@jbrowse/core 2.0.0 → 2.1.2

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 (184) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +9 -3
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +313 -581
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -478
  4. package/BaseFeatureWidget/index.js +88 -126
  5. package/BaseFeatureWidget/types.d.ts +1 -0
  6. package/BaseFeatureWidget/types.js +1 -4
  7. package/BaseFeatureWidget/util.js +40 -75
  8. package/CorePlugin.js +55 -94
  9. package/Plugin.js +9 -34
  10. package/PluginLoader.js +153 -422
  11. package/PluginManager.d.ts +28 -33
  12. package/PluginManager.js +377 -666
  13. package/ReExports/Attributes.js +3 -10
  14. package/ReExports/BaseCard.js +3 -10
  15. package/ReExports/DataGrid.js +5 -12
  16. package/ReExports/FeatureDetails.js +3 -10
  17. package/ReExports/index.js +6 -12
  18. package/ReExports/list.d.ts +5 -0
  19. package/ReExports/list.js +271 -7
  20. package/ReExports/material-ui-colors.js +15 -16
  21. package/ReExports/modules.d.ts +11 -20
  22. package/ReExports/modules.js +453 -798
  23. package/TextSearch/BaseResults.js +51 -123
  24. package/TextSearch/TextSearchManager.js +66 -144
  25. package/assemblyManager/assembly.js +280 -555
  26. package/assemblyManager/assemblyConfigSchema.js +47 -64
  27. package/assemblyManager/assemblyManager.js +126 -272
  28. package/assemblyManager/index.js +9 -22
  29. package/configuration/configurationSchema.js +167 -203
  30. package/configuration/configurationSlot.js +248 -326
  31. package/configuration/index.js +19 -35
  32. package/configuration/util.js +131 -173
  33. package/data_adapters/BaseAdapter.d.ts +2 -2
  34. package/data_adapters/BaseAdapter.js +132 -521
  35. package/data_adapters/CytobandAdapter.js +40 -126
  36. package/data_adapters/dataAdapterCache.js +77 -158
  37. package/package.json +4 -5
  38. package/pluggableElementTypes/AdapterType.js +24 -79
  39. package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  40. package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
  41. package/pluggableElementTypes/ConnectionType.js +22 -65
  42. package/pluggableElementTypes/DisplayType.js +35 -82
  43. package/pluggableElementTypes/InternetAccountType.js +23 -64
  44. package/pluggableElementTypes/PluggableElementBase.js +8 -20
  45. package/pluggableElementTypes/RpcMethodType.js +85 -427
  46. package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
  47. package/pluggableElementTypes/TrackType.js +26 -70
  48. package/pluggableElementTypes/ViewType.js +21 -63
  49. package/pluggableElementTypes/WidgetType.js +21 -64
  50. package/pluggableElementTypes/index.d.ts +4 -3
  51. package/pluggableElementTypes/index.js +42 -125
  52. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
  53. package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
  54. package/pluggableElementTypes/models/BaseTrackModel.js +139 -199
  55. package/pluggableElementTypes/models/BaseViewModel.js +24 -40
  56. package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
  57. package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
  58. package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
  59. package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
  60. package/pluggableElementTypes/models/index.js +21 -70
  61. package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
  62. package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
  63. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
  64. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
  65. package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -255
  66. package/pluggableElementTypes/renderers/RendererType.js +31 -105
  67. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
  68. package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
  69. package/pluggableElementTypes/renderers/index.js +19 -62
  70. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
  71. package/rpc/BaseRpcDriver.js +169 -405
  72. package/rpc/MainThreadRpcDriver.js +27 -150
  73. package/rpc/RpcManager.js +58 -159
  74. package/rpc/WebWorkerRpcDriver.js +54 -171
  75. package/rpc/configSchema.js +25 -49
  76. package/rpc/coreRpcMethods.d.ts +1 -3
  77. package/rpc/coreRpcMethods.js +221 -959
  78. package/rpc/remoteAbortSignals.js +46 -70
  79. package/tsconfig.build.tsbuildinfo +1 -1
  80. package/ui/AboutDialog.js +106 -162
  81. package/ui/App.js +157 -242
  82. package/ui/AssemblySelector.js +59 -120
  83. package/ui/CascadingMenu.js +101 -196
  84. package/ui/ColorPicker.d.ts +16 -0
  85. package/ui/ColorPicker.js +97 -0
  86. package/ui/Drawer.js +28 -61
  87. package/ui/DrawerWidget.js +108 -202
  88. package/ui/DropDownMenu.js +60 -91
  89. package/ui/EditableTypography.js +87 -149
  90. package/ui/ErrorMessage.js +41 -56
  91. package/ui/FactoryResetDialog.js +24 -57
  92. package/ui/FatalErrorDialog.js +59 -91
  93. package/ui/FileSelector/FileSelector.js +123 -189
  94. package/ui/FileSelector/LocalFileChooser.js +44 -75
  95. package/ui/FileSelector/UrlChooser.js +17 -38
  96. package/ui/FileSelector/index.js +6 -12
  97. package/ui/Icons.js +45 -69
  98. package/ui/Logo.js +57 -110
  99. package/ui/Menu.js +232 -354
  100. package/ui/PrerenderedCanvas.js +63 -87
  101. package/ui/ResizeHandle.js +87 -116
  102. package/ui/ReturnToImportFormDialog.js +32 -63
  103. package/ui/SanitizedHTML.js +64 -47
  104. package/ui/Snackbar.js +74 -101
  105. package/ui/SnackbarModel.js +37 -51
  106. package/ui/Tooltip.js +49 -76
  107. package/ui/ViewContainer.js +113 -196
  108. package/ui/colors.d.ts +10 -0
  109. package/ui/colors.js +78 -0
  110. package/ui/index.js +51 -181
  111. package/ui/react-colorful.d.ts +17 -0
  112. package/ui/react-colorful.js +455 -0
  113. package/ui/theme.d.ts +23 -1
  114. package/ui/theme.js +199 -247
  115. package/util/Base1DUtils.d.ts +32 -0
  116. package/util/Base1DUtils.js +174 -0
  117. package/util/Base1DViewModel.d.ts +16 -30
  118. package/util/Base1DViewModel.js +116 -293
  119. package/util/QuickLRU.js +84 -332
  120. package/util/TimeTraveller.d.ts +19 -0
  121. package/util/TimeTraveller.js +86 -0
  122. package/util/aborting.js +49 -127
  123. package/util/analytics.js +91 -154
  124. package/util/blockTypes.js +106 -240
  125. package/util/calculateDynamicBlocks.js +98 -128
  126. package/util/calculateStaticBlocks.js +105 -125
  127. package/util/color/cssColorsLevel4.js +156 -160
  128. package/util/color/index.js +33 -55
  129. package/util/compositeMap.js +49 -333
  130. package/util/formatFastaStrings.js +9 -14
  131. package/util/idMaker.js +18 -31
  132. package/util/index.d.ts +18 -32
  133. package/util/index.js +747 -1226
  134. package/util/io/RemoteFileWithRangeCache.js +88 -257
  135. package/util/io/index.js +95 -169
  136. package/util/jexl.js +60 -115
  137. package/util/jexlStrings.js +24 -29
  138. package/util/layouts/BaseLayout.js +1 -4
  139. package/util/layouts/GranularRectLayout.js +388 -555
  140. package/util/layouts/MultiLayout.js +41 -109
  141. package/util/layouts/PrecomputedLayout.js +56 -112
  142. package/util/layouts/PrecomputedMultiLayout.js +22 -59
  143. package/util/layouts/SceneGraph.js +127 -197
  144. package/util/layouts/index.js +29 -66
  145. package/util/mst-reflection.js +55 -71
  146. package/util/offscreenCanvasPonyfill.js +66 -134
  147. package/util/offscreenCanvasUtils.d.ts +2 -7
  148. package/util/offscreenCanvasUtils.js +49 -146
  149. package/util/range.js +29 -40
  150. package/util/rxjs.js +20 -27
  151. package/util/simpleFeature.js +88 -152
  152. package/util/stats.js +91 -151
  153. package/util/tracks.js +130 -173
  154. package/util/types/index.js +110 -179
  155. package/util/types/mst.js +91 -146
  156. package/util/types/util.js +1 -4
  157. package/util/when.js +54 -101
  158. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
  159. package/BaseFeatureWidget/index.test.js +0 -69
  160. package/TextSearch/BaseResults.test.js +0 -42
  161. package/configuration/configurationSchema.test.js +0 -266
  162. package/configuration/configurationSlot.test.js +0 -69
  163. package/configuration/util.test.js +0 -39
  164. package/data_adapters/BaseAdapter.test.js +0 -200
  165. package/declare.d.js +0 -1
  166. package/pluggableElementTypes/RpcMethodType.test.js +0 -118
  167. package/pluggableElementTypes/renderers/declare.d.js +0 -1
  168. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
  169. package/rpc/BaseRpcDriver.test.js +0 -540
  170. package/rpc/declaration.d.js +0 -1
  171. package/ui/FatalErrorDialog.test.js +0 -82
  172. package/ui/SanitizedHTML.test.js +0 -36
  173. package/ui/theme.test.js +0 -92
  174. package/util/Base1DViewModel.test.js +0 -130
  175. package/util/calculateDynamicBlocks.test.js +0 -74
  176. package/util/calculateStaticBlocks.test.js +0 -297
  177. package/util/declare.d.js +0 -1
  178. package/util/formatFastaStrings.test.js +0 -40
  179. package/util/index.test.js +0 -213
  180. package/util/jexlStrings.test.js +0 -48
  181. package/util/layouts/GranularRectLayout.test.js +0 -99
  182. package/util/range.test.js +0 -64
  183. package/util/simpleFeature.test.js +0 -34
  184. package/util/stats.test.js +0 -172
@@ -1,131 +1,93 @@
1
1
  "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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- exports.configSchema = void 0;
9
- exports.stateModelFactory = exports.default = stateModelFactory;
10
-
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- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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-
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- var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
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-
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- var _mobxStateTree = require("mobx-state-tree");
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-
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- var _mobx = require("mobx");
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-
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- var _configuration = require("../configuration");
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-
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- var _clone = _interopRequireDefault(require("clone"));
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-
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- var _mst = require("../util/types/mst");
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-
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- var _excluded = ["featureData", "finalizedFeatureData"],
26
- _excluded2 = ["unformattedFeatureData", "featureData"];
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-
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- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
29
-
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- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
31
-
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- var configSchema = (0, _configuration.ConfigurationSchema)('BaseFeatureWidget', {});
2
+ 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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+ exports.stateModelFactory = exports.configSchema = void 0;
7
+ const mobx_state_tree_1 = require("mobx-state-tree");
8
+ const mobx_1 = require("mobx");
9
+ const configuration_1 = require("../configuration");
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+ const clone_1 = __importDefault(require("clone"));
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+ const mst_1 = require("../util/types/mst");
12
+ const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
33
13
  exports.configSchema = configSchema;
34
-
35
- function formatSubfeatures(obj, depth, parse) {
36
- var _obj$subfeatures;
37
-
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- var currentDepth = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : 0;
39
- var returnObj = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : {};
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-
41
- if (depth <= currentDepth) {
14
+ function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
15
+ var _a;
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+ if (depth <= currentDepth) {
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+ return returnObj;
18
+ }
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+ returnObj.subfeatures = (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
20
+ formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
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+ return parse(sub);
22
+ });
42
23
  return returnObj;
43
- }
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-
45
- returnObj.subfeatures = (_obj$subfeatures = obj.subfeatures) === null || _obj$subfeatures === void 0 ? void 0 : _obj$subfeatures.map(function (sub) {
46
- formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
47
- return parse(sub);
48
- });
49
- return returnObj;
50
24
  }
51
-
52
25
  function stateModelFactory(pluginManager) {
53
- return _mobxStateTree.types.model('BaseFeatureWidget', {
54
- id: _mst.ElementId,
55
- type: _mobxStateTree.types.literal('BaseFeatureWidget'),
56
- featureData: _mobxStateTree.types.frozen(),
57
- formattedFields: _mobxStateTree.types.frozen(),
58
- unformattedFeatureData: _mobxStateTree.types.frozen(),
59
- view: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
60
- track: _mobxStateTree.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel'))
61
- }).volatile(function () {
62
- return {};
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- }).actions(function (self) {
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- return {
65
- setFeatureData: function setFeatureData(featureData) {
66
- self.unformattedFeatureData = featureData;
67
- },
68
- clearFeatureData: function clearFeatureData() {
69
- self.featureData = undefined;
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- },
71
- setFormattedData: function setFormattedData(feat) {
72
- self.featureData = feat;
73
- }
74
- };
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- }).actions(function (self) {
76
- return {
77
- afterCreate: function afterCreate() {
78
- (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)(function () {
79
- var unformattedFeatureData = self.unformattedFeatureData,
80
- track = self.track;
81
-
82
- if (unformattedFeatureData) {
83
- var feature = (0, _clone.default)(unformattedFeatureData);
84
-
85
- if (track) {
86
- // eslint-disable-next-line no-underscore-dangle
87
- feature.__jbrowsefmt = (0, _configuration.getConf)(track, ['formatDetails', 'feature'], {
88
- feature: feature
89
- });
90
- var depth = (0, _configuration.getConf)(track, ['formatDetails', 'depth']);
91
- formatSubfeatures(feature, depth, function (subfeature) {
92
- // eslint-disable-next-line no-underscore-dangle
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- subfeature.__jbrowsefmt = (0, _configuration.getConf)(track, ['formatDetails', 'subfeatures'], {
94
- feature: subfeature
95
- });
96
- });
97
- }
98
-
99
- self.setFormattedData(feature);
100
- }
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- }));
102
- }
103
- };
104
- }).preProcessSnapshot(function (snap) {
105
- // @ts-ignore
106
- var featureData = snap.featureData,
107
- finalizedFeatureData = snap.finalizedFeatureData,
108
- rest = (0, _objectWithoutProperties2.default)(snap, _excluded);
109
- return _objectSpread({
110
- unformattedFeatureData: featureData,
111
- featureData: finalizedFeatureData
112
- }, rest);
113
- }).postProcessSnapshot(function (snap) {
114
- // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
115
- var _ref = snap,
116
- unformattedFeatureData = _ref.unformattedFeatureData,
117
- featureData = _ref.featureData,
118
- rest = (0, _objectWithoutProperties2.default)(_ref, _excluded2); // finalizedFeatureData avoids running formatter twice if loading from
119
- // snapshot
120
-
121
- return _objectSpread({
122
- // replacing undefined with null helps with allowing fields to be
123
- // hidden, setting null is not allowed by jexl so we set it to
124
- // undefined to hide. see config guide. this replacement happens both
125
- // here and when displaying the featureData in base feature widget
126
- finalizedFeatureData: JSON.parse(JSON.stringify(featureData, function (_, v) {
127
- return typeof v === 'undefined' ? null : v;
128
- }))
129
- }, rest);
130
- });
131
- }
26
+ return mobx_state_tree_1.types
27
+ .model('BaseFeatureWidget', {
28
+ id: mst_1.ElementId,
29
+ type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
30
+ featureData: mobx_state_tree_1.types.frozen(),
31
+ formattedFields: mobx_state_tree_1.types.frozen(),
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+ unformattedFeatureData: mobx_state_tree_1.types.frozen(),
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+ view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
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+ track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
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+ })
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+ .volatile(() => ({}))
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+ .actions(self => ({
38
+ setFeatureData(featureData) {
39
+ self.unformattedFeatureData = featureData;
40
+ },
41
+ clearFeatureData() {
42
+ self.featureData = undefined;
43
+ },
44
+ setFormattedData(feat) {
45
+ self.featureData = feat;
46
+ },
47
+ }))
48
+ .actions(self => ({
49
+ afterCreate() {
50
+ (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
51
+ const { unformattedFeatureData, track } = self;
52
+ if (unformattedFeatureData) {
53
+ const feature = (0, clone_1.default)(unformattedFeatureData);
54
+ if (track) {
55
+ // eslint-disable-next-line no-underscore-dangle
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+ feature.__jbrowsefmt = (0, configuration_1.getConf)(track, ['formatDetails', 'feature'], { feature });
57
+ const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
58
+ formatSubfeatures(feature, depth, subfeature => {
59
+ // eslint-disable-next-line no-underscore-dangle
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+ subfeature.__jbrowsefmt = (0, configuration_1.getConf)(track, ['formatDetails', 'subfeatures'], { feature: subfeature });
61
+ });
62
+ }
63
+ self.setFormattedData(feature);
64
+ }
65
+ }));
66
+ },
67
+ }))
68
+ .preProcessSnapshot(snap => {
69
+ // @ts-ignore
70
+ const { featureData, finalizedFeatureData, ...rest } = snap;
71
+ return {
72
+ unformattedFeatureData: featureData,
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+ featureData: finalizedFeatureData,
74
+ ...rest,
75
+ };
76
+ })
77
+ .postProcessSnapshot(snap => {
78
+ // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
79
+ const { unformattedFeatureData, featureData, ...rest } = snap;
80
+ // finalizedFeatureData avoids running formatter twice if loading from
81
+ // snapshot
82
+ return {
83
+ // replacing undefined with null helps with allowing fields to be
84
+ // hidden, setting null is not allowed by jexl so we set it to
85
+ // undefined to hide. see config guide. this replacement happens both
86
+ // here and when displaying the featureData in base feature widget
87
+ finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => typeof v === 'undefined' ? null : v)),
88
+ ...rest,
89
+ };
90
+ });
91
+ }
92
+ exports.default = stateModelFactory;
93
+ exports.stateModelFactory = stateModelFactory;
@@ -4,6 +4,7 @@ import { SimpleFeatureSerialized } from '../util/simpleFeature';
4
4
  import { AbstractViewModel } from '../util';
5
5
  export interface BaseProps extends BaseCardProps {
6
6
  feature: SimpleFeatureSerialized;
7
+ formatter?: (val: unknown, key: string) => React.ReactNode;
7
8
  descriptions?: Record<string, React.ReactNode>;
8
9
  model?: IAnyStateTreeNode & {
9
10
  view?: AbstractViewModel & {
@@ -1,5 +1,2 @@
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  "use strict";
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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+ Object.defineProperty(exports, "__esModule", { value: true });
@@ -1,84 +1,49 @@
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  "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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- exports.calculateUTRs = calculateUTRs;
9
- exports.dedupe = dedupe;
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- exports.ellipses = ellipses;
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- exports.revlist = revlist;
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- exports.stitch = stitch;
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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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
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-
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- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
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-
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- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
21
-
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.ellipses = exports.calculateUTRs = exports.revlist = exports.dedupe = exports.stitch = void 0;
22
4
  function stitch(subfeats, sequence) {
23
- return subfeats.map(function (sub) {
24
- return sequence.slice(sub.start, sub.end);
25
- }).join('');
26
- } // filter items if they have the same "ID" or location
27
-
28
-
5
+ return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
6
+ }
7
+ exports.stitch = stitch;
8
+ // filter items if they have the same "ID" or location
29
9
  function getItemId(feat) {
30
- return "".concat(feat.start, "-").concat(feat.end);
31
- } // filters if successive elements share same start/end
32
-
33
-
10
+ return `${feat.start}-${feat.end}`;
11
+ }
12
+ // filters if successive elements share same start/end
34
13
  function dedupe(list) {
35
- return list.filter(function (item, pos, ary) {
36
- return !pos || getItemId(item) !== getItemId(ary[pos - 1]);
37
- });
14
+ return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
38
15
  }
39
-
16
+ exports.dedupe = dedupe;
40
17
  function revlist(list, seqlen) {
41
- return list.map(function (sub) {
42
- return _objectSpread(_objectSpread({}, sub), {}, {
43
- start: seqlen - sub.end,
44
- end: seqlen - sub.start
45
- });
46
- }).sort(function (a, b) {
47
- return a.start - b.start;
48
- });
49
- } // calculates UTRs using impliedUTRs logic
50
-
51
-
18
+ return list
19
+ .map(sub => ({
20
+ ...sub,
21
+ start: seqlen - sub.end,
22
+ end: seqlen - sub.start,
23
+ }))
24
+ .sort((a, b) => a.start - b.start);
25
+ }
26
+ exports.revlist = revlist;
27
+ // calculates UTRs using impliedUTRs logic
52
28
  function calculateUTRs(cds, exons) {
53
- var firstCds = cds[0];
54
- var lastCds = cds[cds.length - 1];
55
- var firstCdsIdx = exons.findIndex(function (exon) {
56
- return exon.end >= firstCds.start && exon.start <= firstCds.start;
57
- });
58
- var lastCdsIdx = exons.findIndex(function (exon) {
59
- return exon.end >= lastCds.end && exon.start <= lastCds.end;
60
- });
61
- var lastCdsExon = exons[lastCdsIdx];
62
- var firstCdsExon = exons[firstCdsIdx];
63
- var fiveUTRs = [].concat((0, _toConsumableArray2.default)(exons.slice(0, firstCdsIdx)), [{
64
- start: firstCdsExon.start,
65
- end: firstCds.start
66
- }]).map(function (elt) {
67
- return _objectSpread(_objectSpread({}, elt), {}, {
68
- type: 'five_prime_UTR'
69
- });
70
- });
71
- var threeUTRs = [{
72
- start: lastCds.end,
73
- end: lastCdsExon.end
74
- }].concat((0, _toConsumableArray2.default)(exons.slice(lastCdsIdx + 1))).map(function (elt) {
75
- return _objectSpread(_objectSpread({}, elt), {}, {
76
- type: 'three_prime_UTR'
77
- });
78
- });
79
- return [].concat((0, _toConsumableArray2.default)(fiveUTRs), (0, _toConsumableArray2.default)(threeUTRs));
29
+ const firstCds = cds[0];
30
+ const lastCds = cds[cds.length - 1];
31
+ const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
32
+ const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
33
+ const lastCdsExon = exons[lastCdsIdx];
34
+ const firstCdsExon = exons[firstCdsIdx];
35
+ const fiveUTRs = [
36
+ ...exons.slice(0, firstCdsIdx),
37
+ { start: firstCdsExon.start, end: firstCds.start },
38
+ ].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
39
+ const threeUTRs = [
40
+ { start: lastCds.end, end: lastCdsExon.end },
41
+ ...exons.slice(lastCdsIdx + 1),
42
+ ].map(elt => ({ ...elt, type: 'three_prime_UTR' }));
43
+ return [...fiveUTRs, ...threeUTRs];
80
44
  }
81
-
45
+ exports.calculateUTRs = calculateUTRs;
82
46
  function ellipses(slug) {
83
- return slug.length > 20 ? "".concat(slug.slice(0, 20), "...") : slug;
84
- }
47
+ return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
48
+ }
49
+ exports.ellipses = ellipses;
package/CorePlugin.js CHANGED
@@ -1,103 +1,64 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- var _typeof = require("@babel/runtime/helpers/typeof");
6
-
7
- Object.defineProperty(exports, "__esModule", {
8
- value: true
2
+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
+ if (k2 === undefined) k2 = k;
4
+ var desc = Object.getOwnPropertyDescriptor(m, k);
5
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
+ desc = { enumerable: true, get: function() { return m[k]; } };
7
+ }
8
+ Object.defineProperty(o, k2, desc);
9
+ }) : (function(o, m, k, k2) {
10
+ if (k2 === undefined) k2 = k;
11
+ o[k2] = m[k];
12
+ }));
13
+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
+ Object.defineProperty(o, "default", { enumerable: true, value: v });
15
+ }) : function(o, v) {
16
+ o["default"] = v;
9
17
  });
10
- exports.default = void 0;
11
-
12
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
13
-
14
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
15
-
16
- var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
17
-
18
- var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
19
-
20
- var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
21
-
22
- var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
23
-
24
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
25
-
26
- var _react = require("react");
27
-
28
- var _BaseFeatureWidget = require("./BaseFeatureWidget");
29
-
30
- var _Plugin2 = _interopRequireDefault(require("./Plugin"));
31
-
32
- var coreRpcMethods = _interopRequireWildcard(require("./rpc/coreRpcMethods"));
33
-
34
- var _AdapterType = _interopRequireDefault(require("./pluggableElementTypes/AdapterType"));
35
-
36
- var _WidgetType = _interopRequireDefault(require("./pluggableElementTypes/WidgetType"));
37
-
38
- var _CytobandAdapter = require("./data_adapters/CytobandAdapter");
39
-
40
- 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); }
41
-
42
- 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; }
43
-
44
- 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); }; }
45
-
46
- 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; } }
47
-
18
+ var __importStar = (this && this.__importStar) || function (mod) {
19
+ if (mod && mod.__esModule) return mod;
20
+ var result = {};
21
+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
+ __setModuleDefault(result, mod);
23
+ return result;
24
+ };
25
+ var __importDefault = (this && this.__importDefault) || function (mod) {
26
+ return (mod && mod.__esModule) ? mod : { "default": mod };
27
+ };
28
+ Object.defineProperty(exports, "__esModule", { value: true });
29
+ const react_1 = require("react");
30
+ const BaseFeatureWidget_1 = require("./BaseFeatureWidget");
31
+ const Plugin_1 = __importDefault(require("./Plugin"));
32
+ const coreRpcMethods = __importStar(require("./rpc/coreRpcMethods"));
33
+ const AdapterType_1 = __importDefault(require("./pluggableElementTypes/AdapterType"));
34
+ const WidgetType_1 = __importDefault(require("./pluggableElementTypes/WidgetType"));
35
+ const CytobandAdapter_1 = require("./data_adapters/CytobandAdapter");
48
36
  // the core plugin, which registers types that ALL JBrowse applications are
49
37
  // expected to need.
50
- var CorePlugin = /*#__PURE__*/function (_Plugin) {
51
- (0, _inherits2.default)(CorePlugin, _Plugin);
52
-
53
- var _super = _createSuper(CorePlugin);
54
-
55
- function CorePlugin() {
56
- var _this;
57
-
58
- (0, _classCallCheck2.default)(this, CorePlugin);
59
-
60
- for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
61
- args[_key] = arguments[_key];
38
+ class CorePlugin extends Plugin_1.default {
39
+ constructor() {
40
+ super(...arguments);
41
+ this.name = 'CorePlugin';
62
42
  }
63
-
64
- _this = _super.call.apply(_super, [this].concat(args));
65
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'CorePlugin');
66
- return _this;
67
- }
68
-
69
- (0, _createClass2.default)(CorePlugin, [{
70
- key: "install",
71
- value: function install(pluginManager) {
72
- // register all our core rpc methods
73
- Object.values(coreRpcMethods).forEach(function (RpcMethod) {
74
- pluginManager.addRpcMethod(function () {
75
- return new RpcMethod(pluginManager);
76
- });
77
- });
78
- pluginManager.addAdapterType(function () {
79
- return new _AdapterType.default({
80
- name: 'CytobandAdapter',
81
- configSchema: _CytobandAdapter.configSchema,
82
- AdapterClass: _CytobandAdapter.DataAdapter
43
+ install(pluginManager) {
44
+ // register all our core rpc methods
45
+ Object.values(coreRpcMethods).forEach(RpcMethod => {
46
+ pluginManager.addRpcMethod(() => new RpcMethod(pluginManager));
83
47
  });
84
- });
85
- pluginManager.addWidgetType(function () {
86
- return new _WidgetType.default({
87
- name: 'BaseFeatureWidget',
88
- heading: 'Feature details',
89
- configSchema: _BaseFeatureWidget.configSchema,
90
- stateModel: (0, _BaseFeatureWidget.stateModelFactory)(pluginManager),
91
- ReactComponent: /*#__PURE__*/(0, _react.lazy)(function () {
92
- return Promise.resolve().then(function () {
93
- return _interopRequireWildcard(require('./BaseFeatureWidget/BaseFeatureDetail'));
48
+ pluginManager.addAdapterType(() => new AdapterType_1.default({
49
+ name: 'CytobandAdapter',
50
+ configSchema: CytobandAdapter_1.configSchema,
51
+ AdapterClass: CytobandAdapter_1.DataAdapter,
52
+ }));
53
+ pluginManager.addWidgetType(() => {
54
+ return new WidgetType_1.default({
55
+ name: 'BaseFeatureWidget',
56
+ heading: 'Feature details',
57
+ configSchema: BaseFeatureWidget_1.configSchema,
58
+ stateModel: (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager),
59
+ ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BaseFeatureWidget/BaseFeatureDetail')))),
94
60
  });
95
- })
96
61
  });
97
- });
98
62
  }
99
- }]);
100
- return CorePlugin;
101
- }(_Plugin2.default);
102
-
103
- exports.default = CorePlugin;
63
+ }
64
+ exports.default = CorePlugin;
package/Plugin.js CHANGED
@@ -1,38 +1,13 @@
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
-
2
+ Object.defineProperty(exports, "__esModule", { value: true });
16
3
  /**
17
4
  * base class for a JBrowse plugin
18
5
  */
19
- var Plugin = /*#__PURE__*/function () {
20
- function Plugin() {
21
- (0, _classCallCheck2.default)(this, Plugin);
22
- (0, _defineProperty2.default)(this, "name", void 0);
23
- (0, _defineProperty2.default)(this, "url", void 0);
24
- (0, _defineProperty2.default)(this, "version", void 0);
25
- (0, _defineProperty2.default)(this, "configurationSchema", undefined);
26
- }
27
-
28
- (0, _createClass2.default)(Plugin, [{
29
- key: "install",
30
- value: function install(_pluginManager) {}
31
- }, {
32
- key: "configure",
33
- value: function configure(_pluginManager) {}
34
- }]);
35
- return Plugin;
36
- }();
37
-
38
- exports.default = Plugin;
6
+ class Plugin {
7
+ constructor() {
8
+ this.configurationSchema = undefined;
9
+ }
10
+ install(_pluginManager) { }
11
+ configure(_pluginManager) { }
12
+ }
13
+ exports.default = Plugin;