@jbrowse/core 1.5.1 → 1.5.2

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/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/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.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

@@ -5,12 +5,12 @@ 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;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+exports.createImageBitmap = exports.createCanvas = exports.PonyfillOffscreenContext = exports.PonyfillOffscreenCanvas = exports.ImageBitmapType = void 0;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));

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"));
 

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"));
 

package/util/tracks.js

@@ -3,21 +3,21 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.getTrackAssemblyNames = getTrackAssemblyNames;
-exports.getRpcSessionId = getRpcSessionId;
-exports.getParentRenderProps = getParentRenderProps;
+exports.UNSUPPORTED = exports.UNKNOWN = void 0;
+exports.generateUnknownTrackConf = generateUnknownTrackConf;
+exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
 exports.getBlob = getBlob;
 exports.getBlobMap = getBlobMap;
-exports.setBlobMap = setBlobMap;
-exports.storeBlobLocation = storeBlobLocation;
-exports.makeIndex = makeIndex;
-exports.makeIndexType = makeIndexType;
 exports.getFileName = getFileName;
+exports.getParentRenderProps = getParentRenderProps;
+exports.getRpcSessionId = getRpcSessionId;
+exports.getTrackAssemblyNames = getTrackAssemblyNames;
 exports.guessAdapter = guessAdapter;
 exports.guessTrackType = guessTrackType;
-exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
-exports.generateUnknownTrackConf = generateUnknownTrackConf;
-exports.UNSUPPORTED = exports.UNKNOWN = void 0;
+exports.makeIndex = makeIndex;
+exports.makeIndexType = makeIndexType;
+exports.setBlobMap = setBlobMap;
+exports.storeBlobLocation = storeBlobLocation;
 
 var _mobxStateTree = require("mobx-state-tree");
 

package/util/types/index.d.ts

@@ -29,7 +29,10 @@ export interface JBrowsePlugin {
     authors: string[];
     description: string;
     location: string;
-    url: string;
+    url?: string;
+    umdUrl?: string;
+    esmUrl?: string;
+    cjsUrl?: string;
     license: string;
     image?: string;
 }
@@ -173,6 +176,9 @@ export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion>
 }
 export interface Region extends SnapshotIn<typeof MUIRegion> {
 }
+export interface AugmentedRegion extends Region {
+    originalRefName?: string;
+}
 export interface LocalPathLocation extends SnapshotIn<typeof MULocalPathLocation> {
 }
 export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {

package/util/types/index.js

@@ -25,23 +25,23 @@ var _exportNames = {
   isAuthNeededException: true,
   isRetryException: true
 };
-exports.isViewContainer = isViewContainer;
+exports.RetryError = exports.AuthNeededError = void 0;
+exports.isAbstractMenuManager = isAbstractMenuManager;
+exports.isAppRootModel = isAppRootModel;
+exports.isAuthNeededException = isAuthNeededException;
+exports.isDisplayModel = isDisplayModel;
+exports.isRetryException = isRetryException;
+exports.isSelectionContainer = isSelectionContainer;
 exports.isSessionModel = isSessionModel;
 exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
-exports.isSessionWithAddTracks = isSessionWithAddTracks;
 exports.isSessionModelWithWidgets = isSessionModelWithWidgets;
+exports.isSessionWithAddTracks = isSessionWithAddTracks;
 exports.isSessionWithSessionPlugins = isSessionWithSessionPlugins;
-exports.isSelectionContainer = isSelectionContainer;
-exports.isViewModel = isViewModel;
 exports.isTrackModel = isTrackModel;
-exports.isDisplayModel = isDisplayModel;
 exports.isTrackViewModel = isTrackViewModel;
-exports.isAppRootModel = isAppRootModel;
-exports.isAbstractMenuManager = isAbstractMenuManager;
 exports.isUriLocation = isUriLocation;
-exports.isAuthNeededException = isAuthNeededException;
-exports.isRetryException = isRetryException;
-exports.RetryError = exports.AuthNeededError = void 0;
+exports.isViewContainer = isViewContainer;
+exports.isViewModel = isViewModel;
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 

package/util/types/mst.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.FileLocation = exports.UriLocation = exports.UriLocationRaw = exports.BlobLocation = exports.LocalPathLocation = exports.Region = exports.NoAssemblyRegion = exports.PropTypes = exports.ElementId = void 0;
+exports.UriLocationRaw = exports.UriLocation = exports.Region = exports.PropTypes = exports.NoAssemblyRegion = exports.LocalPathLocation = exports.FileLocation = exports.ElementId = exports.BlobLocation = void 0;
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));