@jbrowse/plugin-variants 1.7.11 → 2.0.0

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 (107) hide show
  1. package/dist/ChordVariantDisplay/index.d.ts +2 -1
  2. package/dist/ChordVariantDisplay/index.js +19 -31
  3. package/dist/ChordVariantDisplay/index.js.map +1 -0
  4. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +94 -2
  5. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js +39 -71
  6. package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map +1 -0
  7. package/dist/LinearVariantDisplay/configSchema.js +9 -16
  8. package/dist/LinearVariantDisplay/configSchema.js.map +1 -0
  9. package/dist/LinearVariantDisplay/index.js +10 -22
  10. package/dist/LinearVariantDisplay/index.js.map +1 -0
  11. package/dist/LinearVariantDisplay/model.d.ts +17 -12
  12. package/dist/LinearVariantDisplay/model.js +83 -73
  13. package/dist/LinearVariantDisplay/model.js.map +1 -0
  14. package/dist/StructuralVariantChordRenderer/ReactComponent.js +193 -214
  15. package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +1 -0
  16. package/dist/StructuralVariantChordRenderer/index.js +36 -46
  17. package/dist/StructuralVariantChordRenderer/index.js.map +1 -0
  18. package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts +1 -1
  19. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +95 -119
  20. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -0
  21. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +193 -240
  22. package/dist/VariantFeatureWidget/VariantFeatureWidget.js.map +1 -0
  23. package/dist/VariantFeatureWidget/index.d.ts +3 -3
  24. package/dist/VariantFeatureWidget/index.js +14 -22
  25. package/dist/VariantFeatureWidget/index.js.map +1 -0
  26. package/dist/VcfAdapter/VcfAdapter.js +232 -372
  27. package/dist/VcfAdapter/VcfAdapter.js.map +1 -0
  28. package/dist/VcfAdapter/configSchema.js +9 -21
  29. package/dist/VcfAdapter/configSchema.js.map +1 -0
  30. package/dist/VcfAdapter/index.js +8 -14
  31. package/dist/VcfAdapter/index.js.map +1 -0
  32. package/dist/VcfTabixAdapter/VcfFeature.js +203 -246
  33. package/dist/VcfTabixAdapter/VcfFeature.js.map +1 -0
  34. package/dist/VcfTabixAdapter/VcfTabixAdapter.js +237 -374
  35. package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -0
  36. package/dist/VcfTabixAdapter/configSchema.js +23 -36
  37. package/dist/VcfTabixAdapter/configSchema.js.map +1 -0
  38. package/dist/VcfTabixAdapter/index.js +8 -14
  39. package/dist/VcfTabixAdapter/index.js.map +1 -0
  40. package/dist/index.js +160 -203
  41. package/dist/index.js.map +1 -0
  42. package/esm/ChordVariantDisplay/index.d.ts +4 -0
  43. package/esm/ChordVariantDisplay/index.js +16 -0
  44. package/esm/ChordVariantDisplay/index.js.map +1 -0
  45. package/esm/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +97 -0
  46. package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js +40 -0
  47. package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js.map +1 -0
  48. package/esm/LinearVariantDisplay/configSchema.d.ts +5 -0
  49. package/esm/LinearVariantDisplay/configSchema.js +7 -0
  50. package/esm/LinearVariantDisplay/configSchema.js.map +1 -0
  51. package/esm/LinearVariantDisplay/index.d.ts +2 -0
  52. package/esm/LinearVariantDisplay/index.js +3 -0
  53. package/esm/LinearVariantDisplay/index.js.map +1 -0
  54. package/esm/LinearVariantDisplay/model.d.ts +212 -0
  55. package/esm/LinearVariantDisplay/model.js +34 -0
  56. package/esm/LinearVariantDisplay/model.js.map +1 -0
  57. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +24 -0
  58. package/esm/StructuralVariantChordRenderer/ReactComponent.js +133 -0
  59. package/esm/StructuralVariantChordRenderer/ReactComponent.js.map +1 -0
  60. package/esm/StructuralVariantChordRenderer/index.d.ts +3 -0
  61. package/esm/StructuralVariantChordRenderer/index.js +33 -0
  62. package/esm/StructuralVariantChordRenderer/index.js.map +1 -0
  63. package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts +10 -0
  64. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +58 -0
  65. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -0
  66. package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +4 -0
  67. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +129 -0
  68. package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map +1 -0
  69. package/esm/VariantFeatureWidget/index.d.ts +37 -0
  70. package/esm/VariantFeatureWidget/index.js +12 -0
  71. package/esm/VariantFeatureWidget/index.js.map +1 -0
  72. package/esm/VcfAdapter/VcfAdapter.d.ts +24 -0
  73. package/esm/VcfAdapter/VcfAdapter.js +99 -0
  74. package/esm/VcfAdapter/VcfAdapter.js.map +1 -0
  75. package/esm/VcfAdapter/configSchema.d.ts +2 -0
  76. package/esm/VcfAdapter/configSchema.js +8 -0
  77. package/esm/VcfAdapter/configSchema.js.map +1 -0
  78. package/esm/VcfAdapter/index.d.ts +1 -0
  79. package/esm/VcfAdapter/index.js +2 -0
  80. package/esm/VcfAdapter/index.js.map +1 -0
  81. package/esm/VcfTabixAdapter/VcfFeature.d.ts +59 -0
  82. package/esm/VcfTabixAdapter/VcfFeature.js +184 -0
  83. package/esm/VcfTabixAdapter/VcfFeature.js.map +1 -0
  84. package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts +35 -0
  85. package/esm/VcfTabixAdapter/VcfTabixAdapter.js +112 -0
  86. package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -0
  87. package/esm/VcfTabixAdapter/configSchema.d.ts +2 -0
  88. package/esm/VcfTabixAdapter/configSchema.js +23 -0
  89. package/esm/VcfTabixAdapter/configSchema.js.map +1 -0
  90. package/esm/VcfTabixAdapter/index.d.ts +1 -0
  91. package/esm/VcfTabixAdapter/index.js +2 -0
  92. package/esm/VcfTabixAdapter/index.js.map +1 -0
  93. package/esm/index.d.ts +7 -0
  94. package/esm/index.js +110 -0
  95. package/esm/index.js.map +1 -0
  96. package/package.json +20 -11
  97. package/src/ChordVariantDisplay/index.ts +4 -4
  98. package/src/ChordVariantDisplay/models/ChordVariantDisplay.js +7 -8
  99. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +8 -9
  100. package/src/VariantFeatureWidget/VariantFeatureWidget.tsx +2 -3
  101. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap +52 -57
  102. package/dist/LinearVariantDisplay/configSchema.test.js +0 -92
  103. package/dist/VariantFeatureWidget/VariantFeatureWidget.test.js +0 -56
  104. package/dist/VcfAdapter/VcfAdapter.test.js +0 -55
  105. package/dist/VcfTabixAdapter/VcfFeature.test.js +0 -106
  106. package/dist/VcfTabixAdapter/VcfTabixAdapter.test.js +0 -99
  107. package/dist/index.test.js +0 -37
@@ -1,228 +1,207 @@
1
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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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- var _typeof = require("@babel/runtime/helpers/typeof");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ var desc = Object.getOwnPropertyDescriptor(m, k);
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+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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+ desc = { enumerable: true, get: function() { return m[k]; } };
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+ }
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+ Object.defineProperty(o, k2, desc);
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+ }) : (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ o[k2] = m[k];
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+ }));
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+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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+ Object.defineProperty(o, "default", { enumerable: true, value: v });
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+ }) : function(o, v) {
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+ o["default"] = v;
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  });
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- exports.default = void 0;
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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 _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 _configuration = require("@jbrowse/core/configuration");
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-
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- var _mst = require("@jbrowse/core/util/types/mst");
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-
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- var _vcf = require("@gmod/vcf");
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-
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- var _propTypes = _interopRequireDefault(require("prop-types"));
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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 || _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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-
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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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-
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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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-
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- function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
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-
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+ var __importStar = (this && this.__importStar) || function (mod) {
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+ if (mod && mod.__esModule) return mod;
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+ var result = {};
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+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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+ __setModuleDefault(result, mod);
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+ return result;
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+ };
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+ var __read = (this && this.__read) || function (o, n) {
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+ var m = typeof Symbol === "function" && o[Symbol.iterator];
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+ if (!m) return o;
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+ var i = m.call(o), r, ar = [], e;
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+ try {
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+ while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
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+ }
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+ catch (error) { e = { error: error }; }
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+ finally {
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+ try {
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+ if (r && !r.done && (m = i["return"])) m.call(i);
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+ }
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+ finally { if (e) throw e.error; }
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+ }
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+ return ar;
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+ };
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+ var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
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+ if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
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+ if (ar || !(i in from)) {
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+ if (!ar) ar = Array.prototype.slice.call(from, 0, i);
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+ ar[i] = from[i];
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+ }
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+ }
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+ return to.concat(ar || Array.prototype.slice.call(from));
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+ };
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+ var __values = (this && this.__values) || function(o) {
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+ var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
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+ if (m) return m.call(o);
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+ if (o && typeof o.length === "number") return {
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+ next: function () {
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+ if (o && i >= o.length) o = void 0;
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+ return { value: o && o[i++], done: !o };
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+ }
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+ };
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+ throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
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+ };
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ var react_1 = __importStar(require("react"));
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+ var mobx_react_1 = require("mobx-react");
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+ var util_1 = require("@jbrowse/core/util");
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+ var configuration_1 = require("@jbrowse/core/configuration");
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+ var mst_1 = require("@jbrowse/core/util/types/mst");
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+ var vcf_1 = require("@gmod/vcf");
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+ var prop_types_1 = __importDefault(require("prop-types"));
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  function bpToRadians(block, pos) {
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- var blockStart = block.region.elided ? 0 : block.region.start;
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- var blockEnd = block.region.elided ? 0 : block.region.end;
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- var bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
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- var radians = bpOffset / block.bpPerRadian + block.startRadians;
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- return radians;
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+ var blockStart = block.region.elided ? 0 : block.region.start;
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+ var blockEnd = block.region.elided ? 0 : block.region.end;
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+ var bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
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+ var radians = bpOffset / block.bpPerRadian + block.startRadians;
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+ return radians;
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  }
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-
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- var Chord = (0, _mobxReact.observer)(function Chord(_ref) {
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- var _feature$get;
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-
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- var feature = _ref.feature,
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- blocksForRefs = _ref.blocksForRefs,
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- radius = _ref.radius,
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- config = _ref.config,
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- bezierRadius = _ref.bezierRadius,
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- selected = _ref.selected,
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- _onClick = _ref.onClick;
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- // find the blocks that our start and end points belong to
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- var startBlock = blocksForRefs[feature.get('refName')];
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-
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- if (!startBlock) {
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+ var Chord = (0, mobx_react_1.observer)(function Chord(_a) {
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+ var _b;
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+ var _c, _d, _e, _f, _g;
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+ var feature = _a.feature, blocksForRefs = _a.blocksForRefs, radius = _a.radius, config = _a.config, bezierRadius = _a.bezierRadius, selected = _a.selected, onClick = _a.onClick;
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+ // find the blocks that our start and end points belong to
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+ var startBlock = blocksForRefs[feature.get('refName')];
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+ if (!startBlock) {
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+ return null;
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+ }
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+ var svType;
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+ if (feature.get('INFO')) {
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+ ;
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+ _b = __read(feature.get('INFO').SVTYPE || [], 1), svType = _b[0];
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+ }
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+ else if (feature.get('mate')) {
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+ svType = 'mate';
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+ }
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+ var endPosition;
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+ var endBlock;
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+ var alt = (_c = feature.get('ALT')) === null || _c === void 0 ? void 0 : _c[0];
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+ var bnd = alt && (0, vcf_1.parseBreakend)(alt);
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+ if (bnd) {
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+ // VCF BND
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+ var matePosition = bnd.MatePosition.split(':');
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+ endPosition = +matePosition[1];
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+ endBlock = blocksForRefs[matePosition[0]];
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+ }
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+ else if (alt === '<TRA>') {
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+ // VCF TRA
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+ var chr2 = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.CHR2) === null || _e === void 0 ? void 0 : _e[0];
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+ var end = (_g = (_f = feature.get('INFO')) === null || _f === void 0 ? void 0 : _f.END) === null || _g === void 0 ? void 0 : _g[0];
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+ endPosition = parseInt(end, 10);
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+ endBlock = blocksForRefs[chr2];
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+ }
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+ else if (svType === 'mate') {
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+ // generic simplefeatures arcs
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+ var mate = feature.get('mate');
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+ var chr2 = mate.refName;
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+ endPosition = mate.start;
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+ endBlock = blocksForRefs[chr2];
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+ }
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+ if (endBlock) {
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+ var startPos = feature.get('start');
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+ var startRadians = bpToRadians(startBlock, startPos);
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+ var endRadians = bpToRadians(endBlock, endPosition);
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+ var startXY = (0, util_1.polarToCartesian)(radius, startRadians);
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+ var endXY = (0, util_1.polarToCartesian)(radius, endRadians);
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+ var controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
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+ var strokeColor_1 = selected
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+ ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature: feature })
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+ : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature: feature });
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+ var hoverStrokeColor_1 = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
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+ feature: feature,
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+ });
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+ return (react_1.default.createElement("path", { "data-testid": "chord-".concat(feature.id()), d: __spreadArray(__spreadArray(__spreadArray(__spreadArray(['M'], __read(startXY), false), ['Q'], false), __read(controlXY), false), __read(endXY), false).join(' '), style: { stroke: strokeColor_1 }, onClick: function (evt) {
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+ return onClick(feature, startBlock.region, endBlock.region, evt);
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+ }, onMouseOver: function (evt) {
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+ if (!selected) {
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+ evt.target.style.stroke = hoverStrokeColor_1;
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+ evt.target.style.strokeWidth = 3;
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+ }
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+ }, onMouseOut: function (evt) {
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+ if (!selected) {
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+ evt.target.style.stroke = strokeColor_1;
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+ evt.target.style.strokeWidth = 1;
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+ }
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+ } }));
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+ }
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  return null;
63
- }
64
-
65
- var svType;
66
-
67
- if (feature.get('INFO')) {
68
- ;
69
-
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- var _ref2 = feature.get('INFO').SVTYPE || [];
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-
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- var _ref3 = (0, _slicedToArray2.default)(_ref2, 1);
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-
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- svType = _ref3[0];
75
- } else if (feature.get('mate')) {
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- svType = 'mate';
77
- }
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-
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- var endPosition;
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- var endBlock;
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- var alt = (_feature$get = feature.get('ALT')) === null || _feature$get === void 0 ? void 0 : _feature$get[0];
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- var bnd = alt && (0, _vcf.parseBreakend)(alt);
83
-
84
- if (bnd) {
85
- // VCF BND
86
- var matePosition = bnd.MatePosition.split(':');
87
- endPosition = +matePosition[1];
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- endBlock = blocksForRefs[matePosition[0]];
89
- } else if (alt === '<TRA>') {
90
- var _feature$get2, _feature$get2$CHR, _feature$get3, _feature$get3$END;
91
-
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- // VCF TRA
93
- var chr2 = (_feature$get2 = feature.get('INFO')) === null || _feature$get2 === void 0 ? void 0 : (_feature$get2$CHR = _feature$get2.CHR2) === null || _feature$get2$CHR === void 0 ? void 0 : _feature$get2$CHR[0];
94
- var end = (_feature$get3 = feature.get('INFO')) === null || _feature$get3 === void 0 ? void 0 : (_feature$get3$END = _feature$get3.END) === null || _feature$get3$END === void 0 ? void 0 : _feature$get3$END[0];
95
- endPosition = parseInt(end, 10);
96
- endBlock = blocksForRefs[chr2];
97
- } else if (svType === 'mate') {
98
- // generic simplefeatures arcs
99
- var mate = feature.get('mate');
100
- var _chr = mate.refName;
101
- endPosition = mate.start;
102
- endBlock = blocksForRefs[_chr];
103
- }
104
-
105
- if (endBlock) {
106
- var startPos = feature.get('start');
107
- var startRadians = bpToRadians(startBlock, startPos);
108
- var endRadians = bpToRadians(endBlock, endPosition);
109
- var startXY = (0, _util.polarToCartesian)(radius, startRadians);
110
- var endXY = (0, _util.polarToCartesian)(radius, endRadians);
111
- var controlXY = (0, _util.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
112
- var strokeColor = selected ? (0, _configuration.readConfObject)(config, 'strokeColorSelected', {
113
- feature: feature
114
- }) : (0, _configuration.readConfObject)(config, 'strokeColor', {
115
- feature: feature
116
- });
117
- var hoverStrokeColor = (0, _configuration.readConfObject)(config, 'strokeColorHover', {
118
- feature: feature
119
- });
120
- return /*#__PURE__*/_react.default.createElement("path", {
121
- "data-testid": "chord-".concat(feature.id()),
122
- d: ['M'].concat((0, _toConsumableArray2.default)(startXY), ['Q'], (0, _toConsumableArray2.default)(controlXY), (0, _toConsumableArray2.default)(endXY)).join(' '),
123
- style: {
124
- stroke: strokeColor
125
- },
126
- onClick: function onClick(evt) {
127
- return _onClick(feature, startBlock.region, endBlock.region, evt);
128
- },
129
- onMouseOver: function onMouseOver(evt) {
130
- if (!selected) {
131
- evt.target.style.stroke = hoverStrokeColor;
132
- evt.target.style.strokeWidth = 3;
133
- }
134
- },
135
- onMouseOut: function onMouseOut(evt) {
136
- if (!selected) {
137
- evt.target.style.stroke = strokeColor;
138
- evt.target.style.strokeWidth = 1;
139
- }
140
- }
141
- });
142
- }
143
-
144
- return null;
145
148
  });
146
-
147
149
  function StructuralVariantChords(props) {
148
- var features = props.features,
149
- config = props.config,
150
- displayModel = props.displayModel,
151
- blockDefinitions = props.blockDefinitions,
152
- radius = props.radius,
153
- bezierRadius = props.bezierRadius,
154
- selectedFeatureId = props.displayModel.selectedFeatureId,
155
- onChordClick = props.onChordClick; // make a map of refName -> blockDefinition
156
-
157
- var blocksForRefsMemo = (0, _react.useMemo)(function () {
158
- var blocksForRefs = {};
159
- blockDefinitions.forEach(function (block) {
160
- var regions = block.region.elided ? block.region.regions : [block.region];
161
- regions.forEach(function (region) {
162
- blocksForRefs[region.refName] = block;
163
- });
164
- });
165
- return blocksForRefs;
166
- }, [blockDefinitions]); // console.log(blocksForRefs)
167
-
168
- var chords = [];
169
-
170
- var _iterator = _createForOfIteratorHelper(features),
171
- _step;
172
-
173
- try {
174
- for (_iterator.s(); !(_step = _iterator.n()).done;) {
175
- var _step$value = (0, _slicedToArray2.default)(_step.value, 2),
176
- id = _step$value[0],
177
- feature = _step$value[1];
178
-
179
- var selected = String(selectedFeatureId) === String(feature.id());
180
- chords.push( /*#__PURE__*/_react.default.createElement(Chord, {
181
- key: id,
182
- feature: feature,
183
- config: config,
184
- displayModel: displayModel,
185
- radius: radius,
186
- bezierRadius: bezierRadius,
187
- blocksForRefs: blocksForRefsMemo,
188
- selected: selected,
189
- onClick: onChordClick
190
- }));
150
+ var e_1, _a;
151
+ var features = props.features, config = props.config, displayModel = props.displayModel, blockDefinitions = props.blockDefinitions, radius = props.radius, bezierRadius = props.bezierRadius, selectedFeatureId = props.displayModel.selectedFeatureId, onChordClick = props.onChordClick;
152
+ // make a map of refName -> blockDefinition
153
+ var blocksForRefsMemo = (0, react_1.useMemo)(function () {
154
+ var blocksForRefs = {};
155
+ blockDefinitions.forEach(function (block) {
156
+ var regions = block.region.elided
157
+ ? block.region.regions
158
+ : [block.region];
159
+ regions.forEach(function (region) {
160
+ blocksForRefs[region.refName] = block;
161
+ });
162
+ });
163
+ return blocksForRefs;
164
+ }, [blockDefinitions]);
165
+ // console.log(blocksForRefs)
166
+ var chords = [];
167
+ try {
168
+ for (var features_1 = __values(features), features_1_1 = features_1.next(); !features_1_1.done; features_1_1 = features_1.next()) {
169
+ var _b = __read(features_1_1.value, 2), id = _b[0], feature = _b[1];
170
+ var selected = String(selectedFeatureId) === String(feature.id());
171
+ chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
172
+ }
191
173
  }
192
- } catch (err) {
193
- _iterator.e(err);
194
- } finally {
195
- _iterator.f();
196
- }
197
-
198
- var trackStyleId = "chords-".concat(displayModel.id);
199
- return /*#__PURE__*/_react.default.createElement("g", {
200
- id: trackStyleId,
201
- "data-testid": "structuralVariantChordRenderer"
202
- }, /*#__PURE__*/_react.default.createElement("style", {
203
- // eslint-disable-next-line react/no-danger
204
- dangerouslySetInnerHTML: {
205
- __html: "\n #".concat(trackStyleId, " > path {\n cursor: crosshair;\n fill: none;\n }\n")
174
+ catch (e_1_1) { e_1 = { error: e_1_1 }; }
175
+ finally {
176
+ try {
177
+ if (features_1_1 && !features_1_1.done && (_a = features_1.return)) _a.call(features_1);
178
+ }
179
+ finally { if (e_1) throw e_1.error; }
206
180
  }
207
- }), chords);
181
+ var trackStyleId = "chords-".concat(displayModel.id);
182
+ return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
183
+ react_1.default.createElement("style", {
184
+ // eslint-disable-next-line react/no-danger
185
+ dangerouslySetInnerHTML: {
186
+ __html: "\n #".concat(trackStyleId, " > path {\n cursor: crosshair;\n fill: none;\n }\n"),
187
+ } }),
188
+ chords));
208
189
  }
209
-
210
190
  StructuralVariantChords.propTypes = {
211
- features: _propTypes.default.instanceOf(Map).isRequired,
212
- config: _mst.PropTypes.ConfigSchema.isRequired,
213
- displayModel: _mobxReact.PropTypes.objectOrObservableObject,
214
- blockDefinitions: _propTypes.default.arrayOf(_mobxReact.PropTypes.objectOrObservableObject).isRequired,
215
- radius: _propTypes.default.number.isRequired,
216
- bezierRadius: _propTypes.default.number.isRequired,
217
- selectedFeatureId: _propTypes.default.string,
218
- onChordClick: _propTypes.default.oneOfType([_propTypes.default.func, _propTypes.default.string])
191
+ features: prop_types_1.default.instanceOf(Map).isRequired,
192
+ config: mst_1.PropTypes.ConfigSchema.isRequired,
193
+ displayModel: mobx_react_1.PropTypes.objectOrObservableObject,
194
+ blockDefinitions: prop_types_1.default.arrayOf(mobx_react_1.PropTypes.objectOrObservableObject)
195
+ .isRequired,
196
+ radius: prop_types_1.default.number.isRequired,
197
+ bezierRadius: prop_types_1.default.number.isRequired,
198
+ selectedFeatureId: prop_types_1.default.string,
199
+ onChordClick: prop_types_1.default.oneOfType([prop_types_1.default.func, prop_types_1.default.string]),
219
200
  };
220
201
  StructuralVariantChords.defaultProps = {
221
- displayModel: undefined,
222
- selectedFeatureId: '',
223
- onChordClick: undefined
202
+ displayModel: undefined,
203
+ selectedFeatureId: '',
204
+ onChordClick: undefined,
224
205
  };
225
-
226
- var _default = (0, _mobxReact.observer)(StructuralVariantChords);
227
-
228
- exports.default = _default;
206
+ exports.default = (0, mobx_react_1.observer)(StructuralVariantChords);
207
+ //# sourceMappingURL=ReactComponent.js.map
@@ -0,0 +1 @@
1
+ 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@@ -1,48 +1,38 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
7
- });
8
- exports.default = void 0;
9
-
10
- var _CircularChordRendererType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
11
-
12
- var _configuration = require("@jbrowse/core/configuration");
13
-
14
- var _ReactComponent = _interopRequireDefault(require("./ReactComponent"));
15
-
16
- var ChordRendererConfigF = function ChordRendererConfigF(pluginManager) {
17
- var configSchema = (0, _configuration.ConfigurationSchema)('StructuralVariantChordRenderer', {
18
- strokeColor: {
19
- type: 'color',
20
- description: 'the line color of each arc',
21
- defaultValue: 'rgba(255,133,0,0.32)',
22
- contextVariable: ['feature']
23
- },
24
- strokeColorSelected: {
25
- type: 'color',
26
- description: 'the line color of an arc that has been selected',
27
- defaultValue: 'black',
28
- contextVariable: ['feature']
29
- },
30
- strokeColorHover: {
31
- type: 'color',
32
- description: 'the line color of an arc that is being hovered over with the mouse',
33
- defaultValue: '#555',
34
- contextVariable: ['feature']
35
- }
36
- }, {
37
- explicitlyTyped: true
38
- });
39
- return new _CircularChordRendererType.default({
40
- name: 'StructuralVariantChordRenderer',
41
- ReactComponent: _ReactComponent.default,
42
- configSchema: configSchema,
43
- pluginManager: pluginManager
44
- });
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
45
4
  };
46
-
47
- var _default = ChordRendererConfigF;
48
- exports.default = _default;
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ var CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
7
+ var configuration_1 = require("@jbrowse/core/configuration");
8
+ var ReactComponent_1 = __importDefault(require("./ReactComponent"));
9
+ var ChordRendererConfigF = function (pluginManager) {
10
+ var configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
11
+ strokeColor: {
12
+ type: 'color',
13
+ description: 'the line color of each arc',
14
+ defaultValue: 'rgba(255,133,0,0.32)',
15
+ contextVariable: ['feature'],
16
+ },
17
+ strokeColorSelected: {
18
+ type: 'color',
19
+ description: 'the line color of an arc that has been selected',
20
+ defaultValue: 'black',
21
+ contextVariable: ['feature'],
22
+ },
23
+ strokeColorHover: {
24
+ type: 'color',
25
+ description: 'the line color of an arc that is being hovered over with the mouse',
26
+ defaultValue: '#555',
27
+ contextVariable: ['feature'],
28
+ },
29
+ }, { explicitlyTyped: true });
30
+ return new CircularChordRendererType_1.default({
31
+ name: 'StructuralVariantChordRenderer',
32
+ ReactComponent: ReactComponent_1.default,
33
+ configSchema: configSchema,
34
+ pluginManager: pluginManager,
35
+ });
36
+ };
37
+ exports.default = ChordRendererConfigF;
38
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.js"],"names":[],"mappings":";;;;;AAAA,sIAAuG;AACvG,6DAAiE;AACjE,oEAA6C;AAE7C,IAAM,oBAAoB,GAAG,UAAA,aAAa;IACxC,IAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,mCAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc,0BAAA;QACd,YAAY,cAAA;QACZ,aAAa,eAAA;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
@@ -1,5 +1,5 @@
1
1
  /// <reference types="react" />
2
- import { Feature } from '@jbrowse/core/util/simpleFeature';
2
+ import { Feature } from '@jbrowse/core/util';
3
3
  declare function BreakendOptionDialog({ model, handleClose, feature, viewType, }: {
4
4
  model: any;
5
5
  handleClose: () => void;