@jbrowse/core 2.0.1 → 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 (179) hide show
  1. package/BaseFeatureWidget/BaseFeatureDetail.d.ts +6 -0
  2. package/BaseFeatureWidget/BaseFeatureDetail.js +313 -592
  3. package/BaseFeatureWidget/SequenceFeatureDetails.js +213 -479
  4. package/BaseFeatureWidget/index.js +88 -126
  5. package/BaseFeatureWidget/types.js +1 -4
  6. package/BaseFeatureWidget/util.js +40 -75
  7. package/CorePlugin.js +55 -94
  8. package/Plugin.js +9 -34
  9. package/PluginLoader.js +153 -422
  10. package/PluginManager.d.ts +17 -14
  11. package/PluginManager.js +377 -666
  12. package/ReExports/Attributes.js +3 -10
  13. package/ReExports/BaseCard.js +3 -10
  14. package/ReExports/DataGrid.js +5 -12
  15. package/ReExports/FeatureDetails.js +3 -10
  16. package/ReExports/index.js +6 -12
  17. package/ReExports/list.d.ts +5 -0
  18. package/ReExports/list.js +271 -7
  19. package/ReExports/material-ui-colors.js +15 -16
  20. package/ReExports/modules.d.ts +0 -1
  21. package/ReExports/modules.js +453 -798
  22. package/TextSearch/BaseResults.js +51 -123
  23. package/TextSearch/TextSearchManager.js +66 -144
  24. package/assemblyManager/assembly.js +280 -555
  25. package/assemblyManager/assemblyConfigSchema.js +47 -64
  26. package/assemblyManager/assemblyManager.js +126 -272
  27. package/assemblyManager/index.js +9 -22
  28. package/configuration/configurationSchema.js +167 -203
  29. package/configuration/configurationSlot.js +248 -326
  30. package/configuration/index.js +19 -35
  31. package/configuration/util.js +131 -173
  32. package/data_adapters/BaseAdapter.d.ts +2 -2
  33. package/data_adapters/BaseAdapter.js +132 -521
  34. package/data_adapters/CytobandAdapter.js +40 -126
  35. package/data_adapters/dataAdapterCache.js +77 -158
  36. package/package.json +4 -5
  37. package/pluggableElementTypes/AdapterType.js +24 -79
  38. package/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  39. package/pluggableElementTypes/AddTrackWorkflowType.js +20 -0
  40. package/pluggableElementTypes/ConnectionType.js +22 -65
  41. package/pluggableElementTypes/DisplayType.js +35 -82
  42. package/pluggableElementTypes/InternetAccountType.js +23 -64
  43. package/pluggableElementTypes/PluggableElementBase.js +8 -20
  44. package/pluggableElementTypes/RpcMethodType.js +85 -427
  45. package/pluggableElementTypes/TextSearchAdapterType.js +16 -55
  46. package/pluggableElementTypes/TrackType.js +26 -70
  47. package/pluggableElementTypes/ViewType.js +21 -63
  48. package/pluggableElementTypes/WidgetType.js +21 -64
  49. package/pluggableElementTypes/index.d.ts +4 -3
  50. package/pluggableElementTypes/index.js +42 -125
  51. package/pluggableElementTypes/models/BaseConnectionModelFactory.js +28 -43
  52. package/pluggableElementTypes/models/BaseDisplayModel.js +58 -95
  53. package/pluggableElementTypes/models/BaseTrackModel.js +139 -199
  54. package/pluggableElementTypes/models/BaseViewModel.js +24 -40
  55. package/pluggableElementTypes/models/InternetAccountModel.js +116 -263
  56. package/pluggableElementTypes/models/baseConnectionConfig.js +14 -25
  57. package/pluggableElementTypes/models/baseInternetAccountConfig.js +29 -38
  58. package/pluggableElementTypes/models/baseTrackConfig.js +106 -133
  59. package/pluggableElementTypes/models/index.js +21 -70
  60. package/pluggableElementTypes/renderers/BoxRendererType.js +132 -291
  61. package/pluggableElementTypes/renderers/CircularChordRendererType.js +8 -38
  62. package/pluggableElementTypes/renderers/ComparativeServerSideRendererType.js +60 -192
  63. package/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -2
  64. package/pluggableElementTypes/renderers/FeatureRendererType.js +89 -264
  65. package/pluggableElementTypes/renderers/RendererType.js +31 -105
  66. package/pluggableElementTypes/renderers/ServerSideRenderedContent.js +61 -72
  67. package/pluggableElementTypes/renderers/ServerSideRendererType.js +112 -265
  68. package/pluggableElementTypes/renderers/index.js +19 -62
  69. package/pluggableElementTypes/renderers/util/serializableFilterChain.js +27 -65
  70. package/rpc/BaseRpcDriver.js +169 -405
  71. package/rpc/MainThreadRpcDriver.js +27 -150
  72. package/rpc/RpcManager.js +58 -159
  73. package/rpc/WebWorkerRpcDriver.js +54 -171
  74. package/rpc/configSchema.js +25 -49
  75. package/rpc/coreRpcMethods.js +221 -959
  76. package/rpc/remoteAbortSignals.js +46 -70
  77. package/tsconfig.build.tsbuildinfo +1 -1
  78. package/ui/AboutDialog.js +106 -162
  79. package/ui/App.js +157 -242
  80. package/ui/AssemblySelector.js +59 -120
  81. package/ui/CascadingMenu.js +101 -196
  82. package/ui/ColorPicker.d.ts +16 -0
  83. package/ui/ColorPicker.js +97 -0
  84. package/ui/Drawer.js +28 -61
  85. package/ui/DrawerWidget.js +108 -202
  86. package/ui/DropDownMenu.js +60 -91
  87. package/ui/EditableTypography.js +87 -149
  88. package/ui/ErrorMessage.js +41 -56
  89. package/ui/FactoryResetDialog.js +24 -57
  90. package/ui/FatalErrorDialog.js +59 -91
  91. package/ui/FileSelector/FileSelector.js +123 -189
  92. package/ui/FileSelector/LocalFileChooser.js +44 -75
  93. package/ui/FileSelector/UrlChooser.js +17 -38
  94. package/ui/FileSelector/index.js +6 -12
  95. package/ui/Icons.js +45 -69
  96. package/ui/Logo.js +57 -110
  97. package/ui/Menu.js +232 -354
  98. package/ui/PrerenderedCanvas.js +63 -87
  99. package/ui/ResizeHandle.js +87 -116
  100. package/ui/ReturnToImportFormDialog.js +32 -63
  101. package/ui/SanitizedHTML.js +64 -47
  102. package/ui/Snackbar.js +74 -101
  103. package/ui/SnackbarModel.js +37 -51
  104. package/ui/Tooltip.js +49 -76
  105. package/ui/ViewContainer.js +113 -196
  106. package/ui/colors.d.ts +10 -0
  107. package/ui/colors.js +78 -0
  108. package/ui/index.js +51 -181
  109. package/ui/react-colorful.d.ts +17 -0
  110. package/ui/react-colorful.js +455 -0
  111. package/ui/theme.js +199 -247
  112. package/util/Base1DUtils.js +163 -202
  113. package/util/Base1DViewModel.js +121 -168
  114. package/util/QuickLRU.js +84 -332
  115. package/util/TimeTraveller.d.ts +19 -0
  116. package/util/TimeTraveller.js +86 -0
  117. package/util/aborting.js +49 -127
  118. package/util/analytics.js +91 -154
  119. package/util/blockTypes.js +106 -240
  120. package/util/calculateDynamicBlocks.js +98 -128
  121. package/util/calculateStaticBlocks.js +105 -125
  122. package/util/color/cssColorsLevel4.js +156 -160
  123. package/util/color/index.js +33 -55
  124. package/util/compositeMap.js +49 -333
  125. package/util/formatFastaStrings.js +9 -14
  126. package/util/idMaker.js +18 -31
  127. package/util/index.d.ts +7 -20
  128. package/util/index.js +742 -1188
  129. package/util/io/RemoteFileWithRangeCache.js +88 -257
  130. package/util/io/index.js +95 -169
  131. package/util/jexl.js +60 -115
  132. package/util/jexlStrings.js +24 -29
  133. package/util/layouts/BaseLayout.js +1 -4
  134. package/util/layouts/GranularRectLayout.js +388 -555
  135. package/util/layouts/MultiLayout.js +41 -109
  136. package/util/layouts/PrecomputedLayout.js +56 -112
  137. package/util/layouts/PrecomputedMultiLayout.js +22 -59
  138. package/util/layouts/SceneGraph.js +127 -197
  139. package/util/layouts/index.js +29 -66
  140. package/util/mst-reflection.js +55 -71
  141. package/util/offscreenCanvasPonyfill.js +66 -134
  142. package/util/offscreenCanvasUtils.d.ts +2 -7
  143. package/util/offscreenCanvasUtils.js +49 -146
  144. package/util/range.js +29 -40
  145. package/util/rxjs.js +20 -27
  146. package/util/simpleFeature.js +88 -152
  147. package/util/stats.js +91 -151
  148. package/util/tracks.js +130 -173
  149. package/util/types/index.js +110 -179
  150. package/util/types/mst.js +91 -146
  151. package/util/types/util.js +1 -4
  152. package/util/when.js +54 -101
  153. package/BaseFeatureWidget/SequenceFeatureDetails.test.js +0 -122
  154. package/BaseFeatureWidget/index.test.js +0 -69
  155. package/TextSearch/BaseResults.test.js +0 -42
  156. package/configuration/configurationSchema.test.js +0 -266
  157. package/configuration/configurationSlot.test.js +0 -69
  158. package/configuration/util.test.js +0 -39
  159. package/data_adapters/BaseAdapter.test.js +0 -200
  160. package/declare.d.js +0 -1
  161. package/pluggableElementTypes/RpcMethodType.test.js +0 -118
  162. package/pluggableElementTypes/renderers/declare.d.js +0 -1
  163. package/pluggableElementTypes/renderers/util/serializableFilterChain.test.js +0 -20
  164. package/rpc/BaseRpcDriver.test.js +0 -540
  165. package/rpc/declaration.d.js +0 -1
  166. package/ui/FatalErrorDialog.test.js +0 -82
  167. package/ui/SanitizedHTML.test.js +0 -36
  168. package/ui/theme.test.js +0 -92
  169. package/util/Base1DViewModel.test.js +0 -130
  170. package/util/calculateDynamicBlocks.test.js +0 -74
  171. package/util/calculateStaticBlocks.test.js +0 -297
  172. package/util/declare.d.js +0 -1
  173. package/util/formatFastaStrings.test.js +0 -40
  174. package/util/index.test.js +0 -213
  175. package/util/jexlStrings.test.js +0 -48
  176. package/util/layouts/GranularRectLayout.test.js +0 -99
  177. package/util/range.test.js +0 -64
  178. package/util/simpleFeature.test.js +0 -34
  179. package/util/stats.test.js +0 -172
@@ -1,131 +1,93 @@
1
1
  "use strict";
2
-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
6
- 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");
20
-
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- var _clone = _interopRequireDefault(require("clone"));
22
-
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- var _mst = require("../util/types/mst");
24
-
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- var _excluded = ["featureData", "finalizedFeatureData"],
26
- _excluded2 = ["unformattedFeatureData", "featureData"];
27
-
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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;
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+ 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$subfeatures;
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-
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- var currentDepth = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : 0;
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- var returnObj = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : {};
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-
41
- if (depth <= currentDepth) {
14
+ function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
15
+ var _a;
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+ if (depth <= currentDepth) {
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+ return returnObj;
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+ }
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+ returnObj.subfeatures = (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
20
+ formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
21
+ return parse(sub);
22
+ });
42
23
  return returnObj;
43
- }
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-
45
- returnObj.subfeatures = (_obj$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);
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- });
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- 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(),
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- 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 {};
63
- }).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;
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- }
74
- };
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- }).actions(function (self) {
76
- return {
77
- afterCreate: function afterCreate() {
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- (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
93
- 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
- }
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- };
104
- }).preProcessSnapshot(function (snap) {
105
- // @ts-ignore
106
- var featureData = snap.featureData,
107
- finalizedFeatureData = snap.finalizedFeatureData,
108
- rest = (0, _objectWithoutProperties2.default)(snap, _excluded);
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- 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')),
35
+ })
36
+ .volatile(() => ({}))
37
+ .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,
73
+ 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;
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+ exports.stateModelFactory = stateModelFactory;
@@ -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; }
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-
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+ Object.defineProperty(exports, "__esModule", { value: true });
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+ exports.ellipses = exports.calculateUTRs = exports.revlist = exports.dedupe = exports.stitch = void 0;
22
4
  function stitch(subfeats, sequence) {
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- 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
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-
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-
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+ return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
6
+ }
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+ exports.stitch = stitch;
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+ // 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;