@jbrowse/plugin-linear-genome-view 1.7.0 → 1.7.4

package/dist/LinearGenomeView/index.js

@@ -9,20 +9,20 @@ exports.RESIZE_HANDLE_HEIGHT = exports.INTER_REGION_PADDING_WIDTH = exports.HEAD
 Object.defineProperty(exports, "ReactComponent", {
   enumerable: true,
   get: function get() {
-    return _LinearGenomeView["default"];
+    return _LinearGenomeView.default;
   }
 });
 Object.defineProperty(exports, "RefNameAutocomplete", {
   enumerable: true,
   get: function get() {
-    return _RefNameAutocomplete["default"];
+    return _RefNameAutocomplete.default;
   }
 });
 exports.SPACING = exports.SCALE_BAR_HEIGHT = void 0;
 Object.defineProperty(exports, "SearchBox", {
   enumerable: true,
   get: function get() {
-    return _SearchBox["default"];
+    return _SearchBox.default;
   }
 });
 exports.WIDGET_HEIGHT = void 0;
@@ -96,7 +96,7 @@ var _ExportSvgDialog = _interopRequireDefault(require("./components/ExportSvgDia
 
 var _LinearGenomeView = _interopRequireDefault(require("./components/LinearGenomeView"));
 
-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 _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); }
 
@@ -104,7 +104,7 @@ function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len
 
 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 _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 calculateVisibleLocStrings(contentBlocks) {
   if (!contentBlocks.length) {
@@ -159,15 +159,15 @@ function stateModelFactory(pluginManager) {
     trackLabels: _mobxStateTree.types.optional(_mobxStateTree.types.string, function () {
       return localStorageGetItem('lgv-trackLabels') || 'overlapping';
     }),
-    showCenterLine: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], function () {
+    showCenterLine: _mobxStateTree.types.optional(_mobxStateTree.types.boolean, function () {
       var setting = localStorageGetItem('lgv-showCenterLine');
       return setting !== undefined && setting !== null ? !!+setting : false;
     }),
-    showCytobandsSetting: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], function () {
+    showCytobandsSetting: _mobxStateTree.types.optional(_mobxStateTree.types.boolean, function () {
       var setting = localStorageGetItem('lgv-showCytobands');
       return setting !== undefined && setting !== null ? !!+setting : true;
     })
-  }))["volatile"](function () {
+  })).volatile(function () {
     return {
       volatileWidth: undefined,
       minimumBlockWidth: 3,
@@ -314,7 +314,7 @@ function stateModelFactory(pluginManager) {
       },
 
       get assemblyNames() {
-        return (0, _toConsumableArray2["default"])(new Set(self.displayedRegions.map(function (region) {
+        return (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
           return region.assemblyName;
         })));
       },
@@ -476,7 +476,7 @@ function stateModelFactory(pluginManager) {
           var trackInMap = allActions.get(track.type);
 
           if (!trackInMap) {
-            var viewMenuActions = (0, _clone["default"])(track.viewMenuActions);
+            var viewMenuActions = (0, _clone.default)(track.viewMenuActions);
 
             _this2.rewriteOnClicks(track.type, viewMenuActions);
 
@@ -954,7 +954,7 @@ function stateModelFactory(pluginManager) {
        * @returns array of Region[]
        */
       getSelectedRegions: function getSelectedRegions(leftOffset, rightOffset) {
-        var simView = _Base1DViewModel["default"].create(_objectSpread(_objectSpread({}, (0, _mobxStateTree.getSnapshot)(self)), {}, {
+        var simView = _Base1DViewModel.default.create(_objectSpread(_objectSpread({}, (0, _mobxStateTree.getSnapshot)(self)), {}, {
           interRegionPaddingWidth: self.interRegionPaddingWidth
         }));
 
@@ -1061,7 +1061,7 @@ function stateModelFactory(pluginManager) {
         var assemblyManager = session.assemblyManager;
 
         if (!assemblyName) {
-          var assemblyNames = (0, _toConsumableArray2["default"])(new Set(self.displayedRegions.map(function (region) {
+          var assemblyNames = (0, _toConsumableArray2.default)(new Set(self.displayedRegions.map(function (region) {
             return region.assemblyName;
           })));
 
@@ -1072,7 +1072,7 @@ function stateModelFactory(pluginManager) {
 
           ;
 
-          var _assemblyNames = (0, _slicedToArray2["default"])(assemblyNames, 1);
+          var _assemblyNames = (0, _slicedToArray2.default)(assemblyNames, 1);
 
           assemblyName = _assemblyNames[0];
         }
@@ -1101,7 +1101,7 @@ function stateModelFactory(pluginManager) {
 
     function slide(viewWidths) {
       var _springAnimate = (0, _util.springAnimate)(self.offsetPx, self.offsetPx + self.width * viewWidths, self.scrollTo),
-          _springAnimate2 = (0, _slicedToArray2["default"])(_springAnimate, 2),
+          _springAnimate2 = (0, _slicedToArray2.default)(_springAnimate, 2),
           animate = _springAnimate2[0],
           cancelAnimation = _springAnimate2[1];
 
@@ -1131,7 +1131,7 @@ function stateModelFactory(pluginManager) {
         self.zoomTo(targetBpPerPx);
         self.setScaleFactor(1);
       }),
-          _springAnimate4 = (0, _slicedToArray2["default"])(_springAnimate3, 2),
+          _springAnimate4 = (0, _slicedToArray2.default)(_springAnimate3, 2),
           animate = _springAnimate4[0],
           cancelAnimation = _springAnimate4[1];
 
@@ -1185,13 +1185,13 @@ function stateModelFactory(pluginManager) {
               }];
             });
           },
-          icon: _FolderOpen["default"]
+          icon: _FolderOpen.default
         }, {
           label: 'Export SVG',
-          icon: _PhotoCamera["default"],
+          icon: _PhotoCamera.default,
           onClick: function onClick() {
             (0, _util.getSession)(self).queueDialog(function (handleClose) {
-              return [_ExportSvgDialog["default"], {
+              return [_ExportSvgDialog.default, {
                 model: self,
                 handleClose: handleClose
               }];
@@ -1203,39 +1203,39 @@ function stateModelFactory(pluginManager) {
           icon: _Icons.TrackSelector
         }, {
           label: 'Horizontally flip',
-          icon: _SyncAlt["default"],
+          icon: _SyncAlt.default,
           onClick: self.horizontallyFlip
         }, {
           type: 'divider'
         }, {
           label: 'Show all regions in assembly',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           onClick: self.showAllRegionsInAssembly
         }, {
           label: 'Show center line',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           type: 'checkbox',
           checked: self.showCenterLine,
           onClick: self.toggleCenterLine
         }, {
           label: 'Show header',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           type: 'checkbox',
           checked: !self.hideHeader,
           onClick: self.toggleHeader
         }, {
           label: 'Show header overview',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           type: 'checkbox',
           checked: !self.hideHeaderOverview,
           onClick: self.toggleHeaderOverview,
           disabled: self.hideHeader
         }, {
           label: 'Track labels',
-          icon: _Label["default"],
+          icon: _Label.default,
           subMenu: [{
             label: 'Overlapping',
-            icon: _Visibility["default"],
+            icon: _Visibility.default,
             type: 'radio',
             checked: self.trackLabels === 'overlapping',
             onClick: function onClick() {
@@ -1243,7 +1243,7 @@ function stateModelFactory(pluginManager) {
             }
           }, {
             label: 'Offset',
-            icon: _Visibility["default"],
+            icon: _Visibility.default,
             type: 'radio',
             checked: self.trackLabels === 'offset',
             onClick: function onClick() {
@@ -1251,14 +1251,14 @@ function stateModelFactory(pluginManager) {
             }
           }, {
             label: 'Hidden',
-            icon: _Visibility["default"],
+            icon: _Visibility.default,
             type: 'radio',
             checked: self.trackLabels === 'hidden',
             onClick: function onClick() {
               return self.setTrackLabels('hidden');
             }
           }]
-        }].concat((0, _toConsumableArray2["default"])(canShowCytobands ? [{
+        }].concat((0, _toConsumableArray2.default)(canShowCytobands ? [{
           label: showCytobands ? 'Hide ideogram' : 'Show ideograms',
           onClick: function onClick() {
             self.setShowCytobands(!showCytobands);
@@ -1270,7 +1270,7 @@ function stateModelFactory(pluginManager) {
 
         try {
           for (_iterator.s(); !(_step = _iterator.n()).done;) {
-            var _step$value = (0, _slicedToArray2["default"])(_step.value, 2),
+            var _step$value = (0, _slicedToArray2.default)(_step.value, 2),
                 _key2 = _step$value[0],
                 value = _step$value[1];
 
@@ -1300,7 +1300,7 @@ function stateModelFactory(pluginManager) {
     var stringifiedCurrentlyCalculatedStaticBlocks = '';
     return {
       get staticBlocks() {
-        var ret = (0, _calculateStaticBlocks["default"])(self);
+        var ret = (0, _calculateStaticBlocks.default)(self);
         var sret = JSON.stringify(ret);
 
         if (stringifiedCurrentlyCalculatedStaticBlocks !== sret) {
@@ -1312,7 +1312,7 @@ function stateModelFactory(pluginManager) {
       },
 
       get dynamicBlocks() {
-        return (0, _calculateDynamicBlocks["default"])(self);
+        return (0, _calculateDynamicBlocks.default)(self);
       },
 
       get roundedDynamicBlocks() {
@@ -1365,9 +1365,9 @@ function stateModelFactory(pluginManager) {
     return {
       exportSvg: function exportSvg() {
         var _arguments = arguments;
-        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
           var opts, html, blob;
-          return _regenerator["default"].wrap(function _callee$(_context) {
+          return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
@@ -1396,7 +1396,7 @@ function stateModelFactory(pluginManager) {
       rubberBandMenuItems: function rubberBandMenuItems() {
         return [{
           label: 'Zoom to region',
-          icon: _ZoomIn["default"],
+          icon: _ZoomIn.default,
           onClick: function onClick() {
             var leftOffset = self.leftOffset,
                 rightOffset = self.rightOffset;
@@ -1407,7 +1407,7 @@ function stateModelFactory(pluginManager) {
           }
         }, {
           label: 'Get sequence',
-          icon: _MenuOpen["default"],
+          icon: _MenuOpen.default,
           onClick: function onClick() {
             self.setSequenceDialogOpen(true);
           }

package/dist/LinearGenomeView/index.test.js

@@ -33,13 +33,13 @@ function initialize() {
   console.warn = jest.fn(); // a stub linear genome view state model that only accepts base track types.
   // used in unit tests.
 
-  var stubManager = new _PluginManager["default"]();
+  var stubManager = new _PluginManager.default();
   stubManager.addTrackType(function () {
     var configSchema = (0, _configuration.ConfigurationSchema)('BasicTrack', {}, {
       baseConfiguration: (0, _models.createBaseTrackConfig)(stubManager),
       explicitIdentifier: 'trackId'
     });
-    return new _TrackType["default"]({
+    return new _TrackType.default({
       name: 'BasicTrack',
       configSchema: configSchema,
       stateModel: (0, _models.createBaseTrackModel)(stubManager, 'BasicTrack', configSchema)
@@ -49,7 +49,7 @@ function initialize() {
     var configSchema = (0, _configuration.ConfigurationSchema)('LinearBareDisplay', {}, {
       explicitlyTyped: true
     });
-    return new _DisplayType["default"]({
+    return new _DisplayType.default({
       name: 'LinearBareDisplay',
       configSchema: configSchema,
       stateModel: (0, _LinearBareDisplay.stateModelFactory)(configSchema),
@@ -61,9 +61,9 @@ function initialize() {
   stubManager.createPluggableElements();
   stubManager.configure();
 
-  var Assembly = _mobxStateTree.types.model({})["volatile"](function () {
+  var Assembly = _mobxStateTree.types.model({}).volatile(function () {
     return {
-      regions: _volvoxDisplayedRegions["default"]
+      regions: _volvoxDisplayedRegions.default
     };
   }).views(function () {
     return {
@@ -100,7 +100,7 @@ function initialize() {
     assemblyManager: _mobxStateTree.types.optional(AssemblyManager, {
       assemblies: {
         volvox: {
-          regions: _volvoxDisplayedRegions["default"]
+          regions: _volvoxDisplayedRegions.default
         }
       }
     })
@@ -235,10 +235,10 @@ test('can instantiate a model that has multiple displayed regions', function ()
   });
   expect(model.offsetPx).toEqual(79401);
 });
-test('can instantiate a model that tests navTo/moveTo', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+test('can instantiate a model that tests navTo/moveTo', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
   var _initialize4, Session, LinearGenomeModel, session, width, model;
 
-  return _regenerator["default"].wrap(function _callee$(_context) {
+  return _regenerator.default.wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
@@ -791,7 +791,7 @@ test('can perform pxToBp on human genome things with ellided blocks (zoomed in)'
   }));
   var width = 800;
   model.setWidth(width);
-  model.setDisplayedRegions(_hg38DisplayedRegions["default"]);
+  model.setDisplayedRegions(_hg38DisplayedRegions.default);
   model.setNewView(6359.273152497633, 503862);
   expect(model.pxToBp(0).refName).toBe('Y');
   expect(model.pxToBp(400).refName).toBe('Y');
@@ -819,7 +819,7 @@ test('can perform pxToBp on human genome things with ellided blocks (zoomed out)
   }));
   var width = 800;
   model.setWidth(width);
-  model.setDisplayedRegions(_hg38DisplayedRegions["default"]);
+  model.setDisplayedRegions(_hg38DisplayedRegions.default);
   model.setNewView(3209286.105, -225.5083315372467); // chr1 to the left
 
   expect(model.pxToBp(0).refName).toBe('1');
@@ -836,10 +836,10 @@ test('can perform pxToBp on human genome things with ellided blocks (zoomed out)
   expect(model.pxToBp(1500).refName).toBe('Y_KI270740v1_random');
   expect(model.pxToBp(1500).oob).toBeTruthy();
 });
-test('can showAllRegionsInAssembly', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+test('can showAllRegionsInAssembly', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
   var _initialize11, Session, LinearGenomeModel, session, width, model;
 
-  return _regenerator["default"].wrap(function _callee2$(_context2) {
+  return _regenerator.default.wrap(function _callee2$(_context2) {
     while (1) {
       switch (_context2.prev = _context2.next) {
         case 0:
@@ -1088,9 +1088,9 @@ test('navToLocString with human assembly', function () {
   var _initialize13 = initialize(),
       LinearGenomeModel = _initialize13.LinearGenomeModel;
 
-  var HumanAssembly = _mobxStateTree.types.model({})["volatile"](function () {
+  var HumanAssembly = _mobxStateTree.types.model({}).volatile(function () {
     return {
-      regions: _hg38DisplayedRegions["default"]
+      regions: _hg38DisplayedRegions.default
     };
   }).views(function () {
     return {
@@ -1126,7 +1126,7 @@ test('navToLocString with human assembly', function () {
     assemblyManager: {
       assemblies: {
         hg38: {
-          regions: _hg38DisplayedRegions["default"]
+          regions: _hg38DisplayedRegions.default
         }
       }
     },
@@ -1135,11 +1135,11 @@ test('navToLocString with human assembly', function () {
     }
   });
   model.view.setWidth(800);
-  model.view.setDisplayedRegions(_hg38DisplayedRegions["default"].slice(0, 1));
+  model.view.setDisplayedRegions(_hg38DisplayedRegions.default.slice(0, 1));
   model.view.navToLocString('2');
-  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions["default"][1].end / model.view.width);
+  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions.default[1].end / model.view.width);
   model.view.navToLocString('chr3');
-  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions["default"][2].end / model.view.width);
+  expect(model.view.bpPerPx).toBe(_hg38DisplayedRegions.default[2].end / model.view.width);
   model.view.navToLocString('chr3:1,000,000,000-1,100,000,000');
   expect(model.view.bpPerPx).toBe(0.02);
   expect(model.view.offsetPx).toBe(9914777550);
@@ -1160,7 +1160,7 @@ test('multi region', function () {
     }]
   }));
   model.setWidth(800);
-  model.setDisplayedRegions(_volvoxDisplayedRegions["default"].slice(0, 1));
+  model.setDisplayedRegions(_volvoxDisplayedRegions.default.slice(0, 1));
   model.navToLocString('ctgA ctgB');
   expect(model.displayedRegions[0].refName).toBe('ctgA');
   expect(model.displayedRegions[1].refName).toBe('ctgB'); // [

package/dist/LinearGenomeView/util.d.ts

@@ -1,14 +1,14 @@
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
-export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
-    majorPitch: number;
-    minorPitch: number;
-};
-export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
-    type: string;
-    base: number;
-    index: number;
-}[];
+/**
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
+ * the gridline pitches to use.
+ */
+export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
+    majorPitch: number;
+    minorPitch: number;
+};
+export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
+    type: string;
+    base: number;
+    index: number;
+}[];