@jbrowse/core 1.4.1 → 1.5.2

package/ui/index.js

@@ -21,76 +21,76 @@ var _exportNames = {
   Menu: true,
   SanitizedHTML: true
 };
-Object.defineProperty(exports, "LogoFull", {
+Object.defineProperty(exports, "App", {
   enumerable: true,
   get: function get() {
-    return _Logo.LogoFull;
+    return _App.default;
   }
 });
-Object.defineProperty(exports, "Logomark", {
+Object.defineProperty(exports, "EditableTypography", {
   enumerable: true,
   get: function get() {
-    return _Logo.Logomark;
+    return _EditableTypography.default;
   }
 });
-Object.defineProperty(exports, "App", {
+Object.defineProperty(exports, "FactoryResetDialog", {
   enumerable: true,
   get: function get() {
-    return _App.default;
+    return _FactoryResetDialog.default;
   }
 });
-Object.defineProperty(exports, "FileSelector", {
+Object.defineProperty(exports, "FatalErrorDialog", {
   enumerable: true,
   get: function get() {
-    return _FileSelector.default;
+    return _FatalErrorDialog.default;
   }
 });
-Object.defineProperty(exports, "PrerenderedCanvas", {
+Object.defineProperty(exports, "FileSelector", {
   enumerable: true,
   get: function get() {
-    return _PrerenderedCanvas.default;
+    return _FileSelector.default;
   }
 });
-Object.defineProperty(exports, "ResizeHandle", {
+Object.defineProperty(exports, "LogoFull", {
   enumerable: true,
   get: function get() {
-    return _ResizeHandle.default;
+    return _Logo.LogoFull;
   }
 });
-Object.defineProperty(exports, "EditableTypography", {
+Object.defineProperty(exports, "Logomark", {
   enumerable: true,
   get: function get() {
-    return _EditableTypography.default;
+    return _Logo.Logomark;
   }
 });
-Object.defineProperty(exports, "FactoryResetDialog", {
+Object.defineProperty(exports, "Menu", {
   enumerable: true,
   get: function get() {
-    return _FactoryResetDialog.default;
+    return _Menu.default;
   }
 });
-Object.defineProperty(exports, "Tooltip", {
+Object.defineProperty(exports, "PrerenderedCanvas", {
   enumerable: true,
   get: function get() {
-    return _Tooltip.default;
+    return _PrerenderedCanvas.default;
   }
 });
-Object.defineProperty(exports, "FatalErrorDialog", {
+Object.defineProperty(exports, "ResizeHandle", {
   enumerable: true,
   get: function get() {
-    return _FatalErrorDialog.default;
+    return _ResizeHandle.default;
   }
 });
-Object.defineProperty(exports, "Menu", {
+Object.defineProperty(exports, "SanitizedHTML", {
   enumerable: true,
   get: function get() {
-    return _Menu.default;
+    return _SanitizedHTML.default;
   }
 });
-Object.defineProperty(exports, "SanitizedHTML", {
+Object.defineProperty(exports, "Tooltip", {
   enumerable: true,
   get: function get() {
-    return _SanitizedHTML.default;
+    return _Tooltip.default;
   }
 });
 

package/ui/theme.js

@@ -5,10 +5,10 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.createJBrowseDefaultProps = createJBrowseDefaultProps;
 exports.createJBrowseDefaultOverrides = createJBrowseDefaultOverrides;
+exports.createJBrowseDefaultProps = createJBrowseDefaultProps;
 exports.createJBrowseTheme = createJBrowseTheme;
-exports.jbrowseBaseTheme = exports.jbrowseDefaultPalette = void 0;
+exports.jbrowseDefaultPalette = exports.jbrowseBaseTheme = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
@@ -54,9 +54,9 @@ var jbrowseDefaultPalette = {
 };
 exports.jbrowseDefaultPalette = jbrowseDefaultPalette;
 
-function createJBrowseDefaultProps()
-/* palette: PaletteOptions = {} */
-{
+function
+  /* palette: PaletteOptions = {} */
+createJBrowseDefaultProps() {
   return {
     MuiButton: {
       size: 'small'

package/util/QuickLRU.d.ts

@@ -19,6 +19,6 @@ declare class QuickLRU {
     clear(): void;
     keys(): Generator<any, void, unknown>;
     values(): Generator<any, void, unknown>;
-    [Symbol.iterator](): Generator<[any, any], void, unknown>;
     get size(): number;
+    [Symbol.iterator](): Generator<[any, any], void, unknown>;
 }

package/util/QuickLRU.js

@@ -28,7 +28,7 @@ function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len
  * (quick-lru didn't work for us because the export wouldn't compile in Webpack
  * properly)
  */
-var QuickLRU = /*#__PURE__*/function () {
+var QuickLRU = /*#__PURE__*/function (_Symbol$iterator) {
   function QuickLRU() {
     var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
     (0, _classCallCheck2.default)(this, QuickLRU);
@@ -225,7 +225,7 @@ var QuickLRU = /*#__PURE__*/function () {
       }, values, this, [[1, 11, 14, 17]]);
     })
   }, {
-    key: Symbol.iterator,
+    key: _Symbol$iterator,
     value: /*#__PURE__*/_regenerator.default.mark(function value() {
       var _iterator3, _step3, item, _iterator4, _step4, _item, _item2, key;
 
@@ -346,7 +346,7 @@ var QuickLRU = /*#__PURE__*/function () {
     }
   }]);
   return QuickLRU;
-}();
+}(Symbol.iterator);
 
 var _default = QuickLRU;
 exports.default = _default;

package/util/aborting.d.ts

@@ -26,5 +26,5 @@ export declare function observeAbortSignal(signal?: AbortSignal): Observable<Eve
  * check if the given exception was caused by an operation being intentionally aborted
  * @param exception -
  */
-export declare function isAbortException(exception: Error): boolean;
+export declare function isAbortException(exception: unknown): boolean;
 export {};

package/util/aborting.js

@@ -5,11 +5,11 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.checkAbortSignal = checkAbortSignal;
 exports.abortBreakPoint = abortBreakPoint;
+exports.checkAbortSignal = checkAbortSignal;
+exports.isAbortException = isAbortException;
 exports.makeAbortError = makeAbortError;
 exports.observeAbortSignal = observeAbortSignal;
-exports.isAbortException = isAbortException;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -145,13 +145,12 @@ function observeAbortSignal(signal) {
 
 
 function isAbortException(exception) {
-  return (// DOMException
-    exception.name === 'AbortError' || // standard-ish non-DOM abort exception
-    exception.code === 'ERR_ABORTED' || // message contains aborted for bubbling through RPC
-    // things we have seen that we want to catch here
-    // Error: aborted
-    // AbortError: aborted
-    // AbortError: The user aborted a request.
-    !!exception.message.match(/\b(aborted|AbortError)\b/i)
-  );
+  return exception instanceof Error && ( // DOMException
+  exception.name === 'AbortError' || // standard-ish non-DOM abort exception
+  exception.code === 'ERR_ABORTED' || // message contains aborted for bubbling through RPC
+  // things we have seen that we want to catch here
+  // Error: aborted
+  // AbortError: aborted
+  // AbortError: The user aborted a request.
+  !!exception.message.match(/\b(aborted|AbortError)\b/i));
 }

package/util/analytics.d.ts

@@ -1,2 +1,2 @@
-export declare function writeAWSAnalytics(rootModel: any, initialTimeStamp: number, sessionQuery?: string | null): Promise<Response>;
-export declare function writeGAAnalytics(rootModel: any, initialTimeStamp: number): Promise<void>;
+export declare function writeAWSAnalytics(rootModel: any, initialTimeStamp: number, sessionQuery?: string | null): Promise<void>;
+export declare function writeGAAnalytics(rootModel: any, initialTimestamp: number): Promise<void>;

package/util/analytics.js

@@ -28,6 +28,7 @@ function _writeAWSAnalytics() {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
+            _context.prev = 0;
             url = 'https://analytics.jbrowse.org/api/v1';
             multiAssemblyTracks = rootModel.jbrowse.tracks.filter(function (track) {
               return ((0, _configuration.readConfObject)(track, 'assemblyNames') || []).length > 1;
@@ -64,24 +65,36 @@ function _writeAWSAnalytics() {
             }; // stringifies the track type counts, gets processed in lambda
 
             tracks.forEach(function (track) {
-              stats["track-types-".concat(track.type)] = stats["track-types-".concat(track.type)] + 1 || 1;
+              var key = "track-types-".concat(track.type);
+              stats[key] = stats[key] + 1 || 1;
             }); // stringifies the session track type counts, gets processed in lambda
 
             session === null || session === void 0 ? void 0 : session.sessionTracks.forEach(function (track) {
-              stats["sessionTrack-types-".concat(track.type)] = stats["sessionTrack-types-".concat(track.type)] + 1 || 1;
+              var key = "sessionTrack-types-".concat(track.type);
+              stats[key] = stats[key] + 1 || 1;
             }); // put stats into a query string for get request
 
             qs = Object.keys(stats).map(function (key) {
               return "".concat(key, "=").concat(stats[key]);
             }).join('&');
-            return _context.abrupt("return", fetch("".concat(url, "?").concat(qs)));
+            _context.next = 12;
+            return fetch("".concat(url, "?").concat(qs));
 
-          case 10:
+          case 12:
+            _context.next = 17;
+            break;
+
+          case 14:
+            _context.prev = 14;
+            _context.t0 = _context["catch"](0);
+            console.error('Failed to write analytics to AWS.', _context.t0);
+
+          case 17:
           case "end":
             return _context.stop();
         }
       }
-    }, _callee);
+    }, _callee, null, [[0, 14]]);
   }));
   return _writeAWSAnalytics.apply(this, arguments);
 }
@@ -91,7 +104,7 @@ function writeGAAnalytics(_x4, _x5) {
 }
 
 function _writeGAAnalytics() {
-  _writeGAAnalytics = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(rootModel, initialTimeStamp) {
+  _writeGAAnalytics = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(rootModel, initialTimestamp) {
     var _rootModel$jbrowse$pl;
 
     var jbrowseUser, stats, analyticsScript, gaData, googleDimensions, analyticsScriptNode;
@@ -105,7 +118,7 @@ function _writeGAAnalytics() {
               // this is all possible tracks
               ver: rootModel.version,
               electron: _util.isElectron,
-              loadTime: Date.now() - initialTimeStamp,
+              loadTime: Date.now() - initialTimestamp,
               pluginNames: ((_rootModel$jbrowse$pl = rootModel.jbrowse.plugins) === null || _rootModel$jbrowse$pl === void 0 ? void 0 : _rootModel$jbrowse$pl.map(function (plugin) {
                 return plugin.name;
               })) || ''

package/util/blockTypes.d.ts

@@ -9,25 +9,29 @@ export declare class BlockSet {
         start: number;
         end: number;
         assemblyName: string;
-        reversed: any;
+        reversed: boolean | undefined;
     }[];
     map<T, U = this>(func: Func<T>, thisarg?: U): T[];
     forEach<T, U = this>(func: Func<T>, thisarg?: U): void;
     get length(): number;
-    get totalWidthPx(): any;
-    get totalWidthPxWithoutBorders(): any;
+    get totalWidthPx(): number;
+    get totalWidthPxWithoutBorders(): number;
     get offsetPx(): number;
     get contentBlocks(): BaseBlock[];
     get totalBp(): number;
 }
 export declare class BaseBlock {
-    [key: string]: any;
+    regionNumber?: number;
+    reversed?: boolean;
     refName: string;
     start: number;
     end: number;
     assemblyName: string;
     key: string;
     offsetPx: number;
+    widthPx: number;
+    variant?: string;
+    isLeftEndOfDisplayedRegion?: boolean;
     /**
      * a block that should be shown as filled with data
      */
@@ -45,7 +49,7 @@ export declare class BaseBlock {
         start: number;
         end: number;
         assemblyName: string;
-        reversed: any;
+        reversed: boolean | undefined;
     };
 }
 export declare class ContentBlock extends BaseBlock {
@@ -56,8 +60,9 @@ export declare class ContentBlock extends BaseBlock {
  */
 export declare class ElidedBlock extends BaseBlock {
     widthPx: number;
+    elidedBlockCount: number;
     constructor(data: Record<string, any>);
-    push(otherBlock: BaseBlock): void;
+    push(otherBlock: ElidedBlock): void;
 }
 /**
  * marker block that sits between two different displayed regions

package/util/blockTypes.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.InterRegionPaddingBlock = exports.ElidedBlock = exports.ContentBlock = exports.BaseBlock = exports.BlockSet = void 0;
+exports.InterRegionPaddingBlock = exports.ElidedBlock = exports.ContentBlock = exports.BlockSet = exports.BaseBlock = void 0;
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
 
@@ -134,12 +134,17 @@ var BaseBlock = /*#__PURE__*/function () {
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   function BaseBlock(data) {
     (0, _classCallCheck2.default)(this, BaseBlock);
+    (0, _defineProperty2.default)(this, "regionNumber", void 0);
+    (0, _defineProperty2.default)(this, "reversed", void 0);
     (0, _defineProperty2.default)(this, "refName", void 0);
     (0, _defineProperty2.default)(this, "start", void 0);
     (0, _defineProperty2.default)(this, "end", void 0);
     (0, _defineProperty2.default)(this, "assemblyName", void 0);
     (0, _defineProperty2.default)(this, "key", void 0);
     (0, _defineProperty2.default)(this, "offsetPx", void 0);
+    (0, _defineProperty2.default)(this, "widthPx", 0);
+    (0, _defineProperty2.default)(this, "variant", void 0);
+    (0, _defineProperty2.default)(this, "isLeftEndOfDisplayedRegion", void 0);
     Object.assign(this, data);
     this.assemblyName = data.assemblyName;
     this.refName = data.refName;
@@ -218,6 +223,7 @@ var ElidedBlock = /*#__PURE__*/function (_BaseBlock2) {
     (0, _classCallCheck2.default)(this, ElidedBlock);
     _this = _super2.call(this, data);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "widthPx", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "elidedBlockCount", 0);
     _this.widthPx = data.widthPx;
     return _this;
   }

package/util/color/cssColorsLevel4.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.namedColorToHex = namedColorToHex;
 exports.isNamedColor = isNamedColor;
+exports.namedColorToHex = namedColorToHex;
 // from https://www.w3.org/TR/css-color-4/#named-colors
 var colors = {
   aliceblue: '#F0F8FF',

package/util/color/index.js

@@ -5,17 +5,17 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.contrastingTextColor = contrastingTextColor;
 exports.emphasize = emphasize;
-exports.makeContrasting = makeContrasting;
-Object.defineProperty(exports, "namedColorToHex", {
+Object.defineProperty(exports, "isNamedColor", {
   enumerable: true,
   get: function get() {
-    return _cssColorsLevel.namedColorToHex;
+    return _cssColorsLevel.isNamedColor;
   }
 });
-Object.defineProperty(exports, "isNamedColor", {
+exports.makeContrasting = makeContrasting;
+Object.defineProperty(exports, "namedColorToHex", {
   enumerable: true,
   get: function get() {
-    return _cssColorsLevel.isNamedColor;
+    return _cssColorsLevel.namedColorToHex;
   }
 });
 

package/util/compositeMap.js

@@ -27,7 +27,7 @@ _Symbol$iterator = Symbol.iterator;
 
 // takes an array or Map or Set (anything iterable with values()) of Maps
 // and lets you query them as one Map
-var CompositeMap = /*#__PURE__*/function () {
+var CompositeMap = /*#__PURE__*/function (_Symbol$iterator2) {
   function CompositeMap(submaps) {
     (0, _classCallCheck2.default)(this, CompositeMap);
     (0, _defineProperty2.default)(this, "submaps", void 0);
@@ -244,7 +244,7 @@ var CompositeMap = /*#__PURE__*/function () {
       return undefined;
     }
   }, {
-    key: _Symbol$iterator,
+    key: _Symbol$iterator2,
     value: /*#__PURE__*/_regenerator.default.mark(function value() {
       var _iterator9, _step9, key;
 
@@ -349,6 +349,6 @@ var CompositeMap = /*#__PURE__*/function () {
     })
   }]);
   return CompositeMap;
-}();
+}(_Symbol$iterator);
 
 exports.default = CompositeMap;

package/util/index.d.ts

@@ -1,26 +1,16 @@
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
-import { Feature } from './simpleFeature';
+import SimpleFeature, { Feature, isFeature } from './simpleFeature';
 import { TypeTestedByPredicate, Region, AssemblyManager } from './types';
 export * from './types';
 export * from './aborting';
 export * from './when';
+export * from './range';
+export { SimpleFeature, isFeature };
 export * from './offscreenCanvasPonyfill';
 export * from './offscreenCanvasUtils';
 export declare const inDevelopment: boolean;
 export declare const inProduction: boolean;
-/**
- * Compress and encode a string as url-safe base64
- * See {@link https://en.wikipedia.org/wiki/Base64#URL_applications}
- * @param str-  a string to compress and encode
- */
-export declare function toUrlSafeB64(str: string): string;
-/**
- * Decode and inflate a url-safe base64 to a string
- * See {@link https://en.wikipedia.org/wiki/Base64#URL_applications}
- * @param b64 - a base64 string to decode and inflate
- */
-export declare function fromUrlSafeB64(b64: string): string;
 export declare function useDebounce<T>(value: T, delay: number): T;
 export declare function useDebouncedCallback<A extends any[]>(callback: (...args: A) => void, wait?: number): (...args: A) => void;
 /** find the first node in the hierarchy that matches the given predicate */
@@ -158,7 +148,7 @@ export declare function bpSpanPx(leftBp: number, rightBp: number, region: {
     reversed?: boolean;
 }, bpPerPx: number): [number, number];
 export declare const objectFromEntries: {
-    <T = any>(entries: Iterable<readonly [string | number | symbol, T]>): {
+    <T = any>(entries: Iterable<readonly [PropertyKey, T]>): {
         [k: string]: T;
     };
     (entries: Iterable<readonly any[]>): any;
@@ -211,7 +201,7 @@ export declare function findLastIndex<T>(array: Array<T>, predicate: (value: T,
  * @param successFunction -
  * @param errorFunction -
  */
-export declare function makeAbortableReaction<T, U, V>(self: T, dataFunction: (arg: T) => U, asyncReactionFunction: (arg: U | undefined, signal: AbortSignal, model: T, handle: IReactionPublic) => Promise<V>, reactionOptions: IReactionOptions, startedFunction: (aborter: AbortController) => void, successFunction: (arg: V) => void, errorFunction: (err: Error) => void): void;
+export declare function makeAbortableReaction<T, U, V>(self: T, dataFunction: (arg: T) => U, asyncReactionFunction: (arg: U | undefined, signal: AbortSignal, model: T, handle: IReactionPublic) => Promise<V>, reactionOptions: IReactionOptions, startedFunction: (aborter: AbortController) => void, successFunction: (arg: V) => void, errorFunction: (err: unknown) => void): void;
 export declare function renameRegionIfNeeded(refNameMap: Record<string, string>, region: Region): Region & {
     originalRefName?: string;
 };
@@ -237,7 +227,7 @@ export declare const isElectron: boolean;
 export declare function revcom(seqString: string): string;
 export declare const complement: (seqString: string) => string;
 export declare function blobToDataURL(blob: Blob): Promise<unknown>;
-export declare const rIC: any;
+export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions | undefined) => number) & typeof requestIdleCallback) | ((cb: Function) => any);
 export declare function measureText(str: unknown, fontSize?: number): number;
 export declare const defaultStarts: string[];
 export declare const defaultStops: string[];