@jbrowse/core 1.5.1 → 1.5.5

package/util/Base1DViewModel.js

@@ -19,9 +19,9 @@ var _calculateDynamicBlocks = _interopRequireDefault(require("./calculateDynamic
 
 var _calculateStaticBlocks = _interopRequireDefault(require("./calculateStaticBlocks"));
 
-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 ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); 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; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 var Base1DView = _mobxStateTree.types.model('Base1DView', {
   displayedRegions: _mobxStateTree.types.array(_mst.Region),

package/util/aborting.js

@@ -5,16 +5,18 @@ 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"));
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -54,7 +56,7 @@ var AbortError = /*#__PURE__*/function (_Error) {
     return _this;
   }
 
-  return AbortError;
+  return (0, _createClass2.default)(AbortError);
 }( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
 /**
  * properly check if the given AbortSignal is aborted.
@@ -145,7 +147,8 @@ 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"));
 
@@ -15,26 +15,23 @@ var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime
 
 var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
 
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
 function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
-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 ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); 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; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 var BlockSet = /*#__PURE__*/function () {
-  function BlockSet() {
-    var blocks = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : [];
+  function BlockSet(blocks = []) {
     (0, _classCallCheck2.default)(this, BlockSet);
-    (0, _defineProperty2.default)(this, "blocks", []);
-    this.blocks = blocks;
   }
 
   (0, _createClass2.default)(BlockSet, [{
@@ -201,7 +198,7 @@ var ContentBlock = /*#__PURE__*/function (_BaseBlock) {
     return _super.apply(this, arguments);
   }
 
-  return ContentBlock;
+  return (0, _createClass2.default)(ContentBlock);
 }(BaseBlock);
 /**
  * marker block representing one or more blocks that are
@@ -261,7 +258,7 @@ var InterRegionPaddingBlock = /*#__PURE__*/function (_BaseBlock3) {
     return _super3.apply(this, arguments);
   }
 
-  return InterRegionPaddingBlock;
+  return (0, _createClass2.default)(InterRegionPaddingBlock);
 }(BaseBlock);
 
 exports.InterRegionPaddingBlock = InterRegionPaddingBlock;

package/util/calculateDynamicBlocks.test.js

@@ -6,9 +6,9 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 var _calculateDynamicBlocks = _interopRequireDefault(require("./calculateDynamicBlocks"));
 
-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 ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); 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; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 var ctgA = {
   assemblyName: 'test',

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

@@ -13,25 +13,17 @@ var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/cl
 
 var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _Symbol$iterator;
-
 function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
 
 function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-_Symbol$iterator = Symbol.iterator;
-
 // takes an array or Map or Set (anything iterable with values()) of Maps
 // and lets you query them as one Map
-var CompositeMap = /*#__PURE__*/function (_Symbol$iterator2) {
+var CompositeMap = /*#__PURE__*/function (_Symbol$iterator) {
   function CompositeMap(submaps) {
     (0, _classCallCheck2.default)(this, CompositeMap);
-    (0, _defineProperty2.default)(this, "submaps", void 0);
-    this.submaps = submaps;
   }
 
   (0, _createClass2.default)(CompositeMap, [{
@@ -244,7 +236,7 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator2) {
       return undefined;
     }
   }, {
-    key: _Symbol$iterator2,
+    key: _Symbol$iterator,
     value: /*#__PURE__*/_regenerator.default.mark(function value() {
       var _iterator9, _step9, key;
 
@@ -349,6 +341,6 @@ var CompositeMap = /*#__PURE__*/function (_Symbol$iterator2) {
     })
   }]);
   return CompositeMap;
-}(_Symbol$iterator);
+}(Symbol.iterator);
 
 exports.default = CompositeMap;

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
 });
@@ -51,46 +53,63 @@ 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;
+exports.useDebounce = useDebounce;
+exports.useDebouncedCallback = useDebouncedCallback;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -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) {
@@ -198,9 +219,13 @@ Object.keys(_offscreenCanvasUtils).forEach(function (key) {
   });
 });
 
-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 _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 _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; }
+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); 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 = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
 
@@ -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)) {
@@ -1245,15 +1274,13 @@ function _updateStatus() {
 
 function hashCode(str) {
   var hash = 0;
-  var i;
-  var chr;
 
   if (str.length === 0) {
     return hash;
   }
 
-  for (i = 0; i < str.length; i++) {
-    chr = str.charCodeAt(i);
+  for (var i = 0; i < str.length; i++) {
+    var chr = str.charCodeAt(i);
     hash = (hash << 5) - hash + chr;
     hash |= 0; // Convert to 32bit integer
   }

package/util/index.test.js

@@ -8,9 +8,9 @@ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/sli
 
 var _index = require("./index");
 
-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 ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); 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; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 describe('parseLocString', function () {
   var cases = [['chr1:1..200', {

package/util/io/RemoteFileWithRangeCache.js

@@ -5,8 +5,8 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.clearCache = clearCache;
 exports.RemoteFileWithRangeCache = void 0;
+exports.clearCache = clearCache;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -40,9 +40,9 @@ function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o =
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-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 ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); 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; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 

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;
 }