@jbrowse/plugin-alignments 1.7.3 → 1.7.4
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/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +26 -26
- package/dist/AlignmentsFeatureDetail/index.js +3 -3
- package/dist/AlignmentsFeatureDetail/index.test.js +2 -2
- package/dist/AlignmentsTrack/index.js +2 -2
- package/dist/BamAdapter/BamAdapter.js +31 -31
- package/dist/BamAdapter/BamAdapter.test.js +10 -10
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +6 -6
- package/dist/BamAdapter/MismatchParser.js +6 -6
- package/dist/BamAdapter/MismatchParser.test.js +2 -2
- package/dist/BamAdapter/configSchema.js +2 -2
- package/dist/BamAdapter/index.js +6 -6
- package/dist/CramAdapter/CramAdapter.js +31 -31
- package/dist/CramAdapter/CramAdapter.test.js +10 -10
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +6 -6
- package/dist/CramAdapter/CramTestAdapters.js +18 -18
- package/dist/CramAdapter/configSchema.js +2 -2
- package/dist/CramAdapter/index.js +6 -6
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +9 -9
- package/dist/HtsgetBamAdapter/configSchema.js +2 -2
- package/dist/HtsgetBamAdapter/index.js +6 -6
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +8 -8
- package/dist/LinearAlignmentsDisplay/index.js +5 -5
- package/dist/LinearAlignmentsDisplay/models/configSchema.js +2 -2
- package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +11 -11
- package/dist/LinearAlignmentsDisplay/models/model.js +15 -15
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +18 -18
- package/dist/LinearPileupDisplay/components/ColorByTag.js +11 -11
- package/dist/LinearPileupDisplay/components/FilterByTag.js +26 -26
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +4 -4
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +12 -12
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +10 -10
- package/dist/LinearPileupDisplay/components/SortByTag.js +10 -10
- package/dist/LinearPileupDisplay/configSchema.js +2 -2
- package/dist/LinearPileupDisplay/configSchema.test.js +12 -12
- package/dist/LinearPileupDisplay/index.js +4 -4
- package/dist/LinearPileupDisplay/model.js +22 -22
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +10 -10
- package/dist/LinearSNPCoverageDisplay/index.js +4 -4
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js +1 -1
- package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +7 -7
- package/dist/LinearSNPCoverageDisplay/models/model.js +11 -11
- package/dist/NestedFrequencyTable.js +7 -7
- package/dist/PileupRPC/rpcMethods.js +23 -23
- package/dist/PileupRenderer/PileupLayoutSession.js +8 -8
- package/dist/PileupRenderer/PileupRenderer.js +37 -37
- package/dist/PileupRenderer/components/PileupRendering.js +13 -13
- package/dist/PileupRenderer/components/PileupRendering.test.js +2 -2
- package/dist/PileupRenderer/configSchema.js +2 -2
- package/dist/PileupRenderer/index.js +4 -4
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +22 -22
- package/dist/SNPCoverageAdapter/configSchema.js +2 -2
- package/dist/SNPCoverageAdapter/index.js +6 -6
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +12 -12
- package/dist/SNPCoverageRenderer/configSchema.js +2 -2
- package/dist/SNPCoverageRenderer/index.js +3 -3
- package/dist/index.js +10 -10
- package/dist/index.test.js +2 -2
- package/dist/shared.js +5 -5
- package/dist/util.js +3 -3
- package/package.json +4 -5
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@@ -20,7 +20,7 @@ var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRend
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var _configSchema = _interopRequireDefault(require("./configSchema"));
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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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@@ -33,26 +33,26 @@ afterEach(function () {
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}); // change renderer
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var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
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(0, _inherits2
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(0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
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var _super = _createSuper(SNPCoverageRendererPlugin);
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function SNPCoverageRendererPlugin() {
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(0, _classCallCheck2
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(0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
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return _super.apply(this, arguments);
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}
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(0, _createClass2
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(0, _createClass2.default)(SNPCoverageRendererPlugin, [{
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key: "install",
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value: function install(pluginManager) {
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(0, _SNPCoverageRenderer
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(0, _SNPCoverageRenderer.default)(pluginManager);
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}
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}]);
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return SNPCoverageRendererPlugin;
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}(_Plugin2
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}(_Plugin2.default);
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test('has a type attr', function () {
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var configSchema = (0, _configSchema
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var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
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var config = configSchema.create({
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type: 'LinearSNPCoverageDisplay',
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displayId: 'display1',
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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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@@ -31,7 +31,7 @@ var _shared = require("../../shared");
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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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// using a map because it preserves order
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var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
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@@ -39,9 +39,9 @@ var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
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var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
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return _mobxStateTree.types.compose('LinearSNPCoverageDisplay', (0, _pluginWiggle.linearWiggleDisplayModelFactory)(pluginManager, configSchema), _mobxStateTree.types.model({
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type: _mobxStateTree.types.literal('LinearSNPCoverageDisplay'),
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drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types
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drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types
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drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types
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drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
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drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
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drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
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filterBy: _mobxStateTree.types.optional(_mobxStateTree.types.model({
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flagInclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
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flagExclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 1540),
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type: _mobxStateTree.types.string,
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tag: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
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}))
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}))
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})).volatile(function () {
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return {
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modificationTagMap: _mobx.observable.map({})
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};
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self.drawArcs = !self.drawArcsSetting;
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},
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afterAttach: function afterAttach() {
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(0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2
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(0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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var colorBy, _ref2, staticBlocks, vals;
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return _regenerator
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return _regenerator.default.wrap(function _callee$(_context) {
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while (1) {
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switch (_context.prev = _context.next) {
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case 0:
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var superTrackMenuItems = self.trackMenuItems;
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return {
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get TooltipComponent() {
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return _Tooltip
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return _Tooltip.default;
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},
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get adapterConfig() {
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return [];
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},
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trackMenuItems: function trackMenuItems() {
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return [].concat((0, _toConsumableArray2
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return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
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label: 'Draw insertion/clipping indicators',
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type: 'checkbox',
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checked: self.drawIndicatorsSetting,
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};
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var _default = stateModelFactory;
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exports
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exports.default = _default;
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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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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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/* eslint-disable @typescript-eslint/no-explicit-any */
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// see perf results on object.keys vs for-in loop
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var NestedFrequencyTable = /*#__PURE__*/function () {
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function NestedFrequencyTable() {
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var initialData = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
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(0, _defineProperty2.default)(this, "categories", void 0);
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(0, _createClass2.default)(NestedFrequencyTable, [{
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// calculate total if necessary
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if (!slot || !slot.categories) {
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this.categories[slotName] = new NestedFrequencyTable(slot ? {
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default: slot + 0
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}
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}();
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exports
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exports.default = NestedFrequencyTable;
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var _MismatchParser = require("../BamAdapter/MismatchParser");
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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 PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
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function PileupGetGlobalValueForTag() {
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(0, _classCallCheck2.default)(this, PileupGetGlobalValueForTag);
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}
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'PileupGetGlobalValueForTag');
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(0, _createClass2.default)(PileupGetGlobalValueForTag, [{
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key: "serializeArguments",
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var _serializeArguments = (0, _asyncToGenerator2
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var _serializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, rpcDriverClassName) {
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var _rootModel$session;
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return _regenerator.default.wrap(function _callee$(_context) {
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exports.PileupGetVisibleModifications = PileupGetVisibleModifications;
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|
@@ -29,33 +29,33 @@ var _BoxRendererType = require("@jbrowse/core/pluggableElementTypes/renderers/Bo
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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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// Sorting and revealing soft clip changes the layout of Pileup renderer
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// Adds extra conditions to see if cached layout is valid
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var PileupLayoutSession = /*#__PURE__*/function (_LayoutSession) {
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(0, _inherits2.default)(PileupLayoutSession, _LayoutSession);
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var _super = _createSuper(PileupLayoutSession);
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function PileupLayoutSession(args) {
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(0, _classCallCheck2.default)(this, PileupLayoutSession);
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "sortedBy", void 0);
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|
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "showSoftClip", false);
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|
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cachedLayout", void 0);
|
|
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|
_this.config = args.config;
|
|
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return _this;
|
|
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|
}
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(0, _createClass2.default)(PileupLayoutSession, [{
|
|
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|
key: "cachedLayoutIsValid",
|
|
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|
value: function cachedLayoutIsValid(cachedLayout) {
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|
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return (0, _get2
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|
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|
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return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual.default)(this.sortedBy, cachedLayout.sortedBy);
|
|
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}
|
|
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}, {
|
|
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key: "layout",
|