@jbrowse/core 1.5.3 → 1.5.7

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Files changed (150) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +4 -2
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +113 -100
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +59 -66
  4. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +9 -9
  5. package/BaseFeatureWidget/index.js +1 -1
  6. package/BaseFeatureWidget/index.test.js +3 -3
  7. package/BaseFeatureWidget/types.js +5 -1
  8. package/BaseFeatureWidget/util.js +9 -13
  9. package/CorePlugin.js +19 -31
  10. package/Plugin.js +11 -13
  11. package/PluginLoader.js +33 -38
  12. package/PluginManager.d.ts +5 -5
  13. package/PluginManager.js +55 -60
  14. package/ReExports/index.js +4 -4
  15. package/ReExports/list.js +2 -2
  16. package/ReExports/material-ui-colors.js +20 -20
  17. package/ReExports/modules.js +47 -51
  18. package/TextSearch/BaseResults.js +24 -34
  19. package/TextSearch/BaseResults.test.js +3 -7
  20. package/TextSearch/TextSearchManager.d.ts +1 -1
  21. package/TextSearch/TextSearchManager.js +15 -18
  22. package/assemblyManager/assembly.js +34 -39
  23. package/assemblyManager/assemblyConfigSchema.js +2 -2
  24. package/assemblyManager/assemblyManager.js +16 -20
  25. package/assemblyManager/index.js +3 -3
  26. package/configuration/configurationSchema.js +17 -19
  27. package/configuration/configurationSlot.js +11 -11
  28. package/configuration/configurationSlot.test.js +5 -5
  29. package/configuration/util.js +5 -5
  30. package/data_adapters/BaseAdapter.d.ts +4 -4
  31. package/data_adapters/BaseAdapter.js +36 -47
  32. package/data_adapters/BaseAdapter.test.js +24 -30
  33. package/data_adapters/CytobandAdapter.js +16 -22
  34. package/data_adapters/dataAdapterCache.js +9 -9
  35. package/package.json +7 -7
  36. package/pluggableElementTypes/AdapterType.js +22 -29
  37. package/pluggableElementTypes/ConnectionType.js +18 -26
  38. package/pluggableElementTypes/DisplayType.js +17 -25
  39. package/pluggableElementTypes/InternetAccountType.js +14 -22
  40. package/pluggableElementTypes/PluggableElementBase.js +9 -10
  41. package/pluggableElementTypes/RpcMethodType.js +40 -56
  42. package/pluggableElementTypes/RpcMethodType.test.js +17 -23
  43. package/pluggableElementTypes/TextSearchAdapterType.js +15 -23
  44. package/pluggableElementTypes/TrackType.js +15 -25
  45. package/pluggableElementTypes/ViewType.js +15 -25
  46. package/pluggableElementTypes/WidgetType.js +17 -25
  47. package/pluggableElementTypes/index.js +11 -11
  48. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +5 -5
  49. package/pluggableElementTypes/models/BaseDisplayModel.js +5 -8
  50. package/pluggableElementTypes/models/BaseTrackModel.js +8 -11
  51. package/pluggableElementTypes/models/BaseViewModel.js +3 -3
  52. package/pluggableElementTypes/models/InternetAccountModel.js +5 -5
  53. package/pluggableElementTypes/models/baseConnectionConfig.js +2 -2
  54. package/pluggableElementTypes/models/baseTrackConfig.js +4 -7
  55. package/pluggableElementTypes/models/index.js +4 -4
  56. package/pluggableElementTypes/renderers/BoxRendererType.js +39 -49
  57. package/pluggableElementTypes/renderers/CircularChordRendererType.js +12 -16
  58. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +27 -35
  59. package/pluggableElementTypes/renderers/FeatureRendererType.js +36 -46
  60. package/pluggableElementTypes/renderers/RendererType.js +21 -31
  61. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +8 -12
  62. package/pluggableElementTypes/renderers/ServerSideRendererType.js +31 -44
  63. package/pluggableElementTypes/renderers/index.js +8 -8
  64. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +8 -10
  65. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +2 -2
  66. package/rpc/BaseRpcDriver.d.ts +1 -1
  67. package/rpc/BaseRpcDriver.js +37 -42
  68. package/rpc/BaseRpcDriver.test.js +49 -63
  69. package/rpc/MainThreadRpcDriver.js +22 -32
  70. package/rpc/RpcManager.d.ts +2 -2
  71. package/rpc/RpcManager.js +20 -25
  72. package/rpc/WebWorkerRpcDriver.d.ts +2 -2
  73. package/rpc/WebWorkerRpcDriver.js +29 -40
  74. package/rpc/configSchema.js +2 -2
  75. package/rpc/coreRpcMethods.js +72 -82
  76. package/rpc/remoteAbortSignals.js +3 -3
  77. package/ui/AboutDialog.js +17 -21
  78. package/ui/App.js +38 -42
  79. package/ui/AssemblySelector.js +5 -5
  80. package/ui/Drawer.js +7 -7
  81. package/ui/DrawerWidget.js +33 -37
  82. package/ui/DropDownMenu.js +9 -21
  83. package/ui/EditableTypography.js +19 -30
  84. package/ui/ErrorMessage.js +5 -5
  85. package/ui/FactoryResetDialog.js +8 -8
  86. package/ui/FatalErrorDialog.js +12 -29
  87. package/ui/FatalErrorDialog.test.js +11 -11
  88. package/ui/FileSelector/FileSelector.js +32 -42
  89. package/ui/FileSelector/LocalFileChooser.js +9 -9
  90. package/ui/FileSelector/UrlChooser.js +4 -4
  91. package/ui/FileSelector/index.js +4 -4
  92. package/ui/Icons.js +9 -9
  93. package/ui/Logo.js +19 -19
  94. package/ui/Menu.js +35 -46
  95. package/ui/NewSessionCards.js +19 -29
  96. package/ui/PrerenderedCanvas.js +10 -27
  97. package/ui/ResizeHandle.js +10 -17
  98. package/ui/SanitizedHTML.js +5 -5
  99. package/ui/SanitizedHTML.test.js +4 -4
  100. package/ui/Snackbar.js +12 -16
  101. package/ui/SnackbarModel.js +1 -1
  102. package/ui/Tooltip.js +7 -11
  103. package/ui/ViewContainer.js +20 -30
  104. package/ui/index.js +13 -17
  105. package/ui/theme.js +11 -15
  106. package/util/Base1DViewModel.js +10 -14
  107. package/util/Base1DViewModel.test.js +5 -5
  108. package/util/QuickLRU.js +27 -31
  109. package/util/aborting.js +16 -24
  110. package/util/analytics.js +7 -7
  111. package/util/blockTypes.js +36 -49
  112. package/util/calculateDynamicBlocks.js +4 -4
  113. package/util/calculateDynamicBlocks.test.js +10 -14
  114. package/util/calculateStaticBlocks.js +1 -1
  115. package/util/calculateStaticBlocks.test.js +15 -15
  116. package/util/compositeMap.js +30 -41
  117. package/util/idMaker.js +4 -4
  118. package/util/index.js +35 -48
  119. package/util/index.test.js +7 -11
  120. package/util/io/RemoteFileWithRangeCache.js +29 -41
  121. package/util/io/index.js +6 -6
  122. package/util/jexl.js +8 -5
  123. package/util/jexlStrings.js +2 -2
  124. package/util/jexlStrings.test.js +2 -2
  125. package/util/layouts/BaseLayout.js +5 -1
  126. package/util/layouts/GranularRectLayout.js +28 -34
  127. package/util/layouts/GranularRectLayout.test.js +10 -10
  128. package/util/layouts/MultiLayout.d.ts +1 -1
  129. package/util/layouts/MultiLayout.js +14 -21
  130. package/util/layouts/PrecomputedLayout.js +14 -16
  131. package/util/layouts/PrecomputedMultiLayout.js +18 -22
  132. package/util/layouts/SceneGraph.d.ts +3 -3
  133. package/util/layouts/SceneGraph.js +17 -31
  134. package/util/layouts/index.js +6 -6
  135. package/util/mst-reflection.d.ts +3 -3
  136. package/util/offscreenCanvasPonyfill.js +29 -31
  137. package/util/offscreenCanvasUtils.js +6 -6
  138. package/util/range.test.js +20 -20
  139. package/util/rxjs.js +2 -2
  140. package/util/simpleFeature.js +19 -24
  141. package/util/simpleFeature.test.js +3 -3
  142. package/util/stats.js +7 -11
  143. package/util/stats.test.js +15 -15
  144. package/util/types/index.d.ts +2 -0
  145. package/util/types/index.js +29 -36
  146. package/util/types/mst.js +15 -19
  147. package/util/types/util.js +5 -1
  148. package/util/when.js +6 -6
  149. package/babel.config.d.ts +0 -15
  150. package/babel.config.js +0 -19
@@ -1,64 +1,64 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
- var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
5
+ var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
6
6
 
7
7
  var _range = require("./range");
8
8
 
9
9
  describe('insersection2', function () {
10
10
  var testCases = [{
11
- in: [1, 3, 5, 10],
11
+ "in": [1, 3, 5, 10],
12
12
  out: []
13
13
  }, {
14
- in: [1, 1, 2, 2],
14
+ "in": [1, 1, 2, 2],
15
15
  out: []
16
16
  }, {
17
- in: [1, 2, 1, 2],
17
+ "in": [1, 2, 1, 2],
18
18
  out: [1, 2]
19
19
  }, {
20
- in: [1, 3, 2, 4],
20
+ "in": [1, 3, 2, 4],
21
21
  out: [2, 3]
22
22
  }, {
23
- in: [2, 4, 1, 3],
23
+ "in": [2, 4, 1, 3],
24
24
  out: [2, 3]
25
25
  }, {
26
- in: [2, 4, 1, 4],
26
+ "in": [2, 4, 1, 4],
27
27
  out: [2, 4]
28
28
  }, {
29
- in: [1, 4, 2, 4],
29
+ "in": [1, 4, 2, 4],
30
30
  out: [2, 4]
31
31
  }, {
32
- in: [1, 3, 1, 4],
32
+ "in": [1, 3, 1, 4],
33
33
  out: [1, 3]
34
34
  }, {
35
- in: [1, 4, 1, 3],
35
+ "in": [1, 4, 1, 3],
36
36
  out: [1, 3]
37
37
  }, {
38
- in: [2, 3, 1, 2],
38
+ "in": [2, 3, 1, 2],
39
39
  out: []
40
40
  }, {
41
- in: [1, 2, 2, 3],
41
+ "in": [1, 2, 2, 3],
42
42
  out: []
43
43
  }, {
44
- in: [1, 1, 1, 1],
44
+ "in": [1, 1, 1, 1],
45
45
  out: []
46
46
  }, {
47
- in: [1, 1, 1, 2],
47
+ "in": [1, 1, 1, 2],
48
48
  out: []
49
49
  }, {
50
- in: [1, 2, 1, 1],
50
+ "in": [1, 2, 1, 1],
51
51
  out: []
52
52
  }, {
53
- in: [1, 3, 2, 2],
53
+ "in": [1, 3, 2, 2],
54
54
  out: []
55
55
  }, {
56
- in: [2, 2, 1, 3],
56
+ "in": [2, 2, 1, 3],
57
57
  out: []
58
58
  }];
59
59
  testCases.forEach(function (testcase) {
60
- test("intersection2(".concat(testcase.in, ") -> ").concat(testcase.out), function () {
61
- expect(_range.intersection2.apply(void 0, (0, _toConsumableArray2.default)(testcase.in))).toEqual(testcase.out);
60
+ test("intersection2(".concat(testcase["in"], ") -> ").concat(testcase.out), function () {
61
+ expect(_range.intersection2.apply(void 0, (0, _toConsumableArray2["default"])(testcase["in"]))).toEqual(testcase.out);
62
62
  });
63
63
  });
64
64
  });
package/util/rxjs.js CHANGED
@@ -21,8 +21,8 @@ function ObservableCreate(func, signal) {
21
21
  try {
22
22
  var ret = func(observer); // catch async errors
23
23
 
24
- if (ret && ret.catch) {
25
- ret.catch(function (error) {
24
+ if (ret && ret["catch"]) {
25
+ ret["catch"](function (error) {
26
26
  return observer.error(error);
27
27
  });
28
28
  }
@@ -1,34 +1,30 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports.default = void 0;
8
+ exports["default"] = void 0;
9
9
  exports.isFeature = isFeature;
10
10
 
11
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
+ var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
12
12
 
13
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
13
+ var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
14
14
 
15
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
15
+ var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
16
16
 
17
- var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
18
-
19
- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
20
-
21
- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
17
+ var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
22
18
 
23
19
  /**
24
20
  * Abstract feature object
25
21
  */
26
22
  function isFeature(thing) {
27
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && typeof thing.get === 'function' && typeof thing.id === 'function';
23
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && typeof thing.get === 'function' && typeof thing.id === 'function';
28
24
  }
29
25
 
30
26
  function isSimpleFeatureSerialized(args) {
31
- return 'uniqueId' in args && (0, _typeof2.default)(args.data) !== 'object';
27
+ return 'uniqueId' in args && (0, _typeof2["default"])(args.data) !== 'object';
32
28
  }
33
29
  /**
34
30
  * Simple implementation of a feature object.
@@ -47,11 +43,11 @@ var SimpleFeature = /*#__PURE__*/function () {
47
43
  function SimpleFeature(args) {
48
44
  var _this = this;
49
45
 
50
- (0, _classCallCheck2.default)(this, SimpleFeature);
51
- (0, _defineProperty2.default)(this, "data", void 0);
52
- (0, _defineProperty2.default)(this, "subfeatures", void 0);
53
- (0, _defineProperty2.default)(this, "parentHandle", void 0);
54
- (0, _defineProperty2.default)(this, "uniqueId", void 0);
46
+ (0, _classCallCheck2["default"])(this, SimpleFeature);
47
+ this.data = void 0;
48
+ this.subfeatures = void 0;
49
+ this.parentHandle = void 0;
50
+ this.uniqueId = void 0;
55
51
 
56
52
  if (isSimpleFeatureSerialized(args)) {
57
53
  this.data = args;
@@ -84,7 +80,7 @@ var SimpleFeature = /*#__PURE__*/function () {
84
80
  function (f, i) {
85
81
  return typeof f.get !== 'function' ? new SimpleFeature({
86
82
  id: f.uniqueId || "".concat(id, "-").concat(i),
87
- data: _objectSpread({
83
+ data: (0, _objectSpread2["default"])({
88
84
  strand: _this.data.strand
89
85
  }, f),
90
86
  parent: _this
@@ -99,10 +95,10 @@ var SimpleFeature = /*#__PURE__*/function () {
99
95
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
100
96
 
101
97
 
102
- (0, _createClass2.default)(SimpleFeature, [{
98
+ (0, _createClass2["default"])(SimpleFeature, [{
103
99
  key: "get",
104
100
  value: function get(name) {
105
- return name === 'subfeatures' ? this.subfeatures : this.data[name];
101
+ return name === 'subfeatures' ? this.subfeatures : name === 'parent' ? this.parent() : this.data[name];
106
102
  }
107
103
  /**
108
104
  * Set an item of data.
@@ -153,10 +149,9 @@ var SimpleFeature = /*#__PURE__*/function () {
153
149
  }, {
154
150
  key: "toJSON",
155
151
  value: function toJSON() {
156
- var d = _objectSpread(_objectSpread({}, this.data), {}, {
152
+ var d = (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, this.data), {}, {
157
153
  uniqueId: this.id()
158
154
  });
159
-
160
155
  var p = this.parent();
161
156
 
162
157
  if (p) {
@@ -176,10 +171,10 @@ var SimpleFeature = /*#__PURE__*/function () {
176
171
  }], [{
177
172
  key: "fromJSON",
178
173
  value: function fromJSON(json) {
179
- return new SimpleFeature(_objectSpread({}, json));
174
+ return new SimpleFeature((0, _objectSpread2["default"])({}, json));
180
175
  }
181
176
  }]);
182
177
  return SimpleFeature;
183
178
  }();
184
179
 
185
- exports.default = SimpleFeature;
180
+ exports["default"] = SimpleFeature;
@@ -1,11 +1,11 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  var _simpleFeature = _interopRequireDefault(require("./simpleFeature"));
6
6
 
7
7
  test('can create a simple feature', function () {
8
- var f = new _simpleFeature.default({
8
+ var f = new _simpleFeature["default"]({
9
9
  uniqueId: 'test',
10
10
  start: 100,
11
11
  end: 200
@@ -15,7 +15,7 @@ test('can create a simple feature', function () {
15
15
  expect(f.get('end')).toEqual(200);
16
16
  });
17
17
  test('can create a simple with subfeatures', function () {
18
- var f = new _simpleFeature.default({
18
+ var f = new _simpleFeature["default"]({
19
19
  uniqueId: 'test',
20
20
  start: 100,
21
21
  end: 500,
package/util/stats.js CHANGED
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
@@ -11,18 +11,14 @@ exports.calcStdFromSums = calcStdFromSums;
11
11
  exports.rectifyStats = rectifyStats;
12
12
  exports.scoresToStats = scoresToStats;
13
13
 
14
- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
14
+ var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
15
15
 
16
- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
16
+ var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
17
17
 
18
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
18
+ var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
19
19
 
20
20
  var _operators = require("rxjs/operators");
21
21
 
22
- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
23
-
24
- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
25
-
26
22
  /*
27
23
  * calculate standard deviation using the 'shortcut method' that accepts
28
24
  * the sum and the sum squares of the elements
@@ -62,7 +58,7 @@ function calcStdFromSums(sum, sumSquares, n) {
62
58
 
63
59
 
64
60
  function rectifyStats(s) {
65
- return _objectSpread(_objectSpread({}, s), {}, {
61
+ return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, s), {}, {
66
62
  scoreMean: (s.scoreSum || 0) / (s.featureCount || s.basesCovered || 1),
67
63
  scoreStdDev: calcStdFromSums(s.scoreSum, s.scoreSumSquares, s.featureCount || s.basesCovered),
68
64
  featureDensity: (s.featureCount || 1) / s.basesCovered
@@ -121,10 +117,10 @@ function scoresToStats(_x, _x2) {
121
117
  }
122
118
 
123
119
  function _scoresToStats() {
124
- _scoresToStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(region, features) {
120
+ _scoresToStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(region, features) {
125
121
  var start, end, _yield$features$pipe$, scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount;
126
122
 
127
- return _regenerator.default.wrap(function _callee$(_context) {
123
+ return _index["default"].wrap(function _callee$(_context) {
128
124
  while (1) {
129
125
  switch (_context.prev = _context.next) {
130
126
  case 0:
@@ -1,10 +1,10 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
5
+ var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
6
6
 
7
- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
7
+ var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
8
8
 
9
9
  var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
10
10
 
@@ -45,9 +45,9 @@ test('test rectify', function () {
45
45
  scoreSumSquares: 14
46
46
  }).scoreStdDev).toEqual(1); // calculated from a webapp about sample standard deviations
47
47
  });
48
- test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
48
+ test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
49
49
  var ret;
50
- return _regenerator.default.wrap(function _callee$(_context) {
50
+ return _index["default"].wrap(function _callee$(_context) {
51
51
  while (1) {
52
52
  switch (_context.prev = _context.next) {
53
53
  case 0:
@@ -56,21 +56,21 @@ test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE_
56
56
  refName: 'ctgA',
57
57
  start: 0,
58
58
  end: 2
59
- }, (0, _rxjs.from)([new _simpleFeature.default({
59
+ }, (0, _rxjs.from)([new _simpleFeature["default"]({
60
60
  id: 1,
61
61
  data: {
62
62
  start: 0,
63
63
  end: 1,
64
64
  score: 1
65
65
  }
66
- }), new _simpleFeature.default({
66
+ }), new _simpleFeature["default"]({
67
67
  id: 2,
68
68
  data: {
69
69
  start: 1,
70
70
  end: 2,
71
71
  score: 2
72
72
  }
73
- }), new _simpleFeature.default({
73
+ }), new _simpleFeature["default"]({
74
74
  id: 3,
75
75
  data: {
76
76
  start: 2,
@@ -101,7 +101,7 @@ test('calc per base stats', function () {
101
101
  refName: 'ctgA',
102
102
  start: 0,
103
103
  end: 9
104
- }, [new _simpleFeature.default({
104
+ }, [new _simpleFeature["default"]({
105
105
  id: 1,
106
106
  data: {
107
107
  start: 0,
@@ -114,14 +114,14 @@ test('calc per base stats', function () {
114
114
  refName: 'ctgA',
115
115
  start: 0,
116
116
  end: 9
117
- }, [new _simpleFeature.default({
117
+ }, [new _simpleFeature["default"]({
118
118
  id: 1,
119
119
  data: {
120
120
  start: 0,
121
121
  end: 1,
122
122
  score: 10
123
123
  }
124
- }), new _simpleFeature.default({
124
+ }), new _simpleFeature["default"]({
125
125
  id: 2,
126
126
  data: {
127
127
  start: 8,
@@ -134,14 +134,14 @@ test('calc per base stats', function () {
134
134
  refName: 'ctgA',
135
135
  start: 15,
136
136
  end: 30
137
- }, [new _simpleFeature.default({
137
+ }, [new _simpleFeature["default"]({
138
138
  id: 1,
139
139
  data: {
140
140
  start: 10,
141
141
  end: 20,
142
142
  score: 10
143
143
  }
144
- }), new _simpleFeature.default({
144
+ }), new _simpleFeature["default"]({
145
145
  id: 2,
146
146
  data: {
147
147
  start: 25,
@@ -154,14 +154,14 @@ test('calc per base stats', function () {
154
154
  refName: 'ctgA',
155
155
  start: 10,
156
156
  end: 19
157
- }, [new _simpleFeature.default({
157
+ }, [new _simpleFeature["default"]({
158
158
  id: 1,
159
159
  data: {
160
160
  start: 5,
161
161
  end: 15,
162
162
  score: 10
163
163
  }
164
- }), new _simpleFeature.default({
164
+ }), new _simpleFeature["default"]({
165
165
  id: 1,
166
166
  data: {
167
167
  start: 18,
@@ -185,10 +185,12 @@ export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
185
185
  }
186
186
  export declare function isUriLocation(location: unknown): location is UriLocation;
187
187
  export declare class AuthNeededError extends Error {
188
+ message: string;
188
189
  location: UriLocation;
189
190
  constructor(message: string, location: UriLocation);
190
191
  }
191
192
  export declare class RetryError extends Error {
193
+ message: string;
192
194
  internetAccountId: string;
193
195
  constructor(message: string, internetAccountId: string);
194
196
  }
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
 
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
3
+ var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
4
4
 
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
@@ -43,21 +43,19 @@ exports.isUriLocation = isUriLocation;
43
43
  exports.isViewContainer = isViewContainer;
44
44
  exports.isViewModel = isViewModel;
45
45
 
46
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
46
+ var _createClass2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createClass.js"));
47
47
 
48
- var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
48
+ var _classCallCheck2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
49
49
 
50
- var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
50
+ var _assertThisInitialized2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/assertThisInitialized.js"));
51
51
 
52
- var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
52
+ var _inherits2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/inherits.js"));
53
53
 
54
- var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
54
+ var _createSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
55
55
 
56
- var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime/helpers/wrapNativeSuper"));
56
+ var _wrapNativeSuper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/wrapNativeSuper.js"));
57
57
 
58
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
59
-
60
- var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
58
+ var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
61
59
 
62
60
  var _mobxStateTree = require("mobx-state-tree");
63
61
 
@@ -75,16 +73,12 @@ Object.keys(_util).forEach(function (key) {
75
73
  });
76
74
  });
77
75
 
78
- function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
79
-
80
- function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
81
-
82
76
  function isViewContainer(thing) {
83
77
  return (0, _mobxStateTree.isStateTreeNode)(thing) && 'removeView' in thing && 'addView' in thing && 'views' in thing;
84
78
  }
85
79
 
86
80
  function isSessionModel(thing) {
87
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'rpcManager' in thing && 'configuration' in thing;
81
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'rpcManager' in thing && 'configuration' in thing;
88
82
  }
89
83
  /** abstract interface for a session allows editing configurations */
90
84
 
@@ -110,39 +104,39 @@ function isSessionWithSessionPlugins(thing) {
110
104
 
111
105
 
112
106
  function isSelectionContainer(thing) {
113
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'selection' in thing && 'setSelection' in thing;
107
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'selection' in thing && 'setSelection' in thing;
114
108
  }
115
109
  /** minimum interface that all view state models must implement */
116
110
 
117
111
 
118
112
  function isViewModel(thing) {
119
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'width' in thing && 'setWidth' in thing;
113
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'width' in thing && 'setWidth' in thing;
120
114
  }
121
115
 
122
116
  function isTrackModel(thing) {
123
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
117
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
124
118
  thing.configuration.trackId;
125
119
  }
126
120
 
127
121
  function isDisplayModel(thing) {
128
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
122
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
129
123
  thing.configuration.displayId;
130
124
  }
131
125
 
132
126
  function isTrackViewModel(thing) {
133
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'showTrack' in thing && 'hideTrack' in thing;
127
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'showTrack' in thing && 'hideTrack' in thing;
134
128
  }
135
129
  /** minimum interface for the root MST model of a JBrowse app */
136
130
 
137
131
 
138
132
  function isAppRootModel(thing) {
139
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'isAssemblyEditing' in thing && 'findAppropriateInternetAccount' in thing;
133
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'isAssemblyEditing' in thing && 'findAppropriateInternetAccount' in thing;
140
134
  }
141
135
  /** a root model that manages global menus */
142
136
 
143
137
 
144
138
  function isAbstractMenuManager(thing) {
145
- return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'appendMenu' in thing && 'appendToSubMenu' in thing;
139
+ return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'appendMenu' in thing && 'appendToSubMenu' in thing;
146
140
  } // Empty interfaces required by mobx-state-tree
147
141
  // See https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
148
142
 
@@ -150,50 +144,49 @@ function isAbstractMenuManager(thing) {
150
144
 
151
145
 
152
146
  function isUriLocation(location) {
153
- return (0, _typeof2.default)(location) === 'object' && location !== null && 'locationType' in location && 'uri' in location;
147
+ return (0, _typeof2["default"])(location) === 'object' && location !== null && 'locationType' in location && 'uri' in location;
154
148
  }
155
149
 
156
150
  var AuthNeededError = /*#__PURE__*/function (_Error) {
157
- (0, _inherits2.default)(AuthNeededError, _Error);
151
+ (0, _inherits2["default"])(AuthNeededError, _Error);
158
152
 
159
- var _super = _createSuper(AuthNeededError);
153
+ var _super = (0, _createSuper2["default"])(AuthNeededError);
160
154
 
161
155
  function AuthNeededError(message, location) {
162
156
  var _this;
163
157
 
164
- (0, _classCallCheck2.default)(this, AuthNeededError);
158
+ (0, _classCallCheck2["default"])(this, AuthNeededError);
165
159
  _this = _super.call(this, message);
166
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "location", void 0);
160
+ _this.message = message;
167
161
  _this.location = location;
168
162
  _this.name = 'AuthNeededError';
169
- Object.setPrototypeOf((0, _assertThisInitialized2.default)(_this), AuthNeededError.prototype);
163
+ Object.setPrototypeOf((0, _assertThisInitialized2["default"])(_this), AuthNeededError.prototype);
170
164
  return _this;
171
165
  }
172
166
 
173
- return AuthNeededError;
174
- }( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
167
+ return (0, _createClass2["default"])(AuthNeededError);
168
+ }( /*#__PURE__*/(0, _wrapNativeSuper2["default"])(Error));
175
169
 
176
170
  exports.AuthNeededError = AuthNeededError;
177
171
 
178
172
  var RetryError = /*#__PURE__*/function (_Error2) {
179
- (0, _inherits2.default)(RetryError, _Error2);
173
+ (0, _inherits2["default"])(RetryError, _Error2);
180
174
 
181
- var _super2 = _createSuper(RetryError);
175
+ var _super2 = (0, _createSuper2["default"])(RetryError);
182
176
 
183
177
  function RetryError(message, internetAccountId) {
184
178
  var _this2;
185
179
 
186
- (0, _classCallCheck2.default)(this, RetryError);
180
+ (0, _classCallCheck2["default"])(this, RetryError);
187
181
  _this2 = _super2.call(this, message);
188
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "internetAccountId", void 0);
189
182
  _this2.message = message;
190
183
  _this2.internetAccountId = internetAccountId;
191
184
  _this2.name = 'RetryError';
192
185
  return _this2;
193
186
  }
194
187
 
195
- return RetryError;
196
- }( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
188
+ return (0, _createClass2["default"])(RetryError);
189
+ }( /*#__PURE__*/(0, _wrapNativeSuper2["default"])(Error));
197
190
 
198
191
  exports.RetryError = RetryError;
199
192