@jbrowse/core 1.5.0 → 1.5.4

package/util/layouts/GranularRectLayout.test.js

@@ -8,7 +8,10 @@ var _GranularRectLayout = _interopRequireDefault(require("./GranularRectLayout")
 
 describe('GranularRectLayout', function () {
   it('lays out non-overlapping features end to end', function () {
-    var l = new _GranularRectLayout.default();
+    var l = new _GranularRectLayout.default({
+      pitchX: 10,
+      pitchY: 4
+    });
     var testRects = [['1,0', 4133, 5923, 16], ['1,1', 11299, 12389, 16], ['1,2', 21050, 22778, 16], ['1,3', 41125, 47459, 16], ['1,4', 47926, 49272, 16], ['1,5', 50240, 52495, 16], ['1,6', 53329, 56283, 16], ['1,7', 59309, 79441, 16], ['1,8', 80359, 83196, 16], ['1,9', 92147, 94188, 16], ['1,10', 96241, 103626, 16], ['1,11', 104396, 108110, 16], ['1,12', 111878, 125251, 16], ['1,13', 125747, 128085, 16], ['1,14', 131492, 132641, 16], ['1,15', 133857, 134931, 16], ['1,16', 137023, 138220, 16], ['1,17', 140703, 145668, 16], ['1,18', 146045, 147059, 16], ['1,19', 162296, 165395, 16], ['1,20', 168531, 170795, 16], ['1,21', 174812, 180475, 16], ['1,22', 184302, 188826, 16], ['1,23', 189609, 191141, 16], ['1,24', 199799, 201389, 16], ['1,25', 203436, 211345, 16], ['1,26', 212100, 212379, 16], ['1,27', 213418, 214627, 16], ['1,28', 215115, 219344, 16], ['1,29', 220067, 222525, 16], ['1,30', 223308, 228141, 16], ['1,31', 234473, 236768, 16], ['1,32', 239691, 245015, 16]];
 
     for (var i = 0; i < testRects.length; i += 1) {
@@ -17,7 +20,10 @@ describe('GranularRectLayout', function () {
     }
   });
   it('stacks up overlapping features', function () {
-    var l = new _GranularRectLayout.default();
+    var l = new _GranularRectLayout.default({
+      pitchX: 10,
+      pitchY: 4
+    });
     var testRects = [];
 
     for (var i = 1; i <= 20; i += 1) {
@@ -26,35 +32,76 @@ describe('GranularRectLayout', function () {
 
     for (var _i = 0; _i < testRects.length; _i += 1) {
       var top = l.addRect.apply(l, (0, _toConsumableArray2.default)(testRects[_i]));
-      expect(top).toEqual(_i % 2 * 3);
+      expect(top).toEqual(_i % 2 * 4);
     }
   });
   it('discards regions', function () {
-    var l = new _GranularRectLayout.default();
+    var l = new _GranularRectLayout.default({
+      pitchX: 10,
+      pitchY: 4
+    });
 
     for (var i = 0; i < 20; i += 1) {
       var top = l.addRect("feature-".concat(i), 10000 * i + 4000, 10000 * i + 16000, 1);
-      expect(top).toEqual(i % 2 * 3);
+      expect(top).toEqual(i % 2 * 4);
     }
+
+    expect(l.bitmap[0].rowState.bits.length).toBe(34812);
+    expect(l.bitmap[1].rowState.bits.length).toBe(34812);
+    l.discardRange(190000, 220000);
+    expect(l.bitmap[0].rowState.bits.length).toBe(24802);
+    expect(l.bitmap[1].rowState.bits.length).toBe(23802);
+    l.discardRange(0, 100000);
+    expect(l.bitmap[0].rowState.bits.length).toBe(19001);
+    expect(l.bitmap[1].rowState.bits.length).toBe(23802);
+    l.discardRange(0, 220000);
+    expect(l.bitmap[0].rowState).toBeUndefined();
   }); // see issue #486
 
   it('tests that adding +/- pitchX fixes resolution causing errors', function () {
-    var l = new _GranularRectLayout.default();
+    var l = new _GranularRectLayout.default({
+      pitchX: 91.21851599727707,
+      pitchY: 3
+    });
     l.addRect('test', 2581541, 2581542, 1);
     expect(l.serializeRegion({
       start: 2581491,
       end: 2818659
     }).rectangles.test).toBeTruthy();
   });
+  it('tests reinitializing layout due to throwing away old one', function () {
+    var spy = jest.spyOn(console, 'warn').mockImplementation(function () {});
+    var l = new _GranularRectLayout.default({
+      pitchX: 1,
+      pitchY: 1,
+      maxHeight: 600
+    });
+    l.addRect('test1', 0, 10000, 1);
+    l.addRect('test2', 1000000, 1000100, 1);
+    l.addRect('test3', 0, 10000, 1);
+    expect(l.rectangles.size).toBe(3);
+    expect(spy).toHaveBeenCalled();
+    spy.mockRestore();
+  });
   it('tests adding a gigantic feature that fills entire row with another smaller added on top', function () {
     var l = new _GranularRectLayout.default({
+      pitchX: 100,
+      pitchY: 1,
       maxHeight: 600
     });
     expect(l.getByCoord(50000, 0)).toEqual(undefined);
-    l.addRect('test1', 0, 10000000, 1);
-    expect(l.getByCoord(50000, 0)).toEqual('test1');
-    l.addRect('test2', 0, 1000, 1);
-    expect(l.getByCoord(500, 2)).toEqual('test2');
+    l.addRect('test1', 0, 100000000, 1, {
+      id: 'feat1'
+    });
+    expect(l.getByCoord(50000, 0)).toEqual({
+      id: 'feat1'
+    });
+    l.addRect('test2', 0, 1000, 1, {
+      id: 'feat2'
+    });
+    expect(l.getByCoord(500, 1)).toEqual({
+      id: 'feat2'
+    });
     expect(l.rectangles.size).toBe(2);
   });
 });

package/util/layouts/MultiLayout.d.ts

@@ -1,7 +1,7 @@
 import { BaseLayout, SerializedLayout } from './BaseLayout';
 export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
-    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS;
+    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     subLayoutConstructorArgs: Record<string, any>;
     /**
      * layout class that just keeps a number of named sub-layouts.

package/util/layouts/MultiLayout.js

@@ -32,10 +32,8 @@ var MultiLayout = /*#__PURE__*/function () {
     var layoutArgs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
     (0, _classCallCheck2.default)(this, MultiLayout);
     (0, _defineProperty2.default)(this, "subLayouts", new Map());
-    (0, _defineProperty2.default)(this, "SubLayoutClass", void 0);
     (0, _defineProperty2.default)(this, "subLayoutConstructorArgs", {});
     this.subLayouts = new Map();
-    this.SubLayoutClass = SubLayoutClass;
     this.subLayoutConstructorArgs = layoutArgs;
   }
 

package/util/layouts/PrecomputedLayout.js

@@ -29,7 +29,8 @@ var PrecomputedLayout = /*#__PURE__*/function () {
     (0, _defineProperty2.default)(this, "totalHeight", void 0);
     (0, _defineProperty2.default)(this, "maxHeightReached", void 0);
     (0, _defineProperty2.default)(this, "rbush", void 0);
-    this.rectangles = new Map(Object.entries(rectangles));
+    this.rectangles = new Map(Object.entries(rectangles)); // rectangles is of the form "featureId": [leftPx, topPx, rightPx, bottomPx]
+
     this.totalHeight = totalHeight;
     this.maxHeightReached = maxHeightReached;
     this.rbush = new _rbush.default();

package/util/layouts/PrecomputedMultiLayout.js

@@ -15,6 +15,8 @@ var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime
 
 var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _MultiLayout2 = _interopRequireDefault(require("./MultiLayout"));
@@ -25,10 +27,10 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
 
 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; } }
 
-var ThrowingLayout = function ThrowingLayout() {
+var ThrowingLayout = /*#__PURE__*/(0, _createClass2.default)(function ThrowingLayout() {
   (0, _classCallCheck2.default)(this, ThrowingLayout);
   throw new Error('invalid layout name');
-};
+});
 
 var PrecomputedMultiLayout = /*#__PURE__*/function (_MultiLayout) {
   (0, _inherits2.default)(PrecomputedMultiLayout, _MultiLayout);
@@ -52,7 +54,7 @@ var PrecomputedMultiLayout = /*#__PURE__*/function (_MultiLayout) {
     return _this;
   }
 
-  return PrecomputedMultiLayout;
+  return (0, _createClass2.default)(PrecomputedMultiLayout);
 }(_MultiLayout2.default);
 
 exports.default = PrecomputedMultiLayout;

package/util/layouts/SceneGraph.d.ts

@@ -8,19 +8,19 @@ interface AbsoluteCache {
     height?: number;
 }
 export default class SceneGraph {
-    private name;
+    name: string;
     left: number;
     top: number;
     width: number;
     height: number;
-    data?: Record<string, any>;
+    data?: Record<string, any> | undefined;
     private children;
     private absoluteCache;
     parent?: SceneGraph;
     /**
      * note: all coordinates are inter-base or inter-pixel coordinates
      */
-    constructor(name: string, left: number, top: number, width: number, height: number, data?: Record<string, any>);
+    constructor(name: string, left: number, top: number, width: number, height: number, data?: Record<string, any> | undefined);
     addChild(nameOrSceneGraph: string | SceneGraph, left: number, top: number, width: number, height: number, data?: Record<string, any>): SceneGraph;
     getSubRecord(name: string): SceneGraph | undefined;
     /**

package/util/layouts/SceneGraph.js

@@ -22,20 +22,12 @@ 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; }
 
 var SceneGraph = /*#__PURE__*/function () {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
   /**
    * note: all coordinates are inter-base or inter-pixel coordinates
    */
   function SceneGraph(name, left, top, width, height, // eslint-disable-next-line @typescript-eslint/no-explicit-any
   data) {
     (0, _classCallCheck2.default)(this, SceneGraph);
-    (0, _defineProperty2.default)(this, "name", void 0);
-    (0, _defineProperty2.default)(this, "left", void 0);
-    (0, _defineProperty2.default)(this, "top", void 0);
-    (0, _defineProperty2.default)(this, "width", void 0);
-    (0, _defineProperty2.default)(this, "height", void 0);
-    (0, _defineProperty2.default)(this, "data", void 0);
     (0, _defineProperty2.default)(this, "children", void 0);
     (0, _defineProperty2.default)(this, "absoluteCache", void 0);
     (0, _defineProperty2.default)(this, "parent", void 0);
@@ -44,12 +36,6 @@ var SceneGraph = /*#__PURE__*/function () {
       throw new TypeError('invalid SceneGraph arguments');
     }
 
-    this.name = name;
-    this.left = left;
-    this.top = top;
-    this.width = width;
-    this.height = height;
-    this.data = data;
     this.children = new Map();
     this.absoluteCache = {
       dirty: true

package/util/layouts/index.d.ts

@@ -0,0 +1,7 @@
+export * from './BaseLayout';
+export { default as GranularRectLayout } from './GranularRectLayout';
+export { default as MultiLayout } from './MultiLayout';
+export { default as PrecomputedLayout } from './PrecomputedLayout';
+export type { Layout } from './PrecomputedLayout';
+export { default as PrecomputedMultiLayout } from './PrecomputedMultiLayout';
+export { default as SceneGraph } from './SceneGraph';

package/util/layouts/index.js

@@ -0,0 +1,68 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+var _exportNames = {
+  GranularRectLayout: true,
+  MultiLayout: true,
+  PrecomputedLayout: true,
+  PrecomputedMultiLayout: true,
+  SceneGraph: true
+};
+Object.defineProperty(exports, "GranularRectLayout", {
+  enumerable: true,
+  get: function get() {
+    return _GranularRectLayout.default;
+  }
+});
+Object.defineProperty(exports, "MultiLayout", {
+  enumerable: true,
+  get: function get() {
+    return _MultiLayout.default;
+  }
+});
+Object.defineProperty(exports, "PrecomputedLayout", {
+  enumerable: true,
+  get: function get() {
+    return _PrecomputedLayout.default;
+  }
+});
+Object.defineProperty(exports, "PrecomputedMultiLayout", {
+  enumerable: true,
+  get: function get() {
+    return _PrecomputedMultiLayout.default;
+  }
+});
+Object.defineProperty(exports, "SceneGraph", {
+  enumerable: true,
+  get: function get() {
+    return _SceneGraph.default;
+  }
+});
+
+var _BaseLayout = require("./BaseLayout");
+
+Object.keys(_BaseLayout).forEach(function (key) {
+  if (key === "default" || key === "__esModule") return;
+  if (Object.prototype.hasOwnProperty.call(_exportNames, key)) return;
+  if (key in exports && exports[key] === _BaseLayout[key]) return;
+  Object.defineProperty(exports, key, {
+    enumerable: true,
+    get: function get() {
+      return _BaseLayout[key];
+    }
+  });
+});
+
+var _GranularRectLayout = _interopRequireDefault(require("./GranularRectLayout"));
+
+var _MultiLayout = _interopRequireDefault(require("./MultiLayout"));
+
+var _PrecomputedLayout = _interopRequireDefault(require("./PrecomputedLayout"));
+
+var _PrecomputedMultiLayout = _interopRequireDefault(require("./PrecomputedMultiLayout"));
+
+var _SceneGraph = _interopRequireDefault(require("./SceneGraph"));

package/util/mst-reflection.d.ts

@@ -4,13 +4,13 @@
  * @param {IModelType} type
  * @returns {IModelType}
  */
-export function getSubType(type: any): any;
+export function getSubType(type: IModelType): IModelType;
 /**
  * get the array of
  * @param {MST Union Type obj} unionType
  * @returns {Array<IModelType>}
  */
-export function getUnionSubTypes(unionType: any): Array<any>;
+export function getUnionSubTypes(unionType: any): Array<IModelType>;
 /**
  * get the type of one of the properties of the given MST model type
  *
@@ -18,7 +18,7 @@ export function getUnionSubTypes(unionType: any): Array<any>;
  * @param {string} propertyName
  * @returns {IModelType}
  */
-export function getPropertyType(type: any, propertyName: string): any;
+export function getPropertyType(type: IModelType, propertyName: string): IModelType;
 /**
  * get the base type from inside an MST optional type
  * @param {*} type

package/util/mst-reflection.js

@@ -3,11 +3,11 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getSubType = getSubType;
-exports.getUnionSubTypes = getUnionSubTypes;
-exports.getPropertyType = getPropertyType;
 exports.getDefaultValue = getDefaultValue;
 exports.getEnumerationValues = getEnumerationValues;
+exports.getPropertyType = getPropertyType;
+exports.getSubType = getSubType;
+exports.getUnionSubTypes = getUnionSubTypes;
 exports.resolveLateType = resolveLateType;
 
 var _mobxStateTree = require("mobx-state-tree");

package/util/offscreenCanvasPonyfill.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.PonyfillOffscreenCanvas = exports.PonyfillOffscreenContext = exports.ImageBitmapType = exports.createImageBitmap = exports.createCanvas = void 0;
+exports.createImageBitmap = exports.createCanvas = exports.PonyfillOffscreenContext = exports.PonyfillOffscreenCanvas = exports.ImageBitmapType = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 

package/util/range.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.intersection2 = intersection2;
 exports.doesIntersect2 = doesIntersect2;
+exports.intersection2 = intersection2;
 exports.isContainedWithin = isContainedWithin;
 
 /**

package/util/simpleFeature.js

@@ -5,8 +5,8 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.isFeature = isFeature;
 exports.default = void 0;
+exports.isFeature = isFeature;
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -16,9 +16,9 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
-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; }
 
 /**
  * Abstract feature object

package/util/stats.js

@@ -5,11 +5,11 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.blankStats = blankStats;
+exports.calcPerBaseStats = calcPerBaseStats;
 exports.calcStdFromSums = calcStdFromSums;
 exports.rectifyStats = rectifyStats;
-exports.calcPerBaseStats = calcPerBaseStats;
 exports.scoresToStats = scoresToStats;
-exports.blankStats = blankStats;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -19,9 +19,9 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 var _operators = require("rxjs/operators");
 
-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; }
 
 /*
  * calculate standard deviation using the 'shortcut method' that accepts