@jbrowse/plugin-wiggle 1.7.1 → 1.7.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BigWigAdapter/BigWigAdapter.js +22 -22
- package/dist/BigWigAdapter/BigWigAdapter.test.js +9 -9
- package/dist/BigWigAdapter/configSchema.js +2 -2
- package/dist/BigWigAdapter/index.js +1 -1
- package/dist/DensityRenderer/DensityRenderer.test.js +6 -6
- package/dist/DensityRenderer/index.js +13 -13
- package/dist/LinePlotRenderer/LinePlotRenderer.js +12 -12
- package/dist/LinePlotRenderer/configSchema.js +2 -2
- package/dist/LinePlotRenderer/index.js +3 -3
- package/dist/LinearWiggleDisplay/components/SetColorDialog.js +14 -14
- package/dist/LinearWiggleDisplay/components/SetMinMaxDialog.js +13 -13
- package/dist/LinearWiggleDisplay/components/Tooltip.js +14 -14
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +5 -5
- package/dist/LinearWiggleDisplay/components/YScaleBar.js +3 -3
- package/dist/LinearWiggleDisplay/index.js +4 -4
- package/dist/LinearWiggleDisplay/models/configSchema.js +1 -1
- package/dist/LinearWiggleDisplay/models/model.d.ts +1 -1
- package/dist/LinearWiggleDisplay/models/model.js +27 -27
- package/dist/WiggleBaseRenderer.js +13 -13
- package/dist/WiggleRPC/rpcMethods.js +27 -27
- package/dist/WiggleRendering.js +7 -7
- package/dist/WiggleRendering.test.js +3 -3
- package/dist/XYPlotRenderer/XYPlotRenderer.js +15 -15
- package/dist/XYPlotRenderer/XYPlotRenderer.test.js +6 -6
- package/dist/XYPlotRenderer/index.js +3 -3
- package/dist/configSchema.js +2 -2
- package/dist/index.d.ts +3 -3
- package/dist/index.js +21 -21
- package/dist/index.test.js +2 -2
- package/dist/util.js +4 -4
- package/package.json +4 -5
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@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
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Object.defineProperty(exports, "__esModule", {
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value: true
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});
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exports
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exports.default = void 0;
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var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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@@ -45,38 +45,38 @@ var _stats = require("@jbrowse/core/util/stats");
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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; }
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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
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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; }
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function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2
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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); }; }
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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; } }
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var BigWigAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
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(0, _inherits2
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(0, _inherits2.default)(BigWigAdapter, _BaseFeatureDataAdapt);
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var _super = _createSuper(BigWigAdapter);
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function BigWigAdapter(config, getSubAdapter, pluginManager) {
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var _this;
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(0, _classCallCheck2
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(0, _classCallCheck2.default)(this, BigWigAdapter);
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_this = _super.call(this, config, getSubAdapter, pluginManager);
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(0, _defineProperty2
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bigwig", void 0);
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_this.bigwig = new _bbi.BigWig({
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filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(config, 'bigWigLocation'), _this.pluginManager)
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});
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return _this;
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}
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(0, _createClass2.default)(BigWigAdapter, [{
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key: "setup",
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value: function () {
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var _setup = (0, _asyncToGenerator2
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var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(opts) {
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var _this2 = this;
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var _ref, _ref$statusCallback, statusCallback;
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}, {
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key: "getRefNames",
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value: function () {
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var _getRefNames = (0, _asyncToGenerator2
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var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
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var _yield$this$setup, refsByName;
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}, {
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key: "refIdToName",
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value: function () {
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var _refIdToName = (0, _asyncToGenerator2
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var _refIdToName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(refId) {
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var _refsByNumber$refId;
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var _yield$this$setup2, refsByNumber;
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}, {
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key: "getGlobalStats",
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value: function () {
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var _getGlobalStats = (0, _asyncToGenerator2
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var _getGlobalStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
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var _yield$this$setup3, totalSummary;
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_opts$statusCallback = opts.statusCallback,
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statusCallback = _opts$statusCallback === void 0 ? function () {} : _opts$statusCallback;
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return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
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var _ref2 = (0, _asyncToGenerator2
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var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(observer) {
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var ob;
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case 3:
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ob = _context5.sent;
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ob.pipe((0, _operators.mergeAll)(), (0, _operators.map)(function (record) {
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return new _simpleFeature
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return new _simpleFeature.default({
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id: "".concat(refName, ":").concat(record.start, "-").concat(record.end),
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data: _objectSpread(_objectSpread({}, record), {}, {
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refName: refName
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}, {
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key: "estimateRegionsStats",
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value: function () {
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var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(_regions) {
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return BigWigAdapter;
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}(_BaseAdapter.BaseFeatureDataAdapter);
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exports
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(0, _defineProperty2
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exports.default = BigWigAdapter;
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(0, _defineProperty2.default)(BigWigAdapter, "capabilities", ['hasResolution', 'hasLocalStats', 'hasGlobalStats']);
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describe('adapter can fetch features from volvox.bw', function () {
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var adapter;
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beforeEach(function () {
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adapter = new _BigWigAdapter
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adapter = new _BigWigAdapter.default(_configSchema.default.create({
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bigWigLocation: {
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localPath: require.resolve('./test_data/volvox.bw'),
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locationType: 'LocalPathLocation'
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}
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}));
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});
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it('test basic aspects of getfeatures', /*#__PURE__*/(0, _asyncToGenerator2
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it('test basic aspects of getfeatures', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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return _regenerator.default.wrap(function _callee$(_context) {
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})));
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it('adapter can fetch stats from volvox.bw', /*#__PURE__*/(0, _asyncToGenerator2
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it('adapter can fetch stats from volvox.bw', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
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})));
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it('get region stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
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})));
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it('get local stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
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test('inverted mode and reversed', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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features: [new _simpleFeature
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features: [new _simpleFeature.default({
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id: 't1',
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data: {
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start: 1,
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end: 100,
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score: 1
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id: 't2',
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data: {
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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; } } }; }
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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; } } }; }
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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); }
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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; }
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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); }; }
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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; } }
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var LinePlotRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
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function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(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; }
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