@jbrowse/core 1.5.1 → 1.5.2

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"));
 
@@ -145,7 +145,8 @@ function observeAbortSignal(signal) {
 
 
 function isAbortException(exception) {
-  return exception instanceof Error && (exception.name === 'AbortError' || // standard-ish non-DOM abort exception
+  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

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"));
 

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/index.d.ts

@@ -1,11 +1,12 @@
 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;

package/util/index.js

@@ -2,6 +2,8 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+var _typeof3 = require("@babel/runtime/helpers/typeof");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
@@ -51,51 +53,68 @@ var _exportNames = {
   generateCodonTable: true,
   updateStatus: true,
   hashCode: true,
-  objectHash: true
+  objectHash: true,
+  SimpleFeature: true,
+  isFeature: true
 };
-exports.useDebounce = useDebounce;
-exports.useDebouncedCallback = useDebouncedCallback;
-exports.findParentThat = findParentThat;
-exports.springAnimate = springAnimate;
-exports.findParentThatIs = findParentThatIs;
-exports.getSession = getSession;
-exports.getContainingView = getContainingView;
-exports.getContainingTrack = getContainingTrack;
-exports.getContainingDisplay = getContainingDisplay;
+Object.defineProperty(exports, "SimpleFeature", {
+  enumerable: true,
+  get: function get() {
+    return _simpleFeature.default;
+  }
+});
 exports.assembleLocString = assembleLocString;
-exports.parseLocStringOneBased = parseLocStringOneBased;
-exports.parseLocString = parseLocString;
-exports.compareLocs = compareLocs;
-exports.compareLocStrings = compareLocStrings;
-exports.clamp = clamp;
+exports.blobToDataURL = blobToDataURL;
+exports.bpSpanPx = bpSpanPx;
 exports.bpToPx = bpToPx;
-exports.radToDeg = radToDeg;
-exports.degToRad = degToRad;
-exports.polarToCartesian = polarToCartesian;
 exports.cartesianToPolar = cartesianToPolar;
+exports.clamp = clamp;
+exports.compareLocStrings = compareLocStrings;
+exports.compareLocs = compareLocs;
+exports.defaultStops = exports.defaultStarts = exports.defaultCodonTable = exports.complement = void 0;
+exports.degToRad = degToRad;
 exports.featureSpanPx = featureSpanPx;
-exports.bpSpanPx = bpSpanPx;
-exports.iterMap = iterMap;
-exports.mergeConfigs = mergeConfigs;
 exports.findLastIndex = findLastIndex;
+exports.findParentThat = findParentThat;
+exports.findParentThatIs = findParentThatIs;
+exports.generateCodonTable = generateCodonTable;
+exports.getContainingDisplay = getContainingDisplay;
+exports.getContainingTrack = getContainingTrack;
+exports.getContainingView = getContainingView;
+exports.getSession = getSession;
+exports.hashCode = hashCode;
+exports.isElectron = exports.inProduction = exports.inDevelopment = void 0;
+Object.defineProperty(exports, "isFeature", {
+  enumerable: true,
+  get: function get() {
+    return _simpleFeature.isFeature;
+  }
+});
+exports.iterMap = iterMap;
 exports.makeAbortableReaction = makeAbortableReaction;
+exports.measureText = measureText;
+exports.mergeConfigs = mergeConfigs;
+exports.minmax = minmax;
+exports.objectFromEntries = void 0;
+exports.objectHash = objectHash;
+exports.parseLocString = parseLocString;
+exports.parseLocStringOneBased = parseLocStringOneBased;
+exports.polarToCartesian = polarToCartesian;
+exports.rIC = void 0;
+exports.radToDeg = radToDeg;
 exports.renameRegionIfNeeded = renameRegionIfNeeded;
 exports.renameRegionsIfNeeded = renameRegionsIfNeeded;
-exports.minmax = minmax;
-exports.stringify = stringify;
 exports.revcom = revcom;
-exports.blobToDataURL = blobToDataURL;
-exports.measureText = measureText;
-exports.generateCodonTable = generateCodonTable;
+exports.springAnimate = springAnimate;
+exports.stringify = stringify;
 exports.updateStatus = updateStatus;
-exports.hashCode = hashCode;
-exports.objectHash = objectHash;
-exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.rIC = exports.complement = exports.isElectron = exports.objectFromEntries = exports.inProduction = exports.inDevelopment = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+exports.useDebounce = useDebounce;
+exports.useDebouncedCallback = useDebouncedCallback;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
@@ -114,6 +133,8 @@ var _react = require("react");
 
 var _deepmerge = _interopRequireDefault(require("deepmerge"));
 
+var _simpleFeature = _interopRequireWildcard(require("./simpleFeature"));
+
 var _types = require("./types");
 
 Object.keys(_types).forEach(function (key) {
@@ -198,6 +219,10 @@ Object.keys(_offscreenCanvasUtils).forEach(function (key) {
   });
 });
 
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof3(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
 
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
@@ -273,7 +298,11 @@ function useDebouncedCallback(callback) {
 
 
 function findParentThat(node, predicate) {
-  var currentNode = node;
+  if (!(0, _mobxStateTree.hasParent)(node)) {
+    throw new Error('node does not have parent');
+  }
+
+  var currentNode = (0, _mobxStateTree.getParent)(node);
 
   while (currentNode && (0, _mobxStateTree.isAlive)(currentNode)) {
     if (predicate(currentNode)) {

package/util/io/RemoteFileWithRangeCache.js

@@ -5,13 +5,13 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.clearCache = clearCache;
 exports.RemoteFileWithRangeCache = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+exports.clearCache = clearCache;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));

package/util/io/index.js

@@ -5,13 +5,13 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.openLocation = openLocation;
 Object.defineProperty(exports, "RemoteFileWithRangeCache", {
   enumerable: true,
   get: function get() {
     return _RemoteFileWithRangeCache.RemoteFileWithRangeCache;
   }
 });
+exports.openLocation = openLocation;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 

package/util/jexl.js

@@ -9,7 +9,9 @@ exports.default = _default;
 
 var _jexl = _interopRequireDefault(require("jexl"));
 
-function _default() {
+function
+  /* config?: any*/
+_default() {
   var j = new _jexl.default.Jexl(); // someday will make sure all of configs callbacks are added in, including
   // ones passed in
   // below are core functions
@@ -40,6 +42,7 @@ function _default() {
   j.addFunction('floor', Math.floor);
   j.addFunction('round', Math.round);
   j.addFunction('abs', Math.abs);
+  j.addFunction('log10', Math.log10);
   j.addFunction('parseInt', Number.parseInt);
   j.addFunction('parseFloat', Number.parseFloat); // string
 

package/util/layouts/BaseLayout.d.ts

@@ -10,11 +10,14 @@ export interface Rectangle<T> {
     r: number;
     top: number | null;
     h: number;
+    originalHeight: number;
     data?: Record<string, T>;
 }
 export interface BaseLayout<T> {
     addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
     collides(rect: Rectangle<T>, top: number): boolean;
+    addRectToBitmap(rect: Rectangle<T>, data: Record<string, T>): void;
+    getRectangles(): Map<string, RectTuple>;
     discardRange(left: number, right: number): void;
     serializeRegion(region: {
         start: number;

package/util/layouts/GranularRectLayout.d.ts

@@ -1,38 +1,47 @@
-import { RectTuple, SerializedLayout, BaseLayout } from './BaseLayout';
+import { RectTuple, SerializedLayout, Rectangle, BaseLayout } from './BaseLayout';
 export default class GranularRectLayout<T> implements BaseLayout<T> {
+    private pitchX;
+    private pitchY;
+    private hardRowLimit;
+    private bitmap;
     private rectangles;
     maxHeightReached: boolean;
     private maxHeight;
-    private rbush;
-    private spacing;
+    private displayMode;
     private pTotalHeight;
-    private pitchX;
-    constructor({ maxHeight, spacing, pitchX, }?: {
-        maxHeight?: number;
-        spacing?: number;
+    constructor({ pitchX, pitchY, maxHeight, hardRowLimit, displayMode, }?: {
         pitchX?: number;
+        pitchY?: number;
+        maxHeight?: number;
+        displayMode?: string;
+        hardRowLimit?: number;
     });
     /**
      * @returns top position for the rect, or Null if laying
      *  out the rect would exceed maxHeight
      */
     addRect(id: string, left: number, right: number, height: number, data?: Record<string, T>): number | null;
-    collides(): boolean;
+    collides(rect: Rectangle<T>, top: number): boolean;
+    /**
+     * make a subarray if it does not exist
+     */
+    private autovivifyRow;
+    addRectToBitmap(rect: Rectangle<T>): void;
     /**
      *  Given a range of X coordinates, deletes all data dealing with
      *  the features.
      */
-    discardRange(): void;
+    discardRange(left: number, right: number): void;
     hasSeen(id: string): boolean;
     getByCoord(x: number, y: number): Record<string, T> | string | undefined;
     getByID(id: string): RectTuple | undefined;
     cleanup(): void;
     getTotalHeight(): number;
     get totalHeight(): number;
+    getRectangles(): Map<string, RectTuple>;
     serializeRegion(region: {
         start: number;
         end: number;
     }): SerializedLayout;
-    getRectangles(): Map<string, RectTuple>;
     toJSON(): SerializedLayout;
 }