@jbrowse/plugin-legacy-jbrowse 1.6.9 → 1.7.3

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/types.js

@@ -0,0 +1,5 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});

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/JBrowse1Connection/util.js

@@ -0,0 +1,177 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.clone = clone;
+exports.deepUpdate = deepUpdate;
+exports.fillTemplate = fillTemplate;
+exports.isSource = isSource;
+exports.isTrack = isTrack;
+
+var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+
+var _getValue = _interopRequireDefault(require("get-value"));
+
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function isTrack(arg) {
+  return arg && arg.label && typeof arg.label === 'string';
+} // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function isSource(arg) {
+  return arg && arg.url && typeof arg.url === 'string';
+}
+/**
+ * updates a with values from b, recursively
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function deepUpdate(a, b) {
+  for (var _i = 0, _Object$keys = Object.keys(b); _i < _Object$keys.length; _i++) {
+    var prop = _Object$keys[_i];
+
+    if (prop in a && (0, _typeof2["default"])(b[prop]) === 'object' && (0, _typeof2["default"])(a[prop]) === 'object') {
+      deepUpdate(a[prop], b[prop]);
+    } else if (typeof a[prop] === 'undefined' || typeof b[prop] !== 'undefined') {
+      a[prop] = b[prop];
+    }
+  }
+
+  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) {
+  var _this = this;
+
+  return template.replace(/\{([\w\s.]+)\}/g, function (match, varName) {
+    varName = varName.replace(/\s+/g, ''); // remove all whitespace
+
+    var fill = (0, _getValue["default"])(fillWith, varName);
+
+    if (fill !== undefined) {
+      if (typeof fill === 'function') {
+        return fill(varName);
+      }
+
+      return fill;
+    }
+
+    if (fillWith.callback) {
+      // @ts-ignore
+      var v = fillWith.callback.call(_this, varName);
+
+      if (v !== undefined) {
+        return v;
+      }
+    }
+
+    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
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+
+function clone(src) {
+  if (!src || (0, _typeof2["default"])(src) !== 'object' || Object.prototype.toString.call(src) === '[object Function]') {
+    // null, undefined, any non-object, or function
+    return src; // anything
+  }
+
+  if (src.nodeType && 'cloneNode' in src) {
+    // DOM Node
+    return src.cloneNode(true); // Node
+  }
+
+  if (src instanceof Date) {
+    // Date
+    return new Date(src.getTime()); // Date
+  }
+
+  if (src instanceof RegExp) {
+    // RegExp
+    return new RegExp(src); // RegExp
+  }
+
+  var r;
+  var i;
+  var l;
+
+  if (Array.isArray(src)) {
+    // array
+    r = [];
+
+    for (i = 0, l = src.length; i < l; ++i) {
+      if (i in src) {
+        r[i] = clone(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);
+}
+/**
+ * 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) {
+  var name;
+  var s;
+  var empty = {};
+
+  for (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
+    s = source[name];
+
+    if (!(name in dest) || // @ts-ignore
+    dest[name] !== s && (!(name in empty) || empty[name] !== s)) {
+      dest[name] = copyFunc ? copyFunc(s) : s;
+    }
+  }
+
+  return dest; // Object
+}

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;
+}