@jbrowse/core 1.7.11 → 2.1.0

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 (204) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +20 -4
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +313 -558
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -473
  4. package/BaseFeatureWidget/index.d.ts +2 -2
  5. package/BaseFeatureWidget/index.js +88 -124
  6. package/BaseFeatureWidget/types.d.ts +1 -0
  7. package/BaseFeatureWidget/types.js +1 -4
  8. package/BaseFeatureWidget/util.js +40 -75
  9. package/CorePlugin.js +55 -94
  10. package/Plugin.js +9 -34
  11. package/PluginLoader.js +153 -422
  12. package/PluginManager.d.ts +84 -117
  13. package/PluginManager.js +377 -666
  14. package/ReExports/Attributes.d.ts +2 -0
  15. package/ReExports/Attributes.js +5 -0
  16. package/ReExports/BaseCard.d.ts +2 -0
  17. package/ReExports/BaseCard.js +5 -0
  18. package/ReExports/DataGrid.d.ts +2 -0
  19. package/ReExports/DataGrid.js +6 -0
  20. package/ReExports/FeatureDetails.d.ts +2 -0
  21. package/ReExports/FeatureDetails.js +5 -0
  22. package/ReExports/index.js +6 -12
  23. package/ReExports/list.d.ts +5 -0
  24. package/ReExports/list.js +271 -7
  25. package/ReExports/material-ui-colors.d.ts +1 -19
  26. package/ReExports/material-ui-colors.js +16 -158
  27. package/ReExports/modules.d.ts +68 -109
  28. package/ReExports/modules.js +455 -244
  29. package/TextSearch/BaseResults.js +51 -123
  30. package/TextSearch/TextSearchManager.d.ts +3 -1
  31. package/TextSearch/TextSearchManager.js +66 -144
  32. package/assemblyManager/assembly.js +280 -554
  33. package/assemblyManager/assemblyConfigSchema.js +47 -64
  34. package/assemblyManager/assemblyManager.d.ts +12 -10
  35. package/assemblyManager/assemblyManager.js +126 -270
  36. package/assemblyManager/index.js +9 -22
  37. package/configuration/configurationSchema.js +167 -203
  38. package/configuration/configurationSlot.js +248 -326
  39. package/configuration/index.js +19 -35
  40. package/configuration/util.d.ts +1 -1
  41. package/configuration/util.js +131 -173
  42. package/data_adapters/BaseAdapter.d.ts +2 -2
  43. package/data_adapters/BaseAdapter.js +132 -521
  44. package/data_adapters/CytobandAdapter.js +40 -126
  45. package/data_adapters/dataAdapterCache.js +77 -158
  46. package/package.json +16 -18
  47. package/pluggableElementTypes/AdapterType.js +24 -79
  48. package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  49. package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
  50. package/pluggableElementTypes/ConnectionType.js +22 -65
  51. package/pluggableElementTypes/DisplayType.js +35 -82
  52. package/pluggableElementTypes/InternetAccountType.js +23 -64
  53. package/pluggableElementTypes/PluggableElementBase.js +8 -20
  54. package/pluggableElementTypes/RpcMethodType.js +85 -427
  55. package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
  56. package/pluggableElementTypes/TrackType.js +26 -70
  57. package/pluggableElementTypes/ViewType.js +21 -63
  58. package/pluggableElementTypes/WidgetType.js +21 -64
  59. package/pluggableElementTypes/index.d.ts +4 -3
  60. package/pluggableElementTypes/index.js +42 -125
  61. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
  62. package/pluggableElementTypes/models/BaseDisplayModel.d.ts +10 -10
  63. package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
  64. package/pluggableElementTypes/models/BaseTrackModel.d.ts +1 -1
  65. package/pluggableElementTypes/models/BaseTrackModel.js +139 -200
  66. package/pluggableElementTypes/models/BaseViewModel.js +24 -40
  67. package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
  68. package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
  69. package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
  70. package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
  71. package/pluggableElementTypes/models/index.js +21 -70
  72. package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
  73. package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
  74. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
  75. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
  76. package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -255
  77. package/pluggableElementTypes/renderers/RendererType.js +31 -105
  78. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
  79. package/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +2 -2
  80. package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
  81. package/pluggableElementTypes/renderers/index.js +19 -62
  82. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
  83. package/rpc/BaseRpcDriver.js +169 -405
  84. package/rpc/MainThreadRpcDriver.js +27 -150
  85. package/rpc/RpcManager.js +58 -159
  86. package/rpc/WebWorkerRpcDriver.js +54 -171
  87. package/rpc/configSchema.js +25 -49
  88. package/rpc/coreRpcMethods.d.ts +1 -3
  89. package/rpc/coreRpcMethods.js +221 -959
  90. package/rpc/remoteAbortSignals.js +46 -70
  91. package/tsconfig.build.tsbuildinfo +1 -1
  92. package/ui/AboutDialog.js +107 -158
  93. package/ui/App.js +157 -261
  94. package/ui/AssemblySelector.d.ts +1 -1
  95. package/ui/AssemblySelector.js +59 -115
  96. package/ui/CascadingMenu.js +100 -199
  97. package/ui/ColorPicker.d.ts +16 -0
  98. package/ui/ColorPicker.js +97 -0
  99. package/ui/Drawer.js +28 -58
  100. package/ui/DrawerWidget.js +109 -209
  101. package/ui/DropDownMenu.d.ts +0 -8
  102. package/ui/DropDownMenu.js +60 -97
  103. package/ui/EditableTypography.d.ts +1 -1
  104. package/ui/EditableTypography.js +87 -155
  105. package/ui/ErrorMessage.js +41 -66
  106. package/ui/FactoryResetDialog.js +24 -57
  107. package/ui/FatalErrorDialog.js +59 -91
  108. package/ui/FileSelector/FileSelector.js +123 -189
  109. package/ui/FileSelector/LocalFileChooser.js +44 -71
  110. package/ui/FileSelector/UrlChooser.js +17 -38
  111. package/ui/FileSelector/index.js +6 -12
  112. package/ui/Icons.d.ts +1 -1
  113. package/ui/Icons.js +45 -69
  114. package/ui/Logo.js +57 -110
  115. package/ui/Menu.d.ts +1 -1
  116. package/ui/Menu.js +232 -355
  117. package/ui/PrerenderedCanvas.js +63 -78
  118. package/ui/ResizeHandle.js +87 -114
  119. package/ui/ReturnToImportFormDialog.js +32 -59
  120. package/ui/SanitizedHTML.js +63 -52
  121. package/ui/Snackbar.js +74 -99
  122. package/ui/SnackbarModel.js +37 -51
  123. package/ui/Tooltip.d.ts +3 -1
  124. package/ui/Tooltip.js +49 -74
  125. package/ui/ViewContainer.js +113 -183
  126. package/ui/colors.d.ts +10 -0
  127. package/ui/colors.js +78 -0
  128. package/ui/index.js +51 -181
  129. package/ui/react-colorful.d.ts +17 -0
  130. package/ui/react-colorful.js +455 -0
  131. package/ui/theme.d.ts +279 -131
  132. package/ui/theme.js +197 -225
  133. package/util/Base1DUtils.d.ts +32 -0
  134. package/util/Base1DUtils.js +174 -0
  135. package/util/Base1DViewModel.d.ts +16 -37
  136. package/util/Base1DViewModel.js +116 -295
  137. package/util/QuickLRU.js +84 -332
  138. package/util/TimeTraveller.d.ts +19 -0
  139. package/util/TimeTraveller.js +86 -0
  140. package/util/aborting.js +49 -127
  141. package/util/analytics.js +91 -154
  142. package/util/blockTypes.js +106 -240
  143. package/util/calculateDynamicBlocks.js +98 -128
  144. package/util/calculateStaticBlocks.js +105 -125
  145. package/util/color/cssColorsLevel4.js +156 -160
  146. package/util/color/index.js +33 -55
  147. package/util/compositeMap.js +49 -333
  148. package/util/formatFastaStrings.js +9 -14
  149. package/util/idMaker.js +18 -31
  150. package/util/index.d.ts +18 -39
  151. package/util/index.js +743 -1236
  152. package/util/io/RemoteFileWithRangeCache.js +88 -257
  153. package/util/io/index.js +95 -169
  154. package/util/jexl.js +60 -115
  155. package/util/jexlStrings.js +24 -29
  156. package/util/layouts/BaseLayout.js +1 -4
  157. package/util/layouts/GranularRectLayout.js +388 -557
  158. package/util/layouts/MultiLayout.js +41 -109
  159. package/util/layouts/PrecomputedLayout.js +56 -114
  160. package/util/layouts/PrecomputedMultiLayout.js +22 -59
  161. package/util/layouts/SceneGraph.js +127 -197
  162. package/util/layouts/index.js +29 -66
  163. package/util/mst-reflection.js +55 -71
  164. package/util/offscreenCanvasPonyfill.js +66 -134
  165. package/util/offscreenCanvasUtils.d.ts +2 -7
  166. package/util/offscreenCanvasUtils.js +49 -146
  167. package/util/range.js +29 -40
  168. package/util/rxjs.js +20 -27
  169. package/util/simpleFeature.js +88 -152
  170. package/util/stats.js +91 -151
  171. package/util/tracks.js +130 -171
  172. package/util/types/index.d.ts +3 -3
  173. package/util/types/index.js +110 -179
  174. package/util/types/mst.d.ts +3 -3
  175. package/util/types/mst.js +91 -142
  176. package/util/types/util.js +1 -4
  177. package/util/when.js +54 -101
  178. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
  179. package/BaseFeatureWidget/index.test.js +0 -51
  180. package/TextSearch/BaseResults.test.js +0 -42
  181. package/configuration/configurationSchema.test.js +0 -266
  182. package/configuration/configurationSlot.test.js +0 -69
  183. package/configuration/util.test.js +0 -39
  184. package/data_adapters/BaseAdapter.test.js +0 -200
  185. package/declare.d.js +0 -1
  186. package/pluggableElementTypes/RpcMethodType.test.js +0 -118
  187. package/pluggableElementTypes/renderers/declare.d.js +0 -1
  188. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
  189. package/rpc/BaseRpcDriver.test.js +0 -540
  190. package/rpc/declaration.d.js +0 -1
  191. package/ui/FatalErrorDialog.test.js +0 -82
  192. package/ui/SanitizedHTML.test.js +0 -36
  193. package/ui/theme.test.js +0 -111
  194. package/util/Base1DViewModel.test.js +0 -130
  195. package/util/calculateDynamicBlocks.test.js +0 -74
  196. package/util/calculateStaticBlocks.test.js +0 -297
  197. package/util/declare.d.js +0 -1
  198. package/util/formatFastaStrings.test.js +0 -40
  199. package/util/index.test.js +0 -213
  200. package/util/jexlStrings.test.js +0 -48
  201. package/util/layouts/GranularRectLayout.test.js +0 -99
  202. package/util/range.test.js +0 -64
  203. package/util/simpleFeature.test.js +0 -34
  204. package/util/stats.test.js +0 -172
@@ -1,63 +1,20 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
7
- });
8
- Object.defineProperty(exports, "BoxRendererType", {
9
- enumerable: true,
10
- get: function get() {
11
- return _BoxRendererType.default;
12
- }
13
- });
14
- Object.defineProperty(exports, "CircularChordRendererType", {
15
- enumerable: true,
16
- get: function get() {
17
- return _CircularChordRendererType.default;
18
- }
19
- });
20
- Object.defineProperty(exports, "ComparativeServerSideRendererType", {
21
- enumerable: true,
22
- get: function get() {
23
- return _ComparativeServerSideRendererType.default;
24
- }
25
- });
26
- Object.defineProperty(exports, "FeatureRendererType", {
27
- enumerable: true,
28
- get: function get() {
29
- return _FeatureRendererType.default;
30
- }
31
- });
32
- Object.defineProperty(exports, "RendererType", {
33
- enumerable: true,
34
- get: function get() {
35
- return _RendererType.default;
36
- }
37
- });
38
- Object.defineProperty(exports, "ServerSideRenderedContent", {
39
- enumerable: true,
40
- get: function get() {
41
- return _ServerSideRenderedContent.default;
42
- }
43
- });
44
- Object.defineProperty(exports, "ServerSideRendererType", {
45
- enumerable: true,
46
- get: function get() {
47
- return _ServerSideRendererType.default;
48
- }
49
- });
50
-
51
- var _BoxRendererType = _interopRequireDefault(require("./BoxRendererType"));
52
-
53
- var _CircularChordRendererType = _interopRequireDefault(require("./CircularChordRendererType"));
54
-
55
- var _ComparativeServerSideRendererType = _interopRequireDefault(require("./ComparativeServerSideRendererType"));
56
-
57
- var _FeatureRendererType = _interopRequireDefault(require("./FeatureRendererType"));
58
-
59
- var _RendererType = _interopRequireDefault(require("./RendererType"));
60
-
61
- var _ServerSideRenderedContent = _interopRequireDefault(require("./ServerSideRenderedContent"));
62
-
63
- var _ServerSideRendererType = _interopRequireDefault(require("./ServerSideRendererType"));
2
+ var __importDefault = (this && this.__importDefault) || function (mod) {
3
+ return (mod && mod.__esModule) ? mod : { "default": mod };
4
+ };
5
+ Object.defineProperty(exports, "__esModule", { value: true });
6
+ exports.ServerSideRendererType = exports.ServerSideRenderedContent = exports.RendererType = exports.FeatureRendererType = exports.ComparativeServerSideRendererType = exports.CircularChordRendererType = exports.BoxRendererType = void 0;
7
+ const BoxRendererType_1 = __importDefault(require("./BoxRendererType"));
8
+ exports.BoxRendererType = BoxRendererType_1.default;
9
+ const CircularChordRendererType_1 = __importDefault(require("./CircularChordRendererType"));
10
+ exports.CircularChordRendererType = CircularChordRendererType_1.default;
11
+ const ComparativeServerSideRendererType_1 = __importDefault(require("./ComparativeServerSideRendererType"));
12
+ exports.ComparativeServerSideRendererType = ComparativeServerSideRendererType_1.default;
13
+ const FeatureRendererType_1 = __importDefault(require("./FeatureRendererType"));
14
+ exports.FeatureRendererType = FeatureRendererType_1.default;
15
+ const RendererType_1 = __importDefault(require("./RendererType"));
16
+ exports.RendererType = RendererType_1.default;
17
+ const ServerSideRenderedContent_1 = __importDefault(require("./ServerSideRenderedContent"));
18
+ exports.ServerSideRenderedContent = ServerSideRenderedContent_1.default;
19
+ const ServerSideRendererType_1 = __importDefault(require("./ServerSideRendererType"));
20
+ exports.ServerSideRendererType = ServerSideRendererType_1.default;
@@ -1,70 +1,32 @@
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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
-
12
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
13
-
14
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
15
-
16
- var _jexlStrings = require("../../../util/jexlStrings");
17
-
18
- var SerializableFilterChain = /*#__PURE__*/function () {
19
- function SerializableFilterChain(_ref) {
20
- var _ref$filters = _ref.filters,
21
- filters = _ref$filters === void 0 ? [] : _ref$filters;
22
- (0, _classCallCheck2.default)(this, SerializableFilterChain);
23
- (0, _defineProperty2.default)(this, "filterChain", void 0);
24
- this.filterChain = filters.map(function (inputFilter) {
25
- if (typeof inputFilter === 'string') {
26
- var expr = (0, _jexlStrings.stringToJexlExpression)(inputFilter);
27
- return {
28
- expr: expr,
29
- string: inputFilter
30
- };
31
- }
32
-
33
- throw new Error("invalid inputFilter string \"".concat(inputFilter, "\""));
34
- });
35
- } // eslint-disable-next-line @typescript-eslint/no-explicit-any
36
-
37
-
38
- (0, _createClass2.default)(SerializableFilterChain, [{
39
- key: "passes",
40
- value: function passes() {
41
- for (var i = 0; i < this.filterChain.length; i += 1) {
42
- if ( // @ts-ignore
43
- !this.filterChain[i].expr.evalSync({
44
- feature: arguments.length <= 0 ? undefined : arguments[0]
45
- })) {
46
- return false;
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ const jexlStrings_1 = require("../../../util/jexlStrings");
4
+ class SerializableFilterChain {
5
+ constructor({ filters = [] }) {
6
+ this.filterChain = filters.map(inputFilter => {
7
+ if (typeof inputFilter === 'string') {
8
+ const expr = (0, jexlStrings_1.stringToJexlExpression)(inputFilter);
9
+ return { expr, string: inputFilter };
10
+ }
11
+ throw new Error(`invalid inputFilter string "${inputFilter}"`);
12
+ });
13
+ }
14
+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
15
+ passes(...args) {
16
+ for (let i = 0; i < this.filterChain.length; i += 1) {
17
+ if (
18
+ // @ts-ignore
19
+ !this.filterChain[i].expr.evalSync({ feature: args[0] })) {
20
+ return false;
21
+ }
47
22
  }
48
- }
49
-
50
- return true;
23
+ return true;
51
24
  }
52
- }, {
53
- key: "toJSON",
54
- value: function toJSON() {
55
- return {
56
- filters: this.filterChain.map(function (f) {
57
- return f.string;
58
- })
59
- };
25
+ toJSON() {
26
+ return { filters: this.filterChain.map(f => f.string) };
60
27
  }
61
- }], [{
62
- key: "fromJSON",
63
- value: function fromJSON(json) {
64
- return new SerializableFilterChain(json);
28
+ static fromJSON(json) {
29
+ return new SerializableFilterChain(json);
65
30
  }
66
- }]);
67
- return SerializableFilterChain;
68
- }();
69
-
70
- exports.default = SerializableFilterChain;
31
+ }
32
+ exports.default = SerializableFilterChain;