@jbrowse/plugin-legacy-jbrowse 1.4.4 → 1.5.3

package/dist/JBrowse1Connection/jb1ToJb2.d.ts

@@ -40,6 +40,7 @@ interface Jb2Location {
     uri?: string;
     localPath?: string;
     blobId?: string;
+    locationType?: string;
 }
 export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string, sequenceAdapter: Jb2Adapter): Jb2Track;
 export declare function createRefSeqsAdapter(refSeqs: string | RefSeqs): Promise<Jb2Adapter>;

package/dist/JBrowse1Connection/types.d.ts

@@ -82,8 +82,10 @@ export interface Config {
 export interface UriLocation {
     uri: string;
     baseUri?: string;
+    locationType: 'UriLocation';
 }
 export interface LocalPathLocation {
     localPath: string;
+    locationType: 'LocalPathLocation';
 }
 export declare type JBLocation = UriLocation | LocalPathLocation;

package/dist/JBrowse1TextSeachAdapter/HttpMap.d.ts

@@ -1,12 +1,7 @@
 export default class HttpMap {
     url: string;
-    isElectron: boolean;
-    hash_hex_characters?: number;
-    compress?: number;
-    tracks?: string[];
     constructor(args: {
         url: string;
-        isElectron: boolean;
     });
     /**
      * loads meta.json file from names directory and reads number of hash_bits used
@@ -15,12 +10,8 @@ export default class HttpMap {
         hashHexCharacters: number;
         compress: any;
         tracks: any;
-    } | {
-        hashHexCharacters?: undefined;
-        compress?: undefined;
-        tracks?: undefined;
     }>;
-    getHashHexCharacters(): Promise<number | undefined>;
+    getHashHexCharacters(): Promise<number>;
     getCompress(): Promise<any>;
     getTrackNames(): Promise<any>;
     /**
@@ -44,10 +35,5 @@ export default class HttpMap {
      * @param hex - hex string
      */
     hexToDirPath(hex: string): Promise<string>;
-    /**
-     * Returns crc32 hash given a string.
-     * (Note: this is using JBrowse1 implementation of crc32.)
-     * @param data - string
-     */
     hash(data: string): string;
 }

package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -3,27 +3,31 @@ import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import { Instance } from 'mobx-state-tree';
 import MyConfigSchema from './configSchema';
 import HttpMap from './HttpMap';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export interface TooManyHits {
     name: string;
     hitLimit: number;
 }
+interface SearchResults {
+    prefix: ({
+        name: string;
+    } | string)[];
+    exact: [string, number, string, string, number, number][];
+}
 export declare type NamesIndexRecord = string | Array<string | number>;
 export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
     httpMap: HttpMap;
     tracksNames?: string[];
-    constructor(config: Instance<typeof MyConfigSchema>);
+    constructor(config: Instance<typeof MyConfigSchema>, 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<Record<string, Record<string, (string | TooManyHits | (string | number)[])[]>>>;
-    /**
-     * Returns list of results
-     * @param args - search options/arguments include: search query
-     * limit of results to return, SearchType...prefix | full | exact", etc.
-     */
+    loadIndexFile(query: string): Promise<Record<string, SearchResults>>;
     searchIndex(args: BaseArgs): Promise<BaseResult[]>;
-    formatResults(results: Array<NamesIndexRecord | TooManyHits>, tracksNames: string[]): BaseResult[];
+    formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
     freeResources(): void;
 }
+export {};

package/dist/NCListAdapter/NCListAdapter.d.ts

@@ -4,10 +4,12 @@ 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';
 export default class NCListAdapter extends BaseFeatureDataAdapter {
     private nclist;
     private configRefNames?;
-    constructor(config: Instance<typeof MyConfigSchema>);
+    constructor(config: Instance<typeof MyConfigSchema>, 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