@jbrowse/plugin-legacy-jbrowse 1.7.0 → 1.7.1

package/dist/JBrowse1Connection/configSchema.d.ts

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

package/dist/JBrowse1Connection/index.d.ts

@@ -1,2 +1,2 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';
+export { default as configSchema } from './configSchema';

package/dist/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -1,36 +1,36 @@
-import { JBLocation, Config } from './types';
-export declare function fetchJb1(dataRoot?: JBLocation, baseConfig?: Config, baseConfigRoot?: JBLocation): Promise<Config>;
-export declare function createFinalConfig(baseConfig: Config, defaults?: {
-    tracks: never[];
-    containerID: string;
-    dataRoot: string;
-    show_tracklist: boolean;
-    show_nav: boolean;
-    show_menu: boolean;
-    show_overview: boolean;
-    show_fullviewlink: boolean;
-    update_browser_title: boolean;
-    updateBrowserURL: boolean;
-    refSeqs: string;
-    include: string[];
-    nameUrl: string;
-    datasets: {
-        _DEFAULT_EXAMPLES: boolean;
-        volvox: {
-            url: string;
-            name: string;
-        };
-        modencode: {
-            url: string;
-            name: string;
-        };
-        yeast: {
-            url: string;
-            name: string;
-        };
-    };
-    highlightSearchedRegions: boolean;
-    highResolutionMode: string;
-}): Promise<Config>;
-export declare function fetchConfigFile(location: JBLocation): Promise<Config>;
-export declare function parseJb1(config: string, url?: string): Config;
+import { JBLocation, Config } from './types';
+export declare function fetchJb1(dataRoot?: JBLocation, baseConfig?: Config, baseConfigRoot?: JBLocation): Promise<Config>;
+export declare function createFinalConfig(baseConfig: Config, defaults?: {
+    tracks: never[];
+    containerID: string;
+    dataRoot: string;
+    show_tracklist: boolean;
+    show_nav: boolean;
+    show_menu: boolean;
+    show_overview: boolean;
+    show_fullviewlink: boolean;
+    update_browser_title: boolean;
+    updateBrowserURL: boolean;
+    refSeqs: string;
+    include: string[];
+    nameUrl: string;
+    datasets: {
+        _DEFAULT_EXAMPLES: boolean;
+        volvox: {
+            url: string;
+            name: string;
+        };
+        modencode: {
+            url: string;
+            name: string;
+        };
+        yeast: {
+            url: string;
+            name: string;
+        };
+    };
+    highlightSearchedRegions: boolean;
+    highResolutionMode: string;
+}): Promise<Config>;
+export declare function fetchConfigFile(location: JBLocation): Promise<Config>;
+export declare function parseJb1(config: string, url?: string): Config;

package/dist/JBrowse1Connection/jb1ConfigParse.d.ts

@@ -1,11 +1,11 @@
-import { Config } from './types';
-export declare function parseJB1Json(config: Config | string, url: string): Config;
-export declare function parseJB1Conf(config: string, url: string): Config;
-/**
- * Applies defaults and any other necessary tweaks to the loaded configuration.
- * @param conf - the object containing the configuration, which it modifies
- * in-place
- * @param url - URL of the config file
- * @returns the same object it was passed
- */
-export declare function regularizeConf(conf: Config, url: string): Config;
+import { Config } from './types';
+export declare function parseJB1Json(config: Config | string, url: string): Config;
+export declare function parseJB1Conf(config: string, url: string): Config;
+/**
+ * Applies defaults and any other necessary tweaks to the loaded configuration.
+ * @param conf - the object containing the configuration, which it modifies
+ * in-place
+ * @param url - URL of the config file
+ * @returns the same object it was passed
+ */
+export declare function regularizeConf(conf: Config, url: string): Config;

package/dist/JBrowse1Connection/jb1ToJb2.d.ts

@@ -1,47 +1,47 @@
-import { Track, RefSeqs } from './types';
-interface Jb2Track {
-    trackId: string;
-    name: string;
-    description?: string;
-    category?: string[];
-    adapter?: Jb2Adapter;
-    type?: string;
-    defaultRendering?: string;
-}
-interface Jb2Adapter {
-    type: string;
-    features?: Jb2Feature[];
-    bamLocation?: Jb2Location;
-    cramLocation?: Jb2Location;
-    craiLocation?: Jb2Location;
-    fastaLocation?: Jb2Location;
-    faiLocation?: Jb2Location;
-    gziLocation?: Jb2Location;
-    twoBitLocation?: Jb2Location;
-    bigWigLocation?: Jb2Location;
-    bigBedLocation?: Jb2Location;
-    vcfGzLocation?: Jb2Location;
-    gffGzLocation?: Jb2Location;
-    bedGzLocation?: Jb2Location;
-    index?: {
-        location: Jb2Location;
-        indexType?: string;
-    };
-    rootUrlTemplate?: Jb2Location;
-    sequenceAdapter?: Jb2Adapter;
-}
-interface Jb2Feature {
-    refName: string;
-    uniqueId: string;
-    start: number;
-    end: number;
-}
-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>;
-export {};
+import { Track, RefSeqs } from './types';
+interface Jb2Track {
+    trackId: string;
+    name: string;
+    description?: string;
+    category?: string[];
+    adapter?: Jb2Adapter;
+    type?: string;
+    defaultRendering?: string;
+}
+interface Jb2Adapter {
+    type: string;
+    features?: Jb2Feature[];
+    bamLocation?: Jb2Location;
+    cramLocation?: Jb2Location;
+    craiLocation?: Jb2Location;
+    fastaLocation?: Jb2Location;
+    faiLocation?: Jb2Location;
+    gziLocation?: Jb2Location;
+    twoBitLocation?: Jb2Location;
+    bigWigLocation?: Jb2Location;
+    bigBedLocation?: Jb2Location;
+    vcfGzLocation?: Jb2Location;
+    gffGzLocation?: Jb2Location;
+    bedGzLocation?: Jb2Location;
+    index?: {
+        location: Jb2Location;
+        indexType?: string;
+    };
+    rootUrlTemplate?: Jb2Location;
+    sequenceAdapter?: Jb2Adapter;
+}
+interface Jb2Feature {
+    refName: string;
+    uniqueId: string;
+    start: number;
+    end: number;
+}
+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>;
+export {};

package/dist/JBrowse1Connection/model.d.ts

@@ -1,4 +1,15 @@
-export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<import("mobx-state-tree").ModelProperties & {
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
-    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
-}, any, any, any>;
+export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+    name: import("mobx-state-tree").ISimpleType<string>;
+    tracks: import("mobx-state-tree").IArrayType<any>;
+} & {
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
+}, {
+    afterAttach(): void;
+    addTrackConf(trackConf: any): any;
+    addTrackConfs(trackConfs: any): any[];
+    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    clear(): void;
+} & {
+    connect(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/JBrowse1Connection/types.d.ts

@@ -1,91 +1,91 @@
-export interface ProtoTrack {
-    backendVersion?: number;
-    baseUrl?: string;
-    category?: string;
-    config?: Track;
-    dataRoot?: string;
-    features?: Feature[];
-    histograms?: Track;
-    index?: number;
-    key?: string;
-    label?: string;
-    metadata?: Metadata;
-    store?: Store | string;
-    storeClass?: string;
-    type?: string;
-    urlTemplate?: string;
-    baiUrlTemplate?: string;
-    craiUrlTemplate?: string;
-    tbiUrlTemplate?: string;
-    csiUrlTemplate?: string;
-    faiUrlTemplate?: string;
-    gziUrlTemplate?: string;
-    useAsRefSeqStore?: boolean;
-}
-export interface Track extends ProtoTrack {
-    label: string;
-}
-export interface Metadata {
-    category?: string;
-    description?: string;
-    Description?: string;
-}
-export interface Feature {
-    seq_id: string;
-    start: number;
-    end: number;
-    name?: string;
-}
-export interface Source {
-    url: string;
-    name?: string;
-    type?: string;
-}
-export interface TrackMetadata {
-    sources?: string | Source | (string | Source)[] | Record<string, Source>;
-}
-export interface Store extends ProtoTrack {
-    name?: string;
-}
-export interface Names {
-    baseUrl?: string;
-}
-export interface RefSeq {
-    name: string;
-    length: number;
-    end: number;
-    start: number;
-}
-export interface RefSeqs {
-    url?: string;
-    data?: RefSeq[];
-}
-export interface Include {
-    url: string;
-    cacheBuster?: boolean;
-    format?: string;
-    version?: number;
-}
-export interface Config {
-    baseUrl?: string;
-    cacheBuster?: boolean;
-    dataRoot?: string;
-    include?: string[];
-    names?: Record<string, string>;
-    nameUrl?: string;
-    refSeqs?: string | RefSeqs;
-    sourceUrl?: string;
-    stores?: Record<string, Store>;
-    trackMetadata?: TrackMetadata;
-    tracks?: Track | Track[] | Record<string, Track | ProtoTrack>;
-}
-export interface UriLocation {
-    uri: string;
-    baseUri?: string;
-    locationType: 'UriLocation';
-}
-export interface LocalPathLocation {
-    localPath: string;
-    locationType: 'LocalPathLocation';
-}
-export declare type JBLocation = UriLocation | LocalPathLocation;
+export interface ProtoTrack {
+    backendVersion?: number;
+    baseUrl?: string;
+    category?: string;
+    config?: Track;
+    dataRoot?: string;
+    features?: Feature[];
+    histograms?: Track;
+    index?: number;
+    key?: string;
+    label?: string;
+    metadata?: Metadata;
+    store?: Store | string;
+    storeClass?: string;
+    type?: string;
+    urlTemplate?: string;
+    baiUrlTemplate?: string;
+    craiUrlTemplate?: string;
+    tbiUrlTemplate?: string;
+    csiUrlTemplate?: string;
+    faiUrlTemplate?: string;
+    gziUrlTemplate?: string;
+    useAsRefSeqStore?: boolean;
+}
+export interface Track extends ProtoTrack {
+    label: string;
+}
+export interface Metadata {
+    category?: string;
+    description?: string;
+    Description?: string;
+}
+export interface Feature {
+    seq_id: string;
+    start: number;
+    end: number;
+    name?: string;
+}
+export interface Source {
+    url: string;
+    name?: string;
+    type?: string;
+}
+export interface TrackMetadata {
+    sources?: string | Source | (string | Source)[] | Record<string, Source>;
+}
+export interface Store extends ProtoTrack {
+    name?: string;
+}
+export interface Names {
+    baseUrl?: string;
+}
+export interface RefSeq {
+    name: string;
+    length: number;
+    end: number;
+    start: number;
+}
+export interface RefSeqs {
+    url?: string;
+    data?: RefSeq[];
+}
+export interface Include {
+    url: string;
+    cacheBuster?: boolean;
+    format?: string;
+    version?: number;
+}
+export interface Config {
+    baseUrl?: string;
+    cacheBuster?: boolean;
+    dataRoot?: string;
+    include?: string[];
+    names?: Record<string, string>;
+    nameUrl?: string;
+    refSeqs?: string | RefSeqs;
+    sourceUrl?: string;
+    stores?: Record<string, Store>;
+    trackMetadata?: TrackMetadata;
+    tracks?: Track | Track[] | Record<string, Track | ProtoTrack>;
+}
+export interface UriLocation {
+    uri: string;
+    baseUri?: string;
+    locationType: 'UriLocation';
+}
+export interface LocalPathLocation {
+    localPath: string;
+    locationType: 'LocalPathLocation';
+}
+export declare type JBLocation = UriLocation | LocalPathLocation;

package/dist/JBrowse1Connection/util.d.ts

@@ -1,26 +1,26 @@
-import { Track, Source } from './types';
-export declare function isTrack(arg: any): arg is Track;
-export declare function isSource(arg: any): arg is Source;
-/**
- * updates a with values from b, recursively
- */
-declare type Obj = Record<string, any>;
-export declare function deepUpdate(a: Obj, b: Obj): Obj;
-/**
- * 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'
- */
-export declare function fillTemplate(template: string, fillWith: Obj): string;
-/**
- * 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
- */
-export declare function clone(src: any): any;
-export {};
+import { Track, Source } from './types';
+export declare function isTrack(arg: any): arg is Track;
+export declare function isSource(arg: any): arg is Source;
+/**
+ * updates a with values from b, recursively
+ */
+declare type Obj = Record<string, any>;
+export declare function deepUpdate(a: Obj, b: Obj): Obj;
+/**
+ * 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'
+ */
+export declare function fillTemplate(template: string, fillWith: Obj): string;
+/**
+ * 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
+ */
+export declare function clone(src: any): any;
+export {};

package/dist/JBrowse1TextSeachAdapter/HttpMap.d.ts

@@ -1,39 +1,39 @@
-export default class HttpMap {
-    url: string;
-    constructor(args: {
-        url: string;
-    });
-    /**
-     * loads meta.json file from names directory and reads number of hash_bits used
-     */
-    readMeta(): Promise<{
-        hashHexCharacters: number;
-        compress: any;
-        tracks: any;
-    }>;
-    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;
-}
+export default class HttpMap {
+    url: string;
+    constructor(args: {
+        url: string;
+    });
+    /**
+     * loads meta.json file from names directory and reads number of hash_bits used
+     */
+    readMeta(): Promise<{
+        hashHexCharacters: number;
+        compress: any;
+        tracks: any;
+    }>;
+    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/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -1,33 +1,33 @@
-import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-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>, 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, SearchResults>>;
-    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
-    formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
-    freeResources(): void;
-}
-export {};
+import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+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>, 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, SearchResults>>;
+    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
+    formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
+    freeResources(): void;
+}
+export {};

package/dist/JBrowse1TextSeachAdapter/configSchema.d.ts

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

package/dist/JBrowse1TextSeachAdapter/index.d.ts

@@ -1,2 +1,2 @@
-export { default as AdapterClass } from './JBrowse1TextSearchAdapter';
-export { default as configSchema } from './configSchema';
+export { default as AdapterClass } from './JBrowse1TextSearchAdapter';
+export { default as configSchema } from './configSchema';