@jbrowse/core 1.7.11 → 2.1.0

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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
package/util/index.d.ts CHANGED
@@ -1,7 +1,8 @@
1
- import { IAnyStateTreeNode } from 'mobx-state-tree';
1
+ import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
2
2
  import { IReactionPublic, IReactionOptions } from 'mobx';
3
3
  import SimpleFeature, { Feature, isFeature } from './simpleFeature';
4
4
  import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
5
+ import { BaseBlock } from './blockTypes';
5
6
  export type { Feature };
6
7
  export * from './types';
7
8
  export * from './aborting';
@@ -149,33 +150,7 @@ export declare function bpSpanPx(leftBp: number, rightBp: number, region: {
149
150
  end: number;
150
151
  reversed?: boolean;
151
152
  }, bpPerPx: number): [number, number];
152
- export declare const objectFromEntries: {
153
- <T = any>(entries: Iterable<readonly [PropertyKey, T]>): {
154
- [k: string]: T;
155
- };
156
- (entries: Iterable<readonly any[]>): any;
157
- };
158
153
  export declare function iterMap<T, U>(iterable: Iterable<T>, func: (item: T) => U, sizeHint?: number): U[];
159
- interface Assembly {
160
- name: string;
161
- [key: string]: any;
162
- }
163
- interface Track {
164
- trackId: string;
165
- [key: string]: any;
166
- }
167
- interface Config {
168
- savedSessions: unknown[];
169
- assemblies: Assembly[];
170
- tracks: Track[];
171
- defaultSession?: {};
172
- }
173
- export declare function mergeConfigs(A: Config, B: Config): {
174
- savedSessions: unknown[];
175
- assemblies: Assembly[];
176
- tracks: Track[];
177
- defaultSession: {};
178
- };
179
154
  /**
180
155
  * Returns the index of the last element in the array where predicate is true,
181
156
  * and -1 otherwise.
@@ -222,7 +197,7 @@ export declare function renameRegionsIfNeeded<ARGTYPE extends {
222
197
  export declare function minmax(a: number, b: number): number[];
223
198
  export declare function stringify({ refName, coord, oob, }: {
224
199
  coord: number;
225
- refName: string;
200
+ refName?: string;
226
201
  oob?: boolean;
227
202
  }): string;
228
203
  export declare const isElectron: boolean;
@@ -324,22 +299,19 @@ export declare type ViewSnap = {
324
299
  interRegionPaddingWidth: number;
325
300
  minimumBlockWidth: number;
326
301
  width: number;
327
- displayedRegions: {
302
+ offsetPx: number;
303
+ staticBlocks: {
304
+ contentBlocks: BaseBlock[];
305
+ blocks: BaseBlock[];
306
+ };
307
+ displayedRegions: (IStateTreeNode & {
328
308
  start: number;
329
309
  end: number;
330
310
  refName: string;
331
311
  reversed: boolean;
332
- }[];
312
+ assemblyName: string;
313
+ })[];
333
314
  };
334
- export declare function viewBpToPx({ refName, coord, regionNumber, self, }: {
335
- refName: string;
336
- coord: number;
337
- regionNumber?: number;
338
- self: ViewSnap;
339
- }): {
340
- index: number;
341
- offsetPx: number;
342
- } | undefined;
343
315
  export declare function supportedIndexingAdapters(type: string): boolean;
344
316
  export declare function getBpDisplayStr(totalBp: number): string;
345
317
  export declare function toLocale(n: number): string;
@@ -354,3 +326,10 @@ export declare function getLayoutId({ sessionId, layoutId, }: {
354
326
  sessionId: string;
355
327
  layoutId: string;
356
328
  }): string;
329
+ export declare const useLocalStorage: (key: string, defaultValue?: string) => [string, (arg: string) => void];
330
+ export declare function getUriLink(value: {
331
+ uri: string;
332
+ baseUri?: string;
333
+ }): string;
334
+ export declare function getStr(obj: unknown): string;
335
+ export declare function measureGridWidth(elements: string[]): number;