@jbrowse/plugin-linear-genome-view 1.6.7 → 1.7.0

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.
Files changed (74) hide show
  1. package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js +232 -0
  2. package/dist/BaseLinearDisplay/components/Block.js +86 -0
  3. package/dist/BaseLinearDisplay/components/LinearBlocks.js +110 -0
  4. package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js +192 -0
  5. package/dist/BaseLinearDisplay/index.js +41 -0
  6. package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +763 -0
  7. package/dist/BaseLinearDisplay/models/baseLinearDisplayConfigSchema.js +24 -0
  8. package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +328 -0
  9. package/dist/LinearBareDisplay/configSchema.js +19 -0
  10. package/dist/LinearBareDisplay/index.js +21 -0
  11. package/dist/LinearBareDisplay/index.test.js +33 -0
  12. package/dist/LinearBareDisplay/model.d.ts +7 -7
  13. package/dist/LinearBareDisplay/model.js +44 -0
  14. package/dist/LinearBasicDisplay/components/SetMaxHeight.js +94 -0
  15. package/dist/LinearBasicDisplay/configSchema.js +25 -0
  16. package/dist/LinearBasicDisplay/index.js +23 -0
  17. package/dist/LinearBasicDisplay/model.d.ts +7 -7
  18. package/dist/LinearBasicDisplay/model.js +162 -0
  19. package/dist/LinearGenomeView/components/CenterLine.js +80 -0
  20. package/dist/LinearGenomeView/components/ExportSvgDialog.js +137 -0
  21. package/dist/LinearGenomeView/components/Header.js +144 -0
  22. package/dist/LinearGenomeView/components/HelpDialog.js +48 -0
  23. package/dist/LinearGenomeView/components/ImportForm.js +330 -0
  24. package/dist/LinearGenomeView/components/LinearGenomeView.js +129 -0
  25. package/dist/LinearGenomeView/components/LinearGenomeView.test.js +234 -0
  26. package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js +349 -0
  27. package/dist/LinearGenomeView/components/MiniControls.js +83 -0
  28. package/dist/LinearGenomeView/components/OverviewRubberBand.js +310 -0
  29. package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts +6 -6
  30. package/dist/LinearGenomeView/components/OverviewScaleBar.js +403 -0
  31. package/dist/LinearGenomeView/components/RefNameAutocomplete.js +331 -0
  32. package/dist/LinearGenomeView/components/RubberBand.js +309 -0
  33. package/dist/LinearGenomeView/components/Ruler.js +101 -0
  34. package/dist/LinearGenomeView/components/ScaleBar.js +184 -0
  35. package/dist/LinearGenomeView/components/ScaleBar.test.js +180 -0
  36. package/dist/LinearGenomeView/components/SearchBox.js +201 -0
  37. package/dist/LinearGenomeView/components/SearchResultsDialog.js +159 -0
  38. package/dist/LinearGenomeView/components/SequenceDialog.js +304 -0
  39. package/dist/LinearGenomeView/components/TrackContainer.js +179 -0
  40. package/dist/LinearGenomeView/components/TrackLabel.js +165 -0
  41. package/dist/LinearGenomeView/components/TracksContainer.js +214 -0
  42. package/dist/LinearGenomeView/components/VerticalGuides.js +116 -0
  43. package/dist/LinearGenomeView/components/ZoomControls.js +92 -0
  44. package/dist/LinearGenomeView/components/util.js +16 -0
  45. package/dist/LinearGenomeView/index.js +1418 -0
  46. package/dist/LinearGenomeView/index.test.js +1170 -0
  47. package/dist/LinearGenomeView/util.js +93 -0
  48. package/dist/LinearGenomeView/util.test.js +78 -0
  49. package/dist/index.d.ts +21 -21
  50. package/dist/index.js +293 -6
  51. package/dist/plugin-linear-genome-view.cjs.development.js +37 -22
  52. package/dist/plugin-linear-genome-view.cjs.development.js.map +1 -1
  53. package/dist/plugin-linear-genome-view.cjs.production.min.js +1 -1
  54. package/dist/plugin-linear-genome-view.cjs.production.min.js.map +1 -1
  55. package/dist/plugin-linear-genome-view.esm.js +37 -22
  56. package/dist/plugin-linear-genome-view.esm.js.map +1 -1
  57. package/package.json +4 -8
  58. package/src/BaseLinearDisplay/components/BaseLinearDisplay.tsx +9 -12
  59. package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +2 -0
  60. package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +10 -8
  61. package/src/LinearBasicDisplay/components/SetMaxHeight.tsx +21 -12
  62. package/src/LinearBasicDisplay/model.ts +17 -18
  63. package/src/LinearGenomeView/components/Header.tsx +1 -1
  64. package/src/LinearGenomeView/components/ImportForm.tsx +10 -4
  65. package/src/LinearGenomeView/components/LinearGenomeView.test.js +1 -0
  66. package/src/LinearGenomeView/components/OverviewScaleBar.tsx +2 -2
  67. package/src/LinearGenomeView/components/RubberBand.tsx +14 -24
  68. package/src/LinearGenomeView/components/ScaleBar.test.tsx +1 -0
  69. package/src/LinearGenomeView/components/ScaleBar.tsx +3 -6
  70. package/src/LinearGenomeView/components/SequenceDialog.tsx +1 -1
  71. package/src/LinearGenomeView/components/TrackContainer.tsx +31 -24
  72. package/src/LinearGenomeView/components/TrackLabel.tsx +1 -1
  73. package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap +23 -47
  74. package/src/LinearGenomeView/index.tsx +2 -3
@@ -0,0 +1,330 @@
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+ "use strict";
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+
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+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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+
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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ });
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+ exports["default"] = void 0;
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+
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+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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+
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+ var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
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+
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+ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
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+
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+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
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+
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+ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
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+
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+ var _react = _interopRequireWildcard(require("react"));
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+
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+ var _mobxReact = require("mobx-react");
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+
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+ var _util = require("@jbrowse/core/util");
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+
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+ var _core = require("@material-ui/core");
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+
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+ var _ErrorMessage = _interopRequireDefault(require("@jbrowse/core/ui/ErrorMessage"));
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+
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+ var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
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+
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+ var _AssemblySelector = _interopRequireDefault(require("@jbrowse/core/ui/AssemblySelector"));
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+
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+ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
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+
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+ var _RefNameAutocomplete = _interopRequireDefault(require("./RefNameAutocomplete"));
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+
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+ var _ = require("..");
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+
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+ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
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+
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+ function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(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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+
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+ var SearchResultsDialog = /*#__PURE__*/(0, _react.lazy)(function () {
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+ return Promise.resolve().then(function () {
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+ return _interopRequireWildcard(require('./SearchResultsDialog'));
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+ });
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+ });
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+ var useStyles = (0, _core.makeStyles)(function (theme) {
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+ return {
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+ importFormContainer: {
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+ padding: theme.spacing(2)
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+ },
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+ button: {
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+ margin: theme.spacing(2)
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+ },
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+ container: {
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+ padding: theme.spacing(4)
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+ }
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+ };
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+ });
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+ var ImportForm = (0, _mobxReact.observer)(function (_ref) {
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+ var _regions$;
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+
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+ var model = _ref.model;
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+ var classes = useStyles();
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+ var session = (0, _util.getSession)(model);
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+ var assemblyNames = session.assemblyNames,
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+ assemblyManager = session.assemblyManager,
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+ textSearchManager = session.textSearchManager;
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+ var rankSearchResults = model.rankSearchResults,
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+ isSearchDialogDisplayed = model.isSearchDialogDisplayed,
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+ modelError = model.error;
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+
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+ var _useState = (0, _react.useState)(assemblyNames[0]),
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+ _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
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+ selectedAsm = _useState2[0],
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+ setSelectedAsm = _useState2[1];
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+
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+ var _useState3 = (0, _react.useState)(modelError),
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+ _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
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+ error = _useState4[0],
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+ setError = _useState4[1];
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+
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+ var searchScope = model.searchScope(selectedAsm);
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+ var assembly = assemblyManager.get(selectedAsm);
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+ var assemblyError = assemblyNames.length ? assembly === null || assembly === void 0 ? void 0 : assembly.error : 'No configured assemblies';
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+ var regions = (assembly === null || assembly === void 0 ? void 0 : assembly.regions) || [];
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+ var err = assemblyError || error;
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+
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+ var _useState5 = (0, _react.useState)(),
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+ _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
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+ myOption = _useState6[0],
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+ setOption = _useState6[1]; // use this instead of useState initializer because the useState initializer
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+ // won't update in response to an observable
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+
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+
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+ var option = myOption || new _BaseResults["default"]({
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+ label: (_regions$ = regions[0]) === null || _regions$ === void 0 ? void 0 : _regions$.refName
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+ });
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+ var selectedRegion = option === null || option === void 0 ? void 0 : option.getLocation();
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+
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+ function fetchResults(_x, _x2) {
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+ return _fetchResults.apply(this, arguments);
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+ } // gets a string as input, or use stored option results from previous query,
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+ // then re-query and
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+ // 1) if it has multiple results: pop a dialog
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+ // 2) if it's a single result navigate to it
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+ // 3) else assume it's a locstring and navigate to it
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+
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+
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+ function _fetchResults() {
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+ _fetchResults = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(query, searchType) {
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+ var _assembly$allRefNames;
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+
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+ var textSearchResults, refNameResults;
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+ return _regenerator["default"].wrap(function _callee$(_context) {
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+ while (1) {
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+ switch (_context.prev = _context.next) {
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+ case 0:
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+ if (!textSearchManager) {
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+ console.warn('No text search manager');
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+ }
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+
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+ _context.next = 3;
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+ return textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
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+ queryString: query,
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+ searchType: searchType
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+ }, searchScope, rankSearchResults);
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+
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+ case 3:
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+ textSearchResults = _context.sent;
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+ refNameResults = assembly === null || assembly === void 0 ? void 0 : (_assembly$allRefNames = assembly.allRefNames) === null || _assembly$allRefNames === void 0 ? void 0 : _assembly$allRefNames.filter(function (refName) {
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+ return refName.startsWith(query);
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+ }).map(function (r) {
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+ return new _BaseResults["default"]({
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+ label: r
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+ });
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+ }).slice(0, 10);
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+ return _context.abrupt("return", [].concat((0, _toConsumableArray2["default"])(refNameResults || []), (0, _toConsumableArray2["default"])(textSearchResults || [])));
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+
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+ case 6:
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+ case "end":
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+ return _context.stop();
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+ }
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+ }
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+ }, _callee);
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+ }));
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+ return _fetchResults.apply(this, arguments);
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+ }
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+
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+ function handleSelectedRegion(_x3) {
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+ return _handleSelectedRegion.apply(this, arguments);
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+ }
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+
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+ function _handleSelectedRegion() {
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+ _handleSelectedRegion = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(input) {
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+ var trackId, location, _assembly$allRefNames2, results;
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+
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+ return _regenerator["default"].wrap(function _callee2$(_context2) {
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+ while (1) {
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+ switch (_context2.prev = _context2.next) {
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+ case 0:
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+ if (option) {
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+ _context2.next = 2;
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+ break;
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+ }
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+
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+ return _context2.abrupt("return");
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+
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+ case 2:
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+ trackId = option.getTrackId();
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+ location = input || option.getLocation() || '';
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+ _context2.prev = 4;
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+
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+ if (!(assembly !== null && assembly !== void 0 && (_assembly$allRefNames2 = assembly.allRefNames) !== null && _assembly$allRefNames2 !== void 0 && _assembly$allRefNames2.includes(location))) {
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+ _context2.next = 9;
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+ break;
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+ }
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+
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+ model.navToLocString(location, selectedAsm);
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+ _context2.next = 20;
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+ break;
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+
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+ case 9:
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+ _context2.next = 11;
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+ return fetchResults(input, 'exact');
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+
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+ case 11:
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+ results = _context2.sent;
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+
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+ if (!(results && results.length > 1)) {
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+ _context2.next = 17;
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+ break;
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+ }
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+
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+ model.setSearchResults(results, input.toLowerCase());
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+ return _context2.abrupt("return");
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+
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+ case 17:
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+ if ((results === null || results === void 0 ? void 0 : results.length) === 1) {
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+ location = results[0].getLocation();
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+ trackId = results[0].getTrackId();
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+ }
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+
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+ case 18:
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+ model.navToLocString(location, selectedAsm);
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+
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+ if (trackId) {
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+ model.showTrack(trackId);
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+ }
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+
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+ case 20:
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+ _context2.next = 26;
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+ break;
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+
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+ case 22:
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+ _context2.prev = 22;
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+ _context2.t0 = _context2["catch"](4);
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+ console.error(_context2.t0);
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+ session.notify("".concat(_context2.t0), 'warning');
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+
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+ case 26:
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+ case "end":
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+ return _context2.stop();
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+ }
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+ }
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+ }, _callee2, null, [[4, 22]]);
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+ }));
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+ return _handleSelectedRegion.apply(this, arguments);
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+ }
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+
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+ var height = _.WIDGET_HEIGHT + 5; // implementation notes:
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+ // having this wrapped in a form allows intuitive use of enter key to submit
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+
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+ return /*#__PURE__*/_react["default"].createElement("div", {
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+ className: classes.container
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+ }, err ? /*#__PURE__*/_react["default"].createElement(_ErrorMessage["default"], {
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+ error: err
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+ }) : null, /*#__PURE__*/_react["default"].createElement(_core.Container, {
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+ className: classes.importFormContainer
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+ }, /*#__PURE__*/_react["default"].createElement("form", {
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+ onSubmit: function onSubmit(event) {
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+ return event.preventDefault();
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+ }
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+ }, /*#__PURE__*/_react["default"].createElement(_core.Grid, {
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+ container: true,
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+ spacing: 1,
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+ justifyContent: "center",
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+ alignItems: "center"
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+ }, /*#__PURE__*/_react["default"].createElement(_core.Grid, {
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+ item: true
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+ }, /*#__PURE__*/_react["default"].createElement(_AssemblySelector["default"], {
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+ onChange: function onChange(val) {
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+ setError(undefined);
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+ setSelectedAsm(val);
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+ },
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+ session: session,
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+ selected: selectedAsm,
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+ InputProps: {
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+ style: {
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+ height: height
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+ }
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+ }
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+ })), /*#__PURE__*/_react["default"].createElement(_core.Grid, {
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+ item: true
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+ }, selectedAsm ? err ? /*#__PURE__*/_react["default"].createElement(_Close["default"], {
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+ style: {
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+ color: 'red'
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+ }
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+ }) : selectedRegion ? /*#__PURE__*/_react["default"].createElement(_RefNameAutocomplete["default"], {
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+ fetchResults: fetchResults,
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+ model: model,
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+ assemblyName: assemblyError ? undefined : selectedAsm,
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+ value: selectedRegion // note: minWidth 270 accomodates full width of helperText
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+ ,
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+ minWidth: 270,
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+ onSelect: function onSelect(option) {
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+ return setOption(option);
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+ },
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+ TextFieldProps: {
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+ variant: 'outlined',
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+ helperText: 'Enter sequence name, feature name, or location',
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+ style: {
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+ minWidth: '175px'
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+ },
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+ InputProps: {
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+ style: {
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+ height: height
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+ }
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+ }
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+ }
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+ }) : /*#__PURE__*/_react["default"].createElement(_core.CircularProgress, {
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+ role: "progressbar",
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+ size: 20,
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+ disableShrink: true
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+ }) : null), /*#__PURE__*/_react["default"].createElement(_core.Grid, {
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+ item: true
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+ }, /*#__PURE__*/_react["default"].createElement(_core.Button, {
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+ type: "submit",
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+ disabled: !selectedRegion,
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+ className: classes.button,
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+ onClick: function onClick() {
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+ model.setError(undefined);
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+
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+ if (selectedRegion) {
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+ handleSelectedRegion(selectedRegion);
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+ }
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+ },
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+ variant: "contained",
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+ color: "primary"
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+ }, "Open"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
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+ disabled: !selectedRegion,
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+ className: classes.button,
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+ onClick: function onClick() {
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+ model.setError(undefined);
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+ model.showAllRegionsInAssembly(selectedAsm);
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+ },
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+ variant: "contained",
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+ color: "secondary"
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+ }, "Show all regions in assembly"))))), isSearchDialogDisplayed ? /*#__PURE__*/_react["default"].createElement(SearchResultsDialog, {
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+ model: model,
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+ optAssemblyName: selectedAsm,
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+ handleClose: function handleClose() {
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+ return model.setSearchResults(undefined, undefined);
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+ }
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+ }) : null);
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+ });
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+ var _default = ImportForm;
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+ exports["default"] = _default;
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+ "use strict";
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+
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+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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+
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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ });
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+ exports["default"] = void 0;
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+
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+ var _react = _interopRequireDefault(require("react"));
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+
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+ var _core = require("@material-ui/core");
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+
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+ var _Icons = require("@jbrowse/core/ui/Icons");
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+
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+ var _mobxReact = require("mobx-react");
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+
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+ var _Header = _interopRequireDefault(require("./Header"));
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+
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+ var _TrackContainer = _interopRequireDefault(require("./TrackContainer"));
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+
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+ var _TracksContainer = _interopRequireDefault(require("./TracksContainer"));
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+
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+ var _ImportForm = _interopRequireDefault(require("./ImportForm"));
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+
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+ var _MiniControls = _interopRequireDefault(require("./MiniControls"));
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+
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+ var _SequenceDialog = _interopRequireDefault(require("./SequenceDialog"));
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+
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+ var _SearchResultsDialog = _interopRequireDefault(require("./SearchResultsDialog"));
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+
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+ var useStyles = (0, _core.makeStyles)(function (theme) {
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+ return {
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+ note: {
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+ textAlign: 'center',
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+ paddingTop: theme.spacing(1),
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+ paddingBottom: theme.spacing(1)
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+ },
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+ dots: {
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+ '&::after': {
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+ display: 'inline-block',
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+ animation: '$ellipsis 1.5s infinite',
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+ content: '"."',
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+ width: '1em',
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+ textAlign: 'left'
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+ }
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+ },
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+ '@keyframes ellipsis': {
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+ '0%': {
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+ content: '"."'
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+ },
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+ '33%': {
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+ content: '".."'
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+ },
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+ '66%': {
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+ content: '"..."'
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+ }
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+ }
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+ };
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+ });
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+ var LinearGenomeView = (0, _mobxReact.observer)(function (_ref) {
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+ var model = _ref.model;
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+ var tracks = model.tracks,
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+ error = model.error,
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+ hideHeader = model.hideHeader,
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+ initialized = model.initialized,
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+ hasDisplayedRegions = model.hasDisplayedRegions;
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+ var classes = useStyles();
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+
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+ if (!initialized && !error) {
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+ return /*#__PURE__*/_react["default"].createElement(_core.Typography, {
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+ className: classes.dots,
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+ variant: "h5"
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+ }, "Loading");
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+ }
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+
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+ if (!hasDisplayedRegions || error) {
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+ return /*#__PURE__*/_react["default"].createElement(_ImportForm["default"], {
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+ model: model
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+ });
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+ }
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+
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+ return /*#__PURE__*/_react["default"].createElement("div", {
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+ style: {
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+ position: 'relative'
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+ }
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+ }, model.seqDialogDisplayed ? /*#__PURE__*/_react["default"].createElement(_SequenceDialog["default"], {
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+ model: model,
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+ handleClose: function handleClose() {
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+ model.setSequenceDialogOpen(false);
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+ }
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+ }) : null, model.isSearchDialogDisplayed ? /*#__PURE__*/_react["default"].createElement(_SearchResultsDialog["default"], {
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+ model: model,
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+ handleClose: function handleClose() {
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+ model.setSearchResults(undefined, undefined);
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+ }
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+ }) : null, !hideHeader ? /*#__PURE__*/_react["default"].createElement(_Header["default"], {
98
+ model: model
99
+ }) : /*#__PURE__*/_react["default"].createElement("div", {
100
+ style: {
101
+ position: 'absolute',
102
+ right: 0,
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+ zIndex: 1001
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+ }
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+ }, /*#__PURE__*/_react["default"].createElement(_MiniControls["default"], {
106
+ model: model
107
+ })), /*#__PURE__*/_react["default"].createElement(_TracksContainer["default"], {
108
+ model: model
109
+ }, !tracks.length ? /*#__PURE__*/_react["default"].createElement(_core.Paper, {
110
+ variant: "outlined",
111
+ className: classes.note
112
+ }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "No tracks active."), /*#__PURE__*/_react["default"].createElement(_core.Button, {
113
+ variant: "contained",
114
+ color: "primary",
115
+ onClick: model.activateTrackSelector,
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+ style: {
117
+ zIndex: 1000
118
+ },
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+ startIcon: /*#__PURE__*/_react["default"].createElement(_Icons.TrackSelector, null)
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+ }, "Open track selector")) : tracks.map(function (track) {
121
+ return /*#__PURE__*/_react["default"].createElement(_TrackContainer["default"], {
122
+ key: track.id,
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+ model: model,
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+ track: track
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+ });
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+ })));
127
+ });
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+ var _default = LinearGenomeView;
129
+ exports["default"] = _default;
@@ -0,0 +1,234 @@
1
+ "use strict";
2
+
3
+ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
+
5
+ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
6
+
7
+ var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
8
+
9
+ var _react = _interopRequireDefault(require("react"));
10
+
11
+ var _react2 = require("@testing-library/react");
12
+
13
+ require("@testing-library/jest-dom/extend-expect");
14
+
15
+ var _rootModel = require("@jbrowse/web/src/rootModel");
16
+
17
+ require("requestidlecallback-polyfill");
18
+
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+ var _LinearGenomeView = _interopRequireDefault(require("./LinearGenomeView"));
20
+
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+ jest.mock('@jbrowse/web/src/makeWorkerInstance', function () {
22
+ return function () {};
23
+ });
24
+ var assemblyConf = {
25
+ name: 'volMyt1',
26
+ sequence: {
27
+ trackId: 'sequenceConfigId',
28
+ type: 'ReferenceSequenceTrack',
29
+ adapter: {
30
+ type: 'FromConfigSequenceAdapter',
31
+ features: [{
32
+ refName: 'ctgA',
33
+ uniqueId: 'firstId',
34
+ start: 0,
35
+ end: 10,
36
+ seq: 'cattgttgcg'
37
+ }]
38
+ }
39
+ }
40
+ };
41
+ describe('<LinearGenomeView />', function () {
42
+ it('renders setup wizard', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
43
+ var session, model, _render, findByText;
44
+
45
+ return _regenerator["default"].wrap(function _callee$(_context) {
46
+ while (1) {
47
+ switch (_context.prev = _context.next) {
48
+ case 0:
49
+ session = (0, _rootModel.createTestSession)();
50
+ session.addAssemblyConf(assemblyConf);
51
+ session.addView('LinearGenomeView', {
52
+ id: 'lgv'
53
+ });
54
+ model = session.views[0];
55
+ model.setWidth(800);
56
+ _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_LinearGenomeView["default"], {
57
+ model: model
58
+ })), findByText = _render.findByText;
59
+ expect(model.displayedRegions.length).toEqual(0);
60
+ _context.t0 = _react2.fireEvent;
61
+ _context.next = 10;
62
+ return findByText('Open');
63
+
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+ case 10:
65
+ _context.t1 = _context.sent;
66
+
67
+ _context.t0.click.call(_context.t0, _context.t1);
68
+
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+ _context.next = 14;
70
+ return (0, _react2.waitFor)(function () {
71
+ expect(model.displayedRegions.length).toEqual(1);
72
+ });
73
+
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+ case 14:
75
+ case "end":
76
+ return _context.stop();
77
+ }
78
+ }
79
+ }, _callee);
80
+ })));
81
+ it('renders one track, one region', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
82
+ var session, model, _render2, container, findByText;
83
+
84
+ return _regenerator["default"].wrap(function _callee2$(_context2) {
85
+ while (1) {
86
+ switch (_context2.prev = _context2.next) {
87
+ case 0:
88
+ session = (0, _rootModel.createTestSession)();
89
+ session.addAssemblyConf(assemblyConf);
90
+ session.addTrackConf({
91
+ trackId: 'testConfig',
92
+ assemblyNames: ['volMyt1'],
93
+ name: 'Foo Track',
94
+ type: 'BasicTrack',
95
+ adapter: {
96
+ type: 'FromConfigAdapter',
97
+ features: []
98
+ }
99
+ });
100
+ session.addView('LinearGenomeView', {
101
+ type: 'LinearGenomeView',
102
+ id: 'lgv',
103
+ offsetPx: 0,
104
+ bpPerPx: 1,
105
+ tracks: [{
106
+ id: 'foo',
107
+ type: 'BasicTrack',
108
+ height: 20,
109
+ configuration: 'testConfig',
110
+ displays: [{
111
+ type: 'LinearBareDisplay',
112
+ configuration: 'testConfig-LinearBareDisplay'
113
+ }]
114
+ }],
115
+ displayedRegions: [{
116
+ assemblyName: 'volMyt1',
117
+ refName: 'ctgA',
118
+ start: 0,
119
+ end: 100
120
+ }]
121
+ });
122
+ model = session.views[0];
123
+ model.setWidth(800);
124
+ _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_LinearGenomeView["default"], {
125
+ model: model
126
+ })), container = _render2.container, findByText = _render2.findByText;
127
+ _context2.next = 9;
128
+ return findByText('Foo Track');
129
+
130
+ case 9:
131
+ _context2.next = 11;
132
+ return findByText('100 bp');
133
+
134
+ case 11:
135
+ expect(container.firstChild).toMatchSnapshot();
136
+
137
+ case 12:
138
+ case "end":
139
+ return _context2.stop();
140
+ }
141
+ }
142
+ }, _callee2);
143
+ })));
144
+ it('renders two tracks, two regions', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
145
+ var session, model, _render3, container, findByText, findAllByTestId;
146
+
147
+ return _regenerator["default"].wrap(function _callee3$(_context3) {
148
+ while (1) {
149
+ switch (_context3.prev = _context3.next) {
150
+ case 0:
151
+ session = (0, _rootModel.createTestSession)();
152
+ session.addAssemblyConf(assemblyConf);
153
+ session.addTrackConf({
154
+ trackId: 'testConfig',
155
+ name: 'Foo Track',
156
+ assemblyNames: ['volMyt1'],
157
+ type: 'BasicTrack',
158
+ adapter: {
159
+ type: 'FromConfigAdapter',
160
+ features: []
161
+ }
162
+ });
163
+ session.addTrackConf({
164
+ trackId: 'testConfig2',
165
+ name: 'Bar Track',
166
+ assemblyNames: ['volMyt1'],
167
+ type: 'BasicTrack',
168
+ adapter: {
169
+ type: 'FromConfigAdapter',
170
+ features: []
171
+ }
172
+ });
173
+ session.addView('LinearGenomeView', {
174
+ id: 'lgv',
175
+ offsetPx: 0,
176
+ bpPerPx: 1,
177
+ displayedRegions: [{
178
+ assemblyName: 'volMyt1',
179
+ refName: 'ctgA',
180
+ start: 0,
181
+ end: 100
182
+ }, {
183
+ assemblyName: 'volMyt1',
184
+ refName: 'ctgB',
185
+ start: 1000,
186
+ end: 2000
187
+ }],
188
+ tracks: [{
189
+ id: 'foo',
190
+ type: 'BasicTrack',
191
+ height: 20,
192
+ configuration: 'testConfig',
193
+ displays: [{
194
+ type: 'LinearBareDisplay',
195
+ configuration: 'testConfig-LinearBareDisplay'
196
+ }]
197
+ }, {
198
+ id: 'bar',
199
+ type: 'BasicTrack',
200
+ height: 20,
201
+ configuration: 'testConfig2',
202
+ displays: [{
203
+ type: 'LinearBareDisplay',
204
+ configuration: 'testConfig2-LinearBareDisplay'
205
+ }]
206
+ }]
207
+ });
208
+ model = session.views[0];
209
+ model.setWidth(800);
210
+ _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_LinearGenomeView["default"], {
211
+ model: model
212
+ })), container = _render3.container, findByText = _render3.findByText, findAllByTestId = _render3.findAllByTestId;
213
+ _context3.next = 10;
214
+ return findByText('Foo Track');
215
+
216
+ case 10:
217
+ _context3.next = 12;
218
+ return findByText('798 bp');
219
+
220
+ case 12:
221
+ _context3.next = 14;
222
+ return findAllByTestId('svgfeatures');
223
+
224
+ case 14:
225
+ expect(container.firstChild).toMatchSnapshot();
226
+
227
+ case 15:
228
+ case "end":
229
+ return _context3.stop();
230
+ }
231
+ }
232
+ }, _callee3);
233
+ })));
234
+ });