: any;
@@ -14,26 +11,9 @@ export default class HttpMap {
     getHashHexCharacters(): Promise<number>;
     getCompress(): Promise<any>;
     getTrackNames(): Promise<any>;
-    /**
-     * Returns contents of a bucket given a key
-     * @param key - string
-     */
     get(key: string): Promise<any>;
-    /**
-     * Returns a bucket given a key
-     * @param key - string
-     */
     getBucket(key: string): Promise<any>;
-    /**
-     * Loads a file using the url and provided id.
-     * Returns response object with contents of the file
-     * @param id - string
-     */
     loadFile(id: string): Promise<any>;
-    /**
-     * Returns the corresponding path of the file given a hex string
-     * @param hex - hex string
-     */
     hexToDirPath(hex: string): Promise<string>;
     hash(data: string): string;
 }

package/dist/JBrowse1TextSearchAdapter/HttpMap.js

@@ -3,20 +3,12 @@ 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
- */
-const crc32_1 = __importDefault(require("crc/crc32"));
 const buffer_1 = require("buffer");
+const crc32_1 = __importDefault(require("crc/crc32"));
 class HttpMap {
     constructor(args) {
-        // make sure url has a trailing slash
         this.url = args.url.endsWith('/') ? args.url : `${args.url}/`;
     }
-    /**
-     * loads meta.json file from names directory and reads number of hash_bits used
-     */
     async readMeta() {
         const meta = await this.loadFile('meta.json');
         const { compress, track_names: tracks } = meta;
@@ -35,28 +27,15 @@ class HttpMap {
         const meta = await this.readMeta();
         return meta.tracks;
     }
-    /**
-     * Returns contents of a bucket given a key
-     * @param key - string
-     */
     async get(key) {
         const bucket = await this.getBucket(key);
         return bucket[key];
     }
-    /**
-     * Returns a bucket given a key
-     * @param key - string
-     */
     async getBucket(key) {
         const bucketIdent = this.hash(key);
         const hexToDirPath = await this.hexToDirPath(bucketIdent);
         return this.loadFile(hexToDirPath);
     }
-    /**
-     * Loads a file using the url and provided id.
-     * Returns response object with contents of the file
-     * @param id - string
-     */
     async loadFile(id) {
         const response = await fetch(`${this.url}${id}`);
         if (!response.ok) {
@@ -64,12 +43,7 @@ class HttpMap {
         }
         return response.json();
     }
-    /**
-     * Returns the corresponding path of the file given a hex string
-     * @param hex - hex string
-     */
     async hexToDirPath(hex) {
-        // zero-pad the hex string to be 8 chars if necessary
         const hashHexCharacters = await this.getHashHexCharacters();
         if (hashHexCharacters) {
             const compress = await this.getCompress();

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -1,9 +1,10 @@
-import { BaseTextSearchAdapter, BaseTextSearchArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import HttpMap from './HttpMap';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseTextSearchAdapter, BaseTextSearchArgs } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export interface TooManyHits {
     name: string;
     hitLimit: number;
@@ -20,11 +21,6 @@ export default class JBrowse1TextSearchAdapter extends BaseAdapter implements Ba
     httpMap: HttpMap;
     tracksNames?: string[];
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    /**
-     * Returns the contents of the file containing the query if it exists
-     * else it returns empty
-     * @param query - string query
-     */
     loadIndexFile(query: string): Promise<IndexFile>;
     searchIndex(args: BaseTextSearchArgs): Promise<BaseResult[]>;
     formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];

package/dist/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.js

@@ -3,11 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
 const configuration_1 = require("@jbrowse/core/configuration");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const HttpMap_1 = __importDefault(require("./HttpMap"));
-// Uses index built by generate-names.pl
 class JBrowse1TextSearchAdapter extends BaseAdapter_1.BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -17,11 +16,6 @@ class JBrowse1TextSearchAdapter extends BaseAdapter_1.BaseAdapter {
             url: baseUri ? new URL(uri, baseUri).href : uri,
         });
     }
-    /**
-     * Returns the contents of the file containing the query if it exists
-     * else it returns empty
-     * @param query - string query
-     */
     async loadIndexFile(query) {
         return this.httpMap.getBucket(query);
     }

package/dist/JBrowse1TextSearchAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     namesIndexLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const _default: import("@jbrowse/core/configuration/configurationSchema"
         };
         description: string;
     };
-    /**
-     * #slot
-     */
     tracks: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/dist/JBrowse1TextSearchAdapter/configSchema.js

@@ -1,31 +1,18 @@
 "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
+function x() { }
 exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1TextSearchAdapter', {
-    /**
-     * #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: [],
@@ -33,8 +20,5 @@ exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1TextSearchAd
     },
 }, {
     explicitlyTyped: true,
-    /**
-     * #identifier
-     */
     explicitIdentifier: 'textSearchAdapterId',
 });

package/dist/JBrowse1TextSearchAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function JBrowse1TextSearchAdapterF(pluginManager: PluginManager): void;

package/dist/JBrowse1TextSearchAdapter/index.js

@@ -28,7 +28,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = JBrowse1TextSearchAdapterF;
 const TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
-// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 function JBrowse1TextSearchAdapterF(pluginManager) {
     pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType_1.default({

package/dist/NCListAdapter/NCListAdapter.d.ts

@@ -1,33 +1,18 @@
-import { Region } from '@jbrowse/core/util/types';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import NCListFeature from './NCListFeature';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
     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
-     * before fetching.
-     * @param region -
-     * @param opts - [signal] optional signalling object for aborting the fetch
-     * @returns Observable of Feature objects in the region
-     */
     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
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }

package/dist/NCListAdapter/NCListAdapter.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const nclist_1 = __importDefault(require("@gmod/nclist"));
 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 stopToken_1 = require("@jbrowse/core/util/stopToken");
 const generic_filehandle_1 = require("generic-filehandle");
 const NCListFeature_1 = __importDefault(require("./NCListFeature"));
 class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -23,19 +23,11 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 : url)).readFile(),
         });
     }
-    /**
-     * Fetch features for a certain region. Use getFeaturesInRegion() if you also
-     * want to verify that the store has features for the given reference sequence
-     * before fetching.
-     * @param region -
-     * @param opts - [signal] optional signalling object for aborting the fetch
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { signal } = opts;
+            const { stopToken } = opts;
             for await (const feature of this.nclist.getFeatures(region, opts)) {
-                (0, util_1.checkAbortSignal)(signal);
+                (0, stopToken_1.checkStopToken)(stopToken);
                 observer.next(this.wrapFeature(feature));
             }
             observer.complete();
@@ -49,17 +41,9 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const root = await this.nclist.getDataRoot(refName);
         return !!((_a = root === null || root === void 0 ? void 0 : root.stats) === null || _a === void 0 ? void 0 : _a.featureCount);
     }
-    /**
-     * NCList is unable to get list of ref names so returns empty
-     */
     async getRefNames() {
         return this.configRefNames || [];
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources() { }
 }
 exports.default = NCListAdapter;

package/dist/NCListAdapter/NCListFeature.d.ts

@@ -1,7 +1,4 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-/**
- * wrapper to adapt nclist features to act like jbrowse 2 features
- */
+import type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 export default class NCListFeature implements Feature {
     private ncFeature;
     private parentHandle?;
@@ -11,21 +8,9 @@ export default class NCListFeature implements Feature {
     jb2TagToJb1Tag(tag: string): string;
     jb1TagToJb2Tag(tag: string): string;
     get(attrName: string): any;
-    /**
-     * Get an array listing which data keys are present in this feature.
-     */
     tags(): string[];
-    /**
-     * Get the unique ID of this feature.
-     */
     id(): string;
-    /**
-     * Get this feature's parent feature, or undefined if none.
-     */
     parent(): Feature | undefined;
-    /**
-     * Get an array of child features, or undefined if none.
-     */
     children(): Feature[] | undefined;
     toJSON(): SimpleFeatureSerialized;
 }

package/dist/NCListAdapter/NCListFeature.js

@@ -2,9 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const jb2ToJb1 = { refName: 'seq_id' };
 const jb1ToJb2 = { seq_id: 'refName' };
-/**
- * wrapper to adapt nclist features to act like jbrowse 2 features
- */
 class NCListFeature {
     constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
@@ -15,13 +12,11 @@ class NCListFeature {
         throw new Error('not implemented');
     }
     jb2TagToJb1Tag(tag) {
-        // @ts-expect-error
         const mapped = jb2ToJb1[tag] || tag;
         return mapped.toLowerCase();
     }
     jb1TagToJb2Tag(tag) {
         const t = tag.toLowerCase();
-        // @ts-expect-error
         return jb1ToJb2[t] || t;
     }
     get(attrName) {
@@ -31,39 +26,25 @@ class NCListFeature {
         }
         return attr;
     }
-    /**
-     * Get an array listing which data keys are present in this feature.
-     */
     tags() {
         return this.ncFeature.tags().map((t) => this.jb1TagToJb2Tag(t));
     }
-    /**
-     * Get the unique ID of this feature.
-     */
     id() {
         return this.uniqueId;
     }
-    /**
-     * Get this feature's parent feature, or undefined if none.
-     */
     parent() {
         return this.parentHandle;
     }
-    /**
-     * Get an array of child features, or undefined if none.
-     */
     children() {
         return this.get('subfeatures');
     }
     toJSON() {
-        // @ts-expect-error
         const data = { uniqueId: this.id() };
         this.ncFeature.tags().forEach((tag) => {
             const mappedTag = this.jb1TagToJb2Tag(tag);
             const value = this.ncFeature.get(tag);
             if (mappedTag === 'subfeatures') {
                 data.subfeatures = (value || []).map((f) => {
-                    // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()
                     return new NCListFeature(f, this).toJSON();
                 });
             }

package/dist/NCListAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     rootUrlTemplate: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     refNames: {
         type: string;
         defaultValue: never[];

package/dist/NCListAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config NCListAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const NCListAdapter = (0, configuration_1.ConfigurationSchema)('NCListAdapter', {
-    /**
-     * #slot
-     */
     rootUrlTemplate: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +10,6 @@ const NCListAdapter = (0, configuration_1.ConfigurationSchema)('NCListAdapter',
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     refNames: {
         type: 'stringArray',
         defaultValue: [],

package/dist/NCListAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function NCListAdapterF(pluginManager: PluginManager): void;

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LegacyJBrowsePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const NCListAdapter_1 = __importDefault(require("./NCListAdapter"));
-const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
-const JBrowse1Connection_1 = __importDefault(require("./JBrowse1Connection"));
 const GuessNCList_1 = __importDefault(require("./GuessNCList"));
+const JBrowse1Connection_1 = __importDefault(require("./JBrowse1Connection"));
+const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
+const NCListAdapter_1 = __importDefault(require("./NCListAdapter"));
 class LegacyJBrowsePlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/esm/GuessNCList/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function GuessNCListF(pluginManager: PluginManager): void;

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     dataDirLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +7,6 @@ declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurat
         };
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         description: string;
         type: string;