@jbrowse/core 4.3.0 → 5.0.0-beta.10

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 (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
  1071. package/esm/util/systemColorScheme.js +27 -0
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  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
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  1077. package/esm/util/temporaryAssembly.js +29 -0
  1078. package/esm/util/thresholdScale.d.ts +91 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
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  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
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  1112. package/esm/util/types/renameIds.d.ts +1 -0
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  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
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  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,167 @@
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { use, useState } from 'react';
3
+ import { getEnv } from '@jbrowse/mobx-state-tree';
4
+ import AddIcon from '@mui/icons-material/Add';
5
+ import { Button, ListItemText, MenuItem, Tab, Tabs, TextField, } from '@mui/material';
6
+ import { observer } from 'mobx-react';
7
+ import { readConfObject } from '../configuration/readConfObject.js';
8
+ import { addRow, describedColumns, readFilterRows, removeRow, replaceRow, resolveFields, stripJexlPrefix, writeFilterRows, } from '../util/jexlFilterRows.js';
9
+ import { activeJexlFilters } from '../util/jexlFilters.js';
10
+ import { ensureJexlPrefix } from '../util/jexlStrings.js';
11
+ import { getContainingTrack } from '../util/mstUtils.js';
12
+ import { makeStyles } from '../util/tss-react/index.js';
13
+ import ExternalLink from './ExternalLink.js';
14
+ import { ConditionRowEditor, TextRowEditor, compileError, } from './JexlFilterRowEditors.js';
15
+ import MonospaceTextField from './MonospaceTextField.js';
16
+ import SubmitDialog from './SubmitDialog.js';
17
+ /**
18
+ * What a display filtering plain annotation features offers as a starting
19
+ * point. A display whose features are a richer record — a VCF, say — passes its
20
+ * own list instead: the examples are the only place the dialog says what is
21
+ * readable off a feature, so a variant track showing `type=='gene'` is teaching
22
+ * the wrong vocabulary.
23
+ */
24
+ const FEATURE_FILTER_EXAMPLES = [
25
+ {
26
+ code: "jexl:get(feature,'name')=='BRCA1'",
27
+ description: 'show only features where the name attribute is BRCA1',
28
+ },
29
+ {
30
+ code: "jexl:startsWith(get(feature,'name'),'PREFIX')",
31
+ description: "show only features where the string 'PREFIX' is the prefix of the feature name. endsWith also works",
32
+ },
33
+ {
34
+ code: "jexl:includes(get(feature,'name'),'PREFIX')",
35
+ description: "show only features where the string 'PREFIX' appears in the feature name",
36
+ },
37
+ {
38
+ code: "jexl:get(feature,'type')=='gene'",
39
+ description: 'show only gene type features in a GFF that has many other feature types',
40
+ },
41
+ {
42
+ code: "jexl:get(feature,'score') > 400",
43
+ description: 'show only features that have a score greater than 400',
44
+ },
45
+ {
46
+ code: "jexl:get(feature,'end') - get(feature,'start') < 1000000",
47
+ description: 'show only features with length less than 1Mbp',
48
+ },
49
+ ];
50
+ const FEATURE_FIELDS = [
51
+ { label: 'name', path: ['name'], type: 'text' },
52
+ { label: 'type', path: ['type'], type: 'text' },
53
+ { label: 'score', path: ['score'], type: 'number' },
54
+ { label: 'start', path: ['start'], type: 'number' },
55
+ { label: 'end', path: ['end'], type: 'number' },
56
+ { label: 'strand', path: ['strand'], type: 'number' },
57
+ ];
58
+ const useStyles = makeStyles()(theme => ({
59
+ body: {
60
+ minHeight: 280,
61
+ },
62
+ tabs: {
63
+ marginBottom: theme.spacing(2),
64
+ },
65
+ hint: {
66
+ marginBottom: theme.spacing(2),
67
+ color: theme.palette.text.secondary,
68
+ },
69
+ examples: {
70
+ minWidth: 220,
71
+ marginBottom: theme.spacing(1),
72
+ },
73
+ }));
74
+ function textLines(text) {
75
+ return text
76
+ .split('\n')
77
+ .map(line => line.trim())
78
+ .filter(line => !!line)
79
+ .map(ensureJexlPrefix);
80
+ }
81
+ function textError(text, jexl) {
82
+ for (const [i, line] of text.split('\n').entries()) {
83
+ const error = line.trim() ? compileError(line, jexl) : undefined;
84
+ if (error) {
85
+ return `Line ${i + 1}: ${error}`;
86
+ }
87
+ }
88
+ return undefined;
89
+ }
90
+ function trackName(model) {
91
+ try {
92
+ return readConfObject(getContainingTrack(model).configuration, 'name');
93
+ }
94
+ catch {
95
+ return undefined;
96
+ }
97
+ }
98
+ function withOneRow(state) {
99
+ return state.rows.length > 0 ? state : addRow(state);
100
+ }
101
+ /**
102
+ * Editor for a display's jexl feature filters, for any display implementing
103
+ * the two-tier {@link JexlFilterModel} contract. The Conditions tab shows each
104
+ * line as rows of field, operator and value where it can, and as text where it
105
+ * cannot; the Text tab is every line as text.
106
+ *
107
+ * `fields` lists what the field picker offers, then the columns `metadata`
108
+ * describes, if it is an adapter's `{column: description}` map. Either one
109
+ * given as a promise suspends the dialog until it resolves, so it must not
110
+ * reject.
111
+ */
112
+ const JexlFilterDialog = observer(function JexlFilterDialog({ model, handleClose, examples = FEATURE_FILTER_EXAMPLES, fields = FEATURE_FIELDS, metadata, }) {
113
+ const { classes } = useStyles();
114
+ const jexl = getEnv(model).pluginManager
115
+ .jexl;
116
+ const fieldList = fields instanceof Promise ? use(fields) : fields;
117
+ const described = metadata && use(metadata);
118
+ const [choices] = useState(() => resolveFields([...fieldList, ...describedColumns(described, fieldList)]));
119
+ const [state, setState] = useState(() => withOneRow(readFilterRows(activeJexlFilters(model), jexl, choices)));
120
+ const [tab, setTab] = useState('conditions');
121
+ const [text, setText] = useState({ value: '', shown: '' });
122
+ const textEdited = text.value !== text.shown;
123
+ const error = tab === 'text'
124
+ ? textError(text.value, jexl)
125
+ : state.rows.some(row => row.kind === 'text' && compileError(row.text, jexl));
126
+ const name = trackName(model);
127
+ return (_jsx(SubmitDialog, { maxWidth: "md", fullWidth: true, open: true, title: name ? `Filter ${name}` : 'Filter features', submitText: "Apply", submitDisabled: !!error, onCancel: handleClose, onSubmit: () => {
128
+ // An emptied list is "show everything", which is NOT the same as
129
+ // following the config slot, so it is set as an override too
130
+ model.setFilter(tab === 'text' && textEdited
131
+ ? textLines(text.value)
132
+ : writeFilterRows(state));
133
+ handleClose();
134
+ }, children: _jsxs("div", { className: classes.body, children: [_jsxs(Tabs, { className: classes.tabs, value: tab, onChange: (_, next) => {
135
+ if (next === 'text') {
136
+ const value = writeFilterRows(state)
137
+ .map(stripJexlPrefix)
138
+ .join('\n');
139
+ setText({ value, shown: value });
140
+ }
141
+ else if (textEdited) {
142
+ setState(withOneRow(readFilterRows(textLines(text.value), jexl, choices)));
143
+ }
144
+ setTab(next);
145
+ }, children: [_jsx(Tab, { value: "conditions", label: "Conditions" }), _jsx(Tab, { value: "text", label: "Text", "data-testid": "jexl-filter-text-tab" })] }), tab === 'conditions' ? (_jsxs(_Fragment, { children: [_jsx("div", { className: classes.hint, children: "Show features that match every condition." }), state.rows.map(row => row.kind === 'text' ? (_jsx(TextRowEditor, { row: row, jexl: jexl, onChange: next => {
146
+ setState(replaceRow(state, next));
147
+ }, onRemove: () => {
148
+ setState(removeRow(state, row.id));
149
+ } }, row.id)) : (_jsx(ConditionRowEditor, { row: row, choices: choices, onChange: next => {
150
+ setState(replaceRow(state, next));
151
+ }, onRemove: () => {
152
+ setState(removeRow(state, row.id));
153
+ } }, row.id))), _jsx(Button, { startIcon: _jsx(AddIcon, {}), onClick: () => {
154
+ setState(addRow(state));
155
+ }, children: "Add condition" })] })) : (_jsxs(_Fragment, { children: [_jsx(TextField, { select: true, size: "small", label: "Insert example\u2026", value: "", className: classes.examples, onChange: event => {
156
+ const code = stripJexlPrefix(event.target.value);
157
+ setText({
158
+ ...text,
159
+ value: text.value.trim()
160
+ ? `${text.value.trimEnd()}\n${code}`
161
+ : code,
162
+ });
163
+ }, children: examples.map(({ code, description }) => (_jsx(MenuItem, { value: code, children: _jsx(ListItemText, { primary: stripJexlPrefix(code), secondary: description }) }, code))) }), _jsx(MonospaceTextField, { fullWidth: true, minRows: 6, maxRows: 14, value: text.value, error: error, helperText: "One filter per line; a feature has to pass every line.", onChange: value => {
164
+ setText({ ...text, value });
165
+ } }), _jsxs("p", { children: ["See the", ' ', _jsx(ExternalLink, { href: "https://jbrowse.org/jb2/docs/config_guides/jexl/", children: "jexl documentation" }), ' ', "for the expression language."] })] }))] }) }));
166
+ });
167
+ export default JexlFilterDialog;
@@ -0,0 +1,15 @@
1
+ import type { ConditionRow, FieldChoice, TextRow } from '../util/jexlFilterRows.ts';
2
+ import type { Jexl } from '@jbrowse/jexl';
3
+ export declare function compileError(line: string, jexl: Pick<Jexl, 'compile'>): string | undefined;
4
+ export declare function ConditionRowEditor({ row, choices, onChange, onRemove, }: {
5
+ row: ConditionRow;
6
+ choices: FieldChoice[];
7
+ onChange: (row: ConditionRow) => void;
8
+ onRemove: () => void;
9
+ }): import("react").JSX.Element;
10
+ export declare function TextRowEditor({ row, jexl, onChange, onRemove, }: {
11
+ row: TextRow;
12
+ jexl: Pick<Jexl, 'compile'>;
13
+ onChange: (row: TextRow) => void;
14
+ onRemove: () => void;
15
+ }): import("react").JSX.Element;
@@ -0,0 +1,90 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import CloseIcon from '@mui/icons-material/Close';
3
+ import { Autocomplete, IconButton, ListItemText, MenuItem, TextField, } from '@mui/material';
4
+ import { OPERATORS, stripJexlPrefix, typedField, withField, withOp, } from '../util/jexlFilterRows.js';
5
+ import { makeStyles } from '../util/tss-react/index.js';
6
+ import MonospaceTextField from './MonospaceTextField.js';
7
+ const useStyles = makeStyles()(theme => ({
8
+ row: {
9
+ display: 'flex',
10
+ alignItems: 'flex-start',
11
+ gap: theme.spacing(1),
12
+ marginBottom: theme.spacing(1),
13
+ },
14
+ field: {
15
+ width: 220,
16
+ flexShrink: 0,
17
+ },
18
+ op: {
19
+ width: 130,
20
+ flexShrink: 0,
21
+ },
22
+ value: {
23
+ flex: 1,
24
+ },
25
+ expression: {
26
+ width: 24,
27
+ flexShrink: 0,
28
+ textAlign: 'center',
29
+ fontStyle: 'italic',
30
+ fontFamily: 'serif',
31
+ fontSize: 18,
32
+ paddingTop: 6,
33
+ color: theme.palette.text.secondary,
34
+ },
35
+ }));
36
+ export function compileError(line, jexl) {
37
+ try {
38
+ jexl.compile(stripJexlPrefix(line.trim()));
39
+ return undefined;
40
+ }
41
+ catch (e) {
42
+ return e instanceof Error ? e.message : String(e);
43
+ }
44
+ }
45
+ function RemoveButton({ onClick }) {
46
+ return (_jsx(IconButton, { size: "small", "aria-label": "Remove condition", onClick: onClick, children: _jsx(CloseIcon, { fontSize: "small" }) }));
47
+ }
48
+ function ValueInput({ row, onChange, }) {
49
+ const { classes } = useStyles();
50
+ const { field, op, value } = row;
51
+ if (op === 'set' || op === '!set') {
52
+ return _jsx("div", { className: classes.value });
53
+ }
54
+ const suggestions = field?.values ?? [];
55
+ if (op === 'in') {
56
+ return (_jsx(Autocomplete, { className: classes.value, size: "small", multiple: true, freeSolo: true, autoSelect: true, options: suggestions, value: [value].flat(), onChange: (_, next) => {
57
+ onChange({ ...row, value: next });
58
+ }, renderInput: params => (_jsx(TextField, { ...params, placeholder: "Values, Enter after each" })) }));
59
+ }
60
+ const text = [value].flat()[0] ?? '';
61
+ return suggestions.length > 0 && op !== '~' ? (_jsx(Autocomplete, { className: classes.value, size: "small", freeSolo: true, options: suggestions, inputValue: text, onInputChange: (_, next) => {
62
+ onChange({ ...row, value: next });
63
+ }, renderInput: params => _jsx(TextField, { ...params, placeholder: "Value" }) })) : (_jsx(TextField, { className: classes.value, size: "small", placeholder: op === '~' ? 'Regular expression' : 'Value', type: field?.type === 'number' ? 'number' : 'text', disabled: !field, value: text, onChange: event => {
64
+ onChange({ ...row, value: event.target.value });
65
+ } }));
66
+ }
67
+ export function ConditionRowEditor({ row, choices, onChange, onRemove, }) {
68
+ const { classes } = useStyles();
69
+ const { field } = row;
70
+ const grouped = choices.some(choice => choice.group);
71
+ return (_jsxs("div", { className: classes.row, children: [_jsx(Autocomplete, { className: classes.field, size: "small", freeSolo: true, autoSelect: true, options: choices, groupBy: grouped ? choice => choice.group ?? '' : undefined, getOptionLabel: choice => typeof choice === 'string' ? choice : choice.label, getOptionKey: choice => typeof choice === 'string' ? choice : choice.key, isOptionEqualToValue: (a, b) => typeof b !== 'string' && a.key === b.key, value: field ?? null, onChange: (_, next) => {
72
+ const chosen = typeof next !== 'string'
73
+ ? next
74
+ : next === field?.label
75
+ ? field
76
+ : (choices.find(choice => choice.label === next) ??
77
+ typedField(next));
78
+ if (chosen && chosen.key !== field?.key) {
79
+ onChange(withField(row, chosen));
80
+ }
81
+ }, renderOption: ({ key, ...props }, choice) => (_jsx("li", { ...props, children: _jsx(ListItemText, { primary: choice.label, secondary: choice.description }) }, key)), renderInput: params => _jsx(TextField, { ...params, placeholder: "Field" }) }), _jsx(TextField, { className: classes.op, select: true, size: "small", disabled: !field, value: row.op, helperText: field?.multi ? 'any value' : undefined, onChange: event => {
82
+ onChange(withOp(row, event.target.value));
83
+ }, children: OPERATORS[field?.type ?? 'any'].map(({ op, label }) => (_jsx(MenuItem, { value: op, children: label }, op))) }), _jsx(ValueInput, { row: row, onChange: onChange }), _jsx(RemoveButton, { onClick: onRemove })] }));
84
+ }
85
+ export function TextRowEditor({ row, jexl, onChange, onRemove, }) {
86
+ const { classes } = useStyles();
87
+ return (_jsxs("div", { className: classes.row, children: [_jsx("div", { className: classes.expression, title: "An expression the field pickers cannot show", children: "\u0192" }), _jsx(MonospaceTextField, { className: classes.value, variant: "standard", fullWidth: true, value: row.text, error: compileError(row.text, jexl), onChange: text => {
88
+ onChange({ ...row, text });
89
+ } }), _jsx(RemoveButton, { onClick: onRemove })] }));
90
+ }
@@ -0,0 +1,9 @@
1
+ import type { ReactNode } from 'react';
2
+ export default function LabeledCheckbox({ checked, onChange, label, className, disabled, size, }: {
3
+ checked: boolean;
4
+ onChange: (checked: boolean) => void;
5
+ label: ReactNode;
6
+ className?: string;
7
+ disabled?: boolean;
8
+ size?: 'small' | 'medium';
9
+ }): import("react").JSX.Element;
@@ -0,0 +1,7 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Checkbox, FormControlLabel } from '@mui/material';
3
+ export default function LabeledCheckbox({ checked, onChange, label, className, disabled, size, }) {
4
+ return (_jsx(FormControlLabel, { className: className, disabled: disabled, control: _jsx(Checkbox, { size: size, checked: checked, onChange: event => {
5
+ onChange(event.target.checked);
6
+ } }), label: label }));
7
+ }
@@ -0,0 +1,4 @@
1
+ import type { ComponentProps } from 'react';
2
+ declare const Lazy: import("react").LazyExoticComponent<typeof import("./BaseTooltip.tsx").default>;
3
+ export default function LazyBaseTooltip(props: ComponentProps<typeof Lazy>): import("react").JSX.Element;
4
+ export {};
@@ -0,0 +1,9 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Suspense, lazy } from 'react';
3
+ // The tooltip, behind its own chunk: @floating-ui is ~266KB and this is what
4
+ // lets the ui barrel export it without putting that on the startup path. A
5
+ // consumer that wants the eager component deep-imports './BaseTooltip.tsx'.
6
+ const Lazy = lazy(() => import('./BaseTooltip.js'));
7
+ export default function LazyBaseTooltip(props) {
8
+ return (_jsx(Suspense, { fallback: null, children: _jsx(Lazy, { ...props }) }));
9
+ }
@@ -0,0 +1,7 @@
1
+ import type { LegendSwatch } from './legendSpec.ts';
2
+ export declare function LegendSwatchGlyph({ swatch, size, x, y, }: {
3
+ swatch: LegendSwatch;
4
+ size: number;
5
+ x?: number;
6
+ y?: number;
7
+ }): import("react").JSX.Element;
@@ -0,0 +1,30 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { appendGlyph } from '@jbrowse/render-core/marks/glyphPaint';
3
+ import { DIAMOND_GLYPH_SCALE } from '@jbrowse/render-core/shaders/pointMarkConsts';
4
+ import { SHAPE_CODES } from '../util/shapeNames.js';
5
+ // The point mark's own painter, recorded as SVG path data, so the key draws
6
+ // the glyph the plot draws. The diamond paints wider than its diameter and
7
+ // is scaled down to fit the box.
8
+ function glyphPathData(shape, size, x, y) {
9
+ const d = [];
10
+ const path = {
11
+ moveTo: (px, py) => d.push(`M${px} ${py}`),
12
+ lineTo: (px, py) => d.push(`L${px} ${py}`),
13
+ closePath: () => d.push('Z'),
14
+ rect: (px, py, w, h) => d.push(`M${px} ${py}h${w}v${h}h${-w}Z`),
15
+ arc: (cx, cy, r) => d.push(`A${r} ${r} 0 1 0 ${cx - r} ${cy}A${r} ${r} 0 1 0 ${cx + r} ${cy}Z`),
16
+ };
17
+ const diameter = shape === 'diamond' ? size / DIAMOND_GLYPH_SCALE : size;
18
+ appendGlyph(path, SHAPE_CODES[shape], x + size / 2, y + size / 2, diameter);
19
+ return d.join('');
20
+ }
21
+ // The one place that decides what a legend swatch looks like. Returns a bare
22
+ // shape rather than a rooted <svg>, so the floating legend (which wraps it in an
23
+ // inline <svg>) and the SVG export (which drops it into a row <g>) draw the
24
+ // identical box.
25
+ //
26
+ // The shape fills the `size` box from (x, y) so a caller can lay swatches out on
27
+ // a fixed pitch.
28
+ export function LegendSwatchGlyph({ swatch, size, x = 0, y = 0, }) {
29
+ return swatch.shape ? (_jsx("path", { d: glyphPathData(swatch.shape, size, x, y), fill: swatch.color })) : (_jsx("rect", { x: x, y: y, width: size, height: size, fill: swatch.color }));
30
+ }
@@ -0,0 +1 @@
1
+ export default function LoadingDots(): import("react").JSX.Element;
@@ -0,0 +1,30 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { makeStyles } from '../util/tss-react/index.js';
3
+ import { dot1, dot2, dot3 } from './loadingDotKeyframes.js';
4
+ const useStyles = makeStyles()({
5
+ dots: {
6
+ display: 'inline-block',
7
+ width: '1em',
8
+ textAlign: 'left',
9
+ '& span': {
10
+ display: 'inline-block',
11
+ opacity: 0,
12
+ // promote each dot to its own compositor layer so the opacity animation
13
+ // is offloaded from the main thread and keeps running during jank
14
+ willChange: 'opacity',
15
+ '&:nth-of-type(1)': {
16
+ animation: `${dot1} 1.2s infinite`,
17
+ },
18
+ '&:nth-of-type(2)': {
19
+ animation: `${dot2} 1.2s infinite`,
20
+ },
21
+ '&:nth-of-type(3)': {
22
+ animation: `${dot3} 1.2s infinite`,
23
+ },
24
+ },
25
+ },
26
+ });
27
+ export default function LoadingDots() {
28
+ const { classes } = useStyles();
29
+ return (_jsxs("span", { className: classes.dots, children: [_jsx("span", { children: "." }), _jsx("span", { children: "." }), _jsx("span", { children: "." })] }));
30
+ }
@@ -3,5 +3,21 @@ interface Props extends TypographyProps {
3
3
  message?: string;
4
4
  children?: never;
5
5
  }
6
- export default function LoadingEllipses({ message, children, variant, ...rest }: Props): import("react/jsx-runtime").JSX.Element;
6
+ /**
7
+ * The label every part of the app shows while it is working, and — through
8
+ * `data-busy` — the only thing an automated capture has to look at to know that
9
+ * it is.
10
+ *
11
+ * The attribute is the contract that replaces reading the label. A harness
12
+ * waiting for a page to finish used to scan visible text for /^loading/ and
13
+ * resolve `getComputedStyle` to decide whether each match was on screen, which
14
+ * makes a rendering detail load-bearing: a reworded message, a translation, or
15
+ * an element that animates its opacity all change the answer. `[data-busy]` is
16
+ * published by the component that knows, so a wait is one selector.
17
+ *
18
+ * Anything that renders its own in-flight banner instead of this component
19
+ * should carry the attribute too — see `isPageBusyInPage` in
20
+ * `@jbrowse/capture`, which is what reads it.
21
+ */
22
+ export default function LoadingEllipses({ message, variant, ...rest }: Props): import("react").JSX.Element;
7
23
  export {};
@@ -1,31 +1,22 @@
1
- import { jsx as _jsx } from "react/jsx-runtime";
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import { Typography } from '@mui/material';
3
- import { cx, keyframes, makeStyles } from "../util/tss-react/index.js";
4
- const useStyles = makeStyles()({
5
- dots: {
6
- '&::after': {
7
- display: 'inline-block',
8
- content: '""',
9
- width: '1em',
10
- textAlign: 'left',
11
- animation: `${keyframes `
12
- 0% {
13
- content: '';
14
- }
15
- 25% {
16
- content: '.';
17
- }
18
- 50% {
19
- content: '..';
20
- }
21
- 75% {
22
- content: '...';
23
- }
24
- `} 1.2s infinite ease-in-out`,
25
- },
26
- },
27
- });
28
- export default function LoadingEllipses({ message, children, variant = 'body2', ...rest }) {
29
- const { classes } = useStyles();
30
- return (_jsx(Typography, { className: cx(classes.dots, rest.className), ...rest, variant: variant, children: message || 'Loading' }));
3
+ import LoadingDots from './LoadingDots.js';
4
+ /**
5
+ * The label every part of the app shows while it is working, and — through
6
+ * `data-busy` — the only thing an automated capture has to look at to know that
7
+ * it is.
8
+ *
9
+ * The attribute is the contract that replaces reading the label. A harness
10
+ * waiting for a page to finish used to scan visible text for /^loading/ and
11
+ * resolve `getComputedStyle` to decide whether each match was on screen, which
12
+ * makes a rendering detail load-bearing: a reworded message, a translation, or
13
+ * an element that animates its opacity all change the answer. `[data-busy]` is
14
+ * published by the component that knows, so a wait is one selector.
15
+ *
16
+ * Anything that renders its own in-flight banner instead of this component
17
+ * should carry the attribute too — see `isPageBusyInPage` in
18
+ * `@jbrowse/capture`, which is what reads it.
19
+ */
20
+ export default function LoadingEllipses({ message, variant = 'body2', ...rest }) {
21
+ return (_jsxs(Typography, { ...rest, variant: variant, "data-busy": "true", children: [message || 'Loading', _jsx(LoadingDots, {})] }));
31
22
  }
@@ -0,0 +1,23 @@
1
+ /**
2
+ * Returns false, then flips true once `active` has stayed true continuously for
3
+ * `delayMs`. Each activation gets a fresh delay, and the flag drops the moment
4
+ * `active` does.
5
+ *
6
+ * Keyed on a count of RISING edges rather than on `active` itself, so the
7
+ * falling edge does no work at all. A display refetching through a wheel zoom
8
+ * flips `active` several times a second — it finishes a fetch, waits out the
9
+ * debounce, starts the next — and an effect depending on `active` tore its timer
10
+ * down and built a new one on each of those, twice over, for a scrim that by
11
+ * construction never appears. Deriving the flag from a comparison instead means
12
+ * one `setTimeout` per loading pulse, which is the floor for these semantics.
13
+ */
14
+ export declare function useDelayedFlag(active: boolean, delayMs: number): boolean;
15
+ export default function LoadingOverlay({ statusMessage, progress, isVisible, immediate, canceled, onCancel, onRetry, }: {
16
+ statusMessage?: string;
17
+ progress?: number;
18
+ isVisible?: boolean;
19
+ immediate?: boolean;
20
+ canceled?: boolean;
21
+ onCancel?: () => void;
22
+ onRetry?: () => void;
23
+ }): import("react").JSX.Element | null;
@@ -0,0 +1,139 @@
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { useEffect, useState } from 'react';
3
+ import CloseIcon from '@mui/icons-material/Close';
4
+ import RefreshIcon from '@mui/icons-material/Refresh';
5
+ import { IconButton, Tooltip } from '@mui/material';
6
+ import { progressLabel } from '../util/progress.js';
7
+ import { makeStyles } from '../util/tss-react/index.js';
8
+ import LoadingDots from './LoadingDots.js';
9
+ import StatusProgressBar from './StatusProgressBar.js';
10
+ import { alpha } from './palette.js';
11
+ const cancelDelayMs = 5000;
12
+ // suppress the overlay for the first moments of a refetch so quick zoom/pan
13
+ // loads stay silent and only genuinely slow loads ever draw the indicator.
14
+ // Skipped when `immediate` is set (initial load with nothing on screen yet) —
15
+ // there's no content to flash over, so the indicator shows right away.
16
+ const flashDelayMs = 250;
17
+ /**
18
+ * Returns false, then flips true once `active` has stayed true continuously for
19
+ * `delayMs`. Each activation gets a fresh delay, and the flag drops the moment
20
+ * `active` does.
21
+ *
22
+ * Keyed on a count of RISING edges rather than on `active` itself, so the
23
+ * falling edge does no work at all. A display refetching through a wheel zoom
24
+ * flips `active` several times a second — it finishes a fetch, waits out the
25
+ * debounce, starts the next — and an effect depending on `active` tore its timer
26
+ * down and built a new one on each of those, twice over, for a scrim that by
27
+ * construction never appears. Deriving the flag from a comparison instead means
28
+ * one `setTimeout` per loading pulse, which is the floor for these semantics.
29
+ */
30
+ export function useDelayedFlag(active, delayMs) {
31
+ const [previous, setPrevious] = useState(active);
32
+ const [activation, setActivation] = useState(0);
33
+ if (previous !== active) {
34
+ setPrevious(active);
35
+ if (active) {
36
+ setActivation(n => n + 1);
37
+ }
38
+ }
39
+ const [elapsedFor, setElapsedFor] = useState(-1);
40
+ useEffect(() => {
41
+ const id = setTimeout(() => {
42
+ setElapsedFor(activation);
43
+ }, delayMs);
44
+ return () => {
45
+ clearTimeout(id);
46
+ };
47
+ }, [activation, delayMs]);
48
+ return active && elapsedFor === activation;
49
+ }
50
+ const useStyles = makeStyles()(theme => {
51
+ // derive the stripe + chip tints from the theme so the "something's happening"
52
+ // signal stays subtle and equally visible in light and dark mode
53
+ const stripe = alpha(theme.palette.text.primary, 0.05);
54
+ return {
55
+ overlay: {
56
+ position: 'absolute',
57
+ top: 0,
58
+ left: 0,
59
+ right: 0,
60
+ bottom: 0,
61
+ background: `repeating-linear-gradient(45deg, transparent, transparent 8px, ${stripe} 8px, ${stripe} 16px)`,
62
+ pointerEvents: 'none',
63
+ zIndex: 1,
64
+ display: 'flex',
65
+ justifyContent: 'center',
66
+ alignItems: 'flex-start',
67
+ paddingTop: '20px',
68
+ },
69
+ // the status chip is the only interactive element; the striped backdrop stays
70
+ // click-through so it never swallows track interactions.
71
+ //
72
+ // Mostly-opaque paper (was 0.4, which let dense features and the striping
73
+ // read straight through the label): the chip sits over a canvas whose colors
74
+ // aren't known here, so the text needs its own backing to stay legible.
75
+ // `background.paper` rather than a literal white so dark mode gets the dark
76
+ // equivalent, and short of fully opaque so it still reads as an overlay.
77
+ content: {
78
+ pointerEvents: 'auto',
79
+ display: 'flex',
80
+ flexDirection: 'column',
81
+ alignItems: 'center',
82
+ gap: 2,
83
+ background: alpha(theme.palette.background.paper, 0.85),
84
+ borderRadius: 4,
85
+ padding: '2px 8px',
86
+ },
87
+ row: {
88
+ display: 'flex',
89
+ alignItems: 'center',
90
+ gap: 4,
91
+ },
92
+ text: {
93
+ fontSize: '0.8rem',
94
+ fontWeight: 300,
95
+ },
96
+ bar: {
97
+ width: 160,
98
+ },
99
+ };
100
+ });
101
+ export default function LoadingOverlay({ statusMessage, progress, isVisible, immediate, canceled, onCancel, onRetry, }) {
102
+ const { classes } = useStyles();
103
+ const hasProgress = progress !== undefined;
104
+ // anti-flash: only render after the load has run long enough to be worth
105
+ // signaling, so fast loads show nothing at all. `immediate` bypasses this for
106
+ // initial loads, where nothing is on screen to flash over yet.
107
+ //
108
+ // The delay runs off `isVisible` ALONE. Feeding `!immediate` in as well made
109
+ // `immediate` *restart* the timer rather than merely bypass it, and the chrome
110
+ // flips `immediate` mid-load: it passes `immediate={!painted}`, so first paint
111
+ // drops it while the phase is still `loading` — region 1 drawn, regions 2..n
112
+ // in flight. The scrim then blinked out for a fresh 250 ms in the middle of
113
+ // one continuous load.
114
+ const shownAfterDelay = useDelayedFlag(!!isVisible, flashDelayMs);
115
+ const shown = !!isVisible && (!!immediate || shownAfterDelay);
116
+ // only offer cancel after the overlay has been continuously visible for a few
117
+ // seconds, so a quick load can't be canceled by an accidental click.
118
+ //
119
+ // Keyed on `shown` rather than `isVisible`, which is what "continuously
120
+ // visible" means and is also what keeps this timer out of a zoom: a display
121
+ // refetching per animation frame flips `isVisible` a couple of times a frame,
122
+ // and each flip was a clearTimeout/setTimeout pair for a five-second delay
123
+ // that could never elapse — 368 timer installs over a ten-second gesture,
124
+ // half of them these.
125
+ const cancelableAfterDelay = useDelayedFlag(shown, cancelDelayMs);
126
+ const cancelable = shown && cancelableAfterDelay;
127
+ // Rendered only while shown. The content chip is `pointerEvents:auto`, so
128
+ // leaving it mounted (merely transparent) in the idle state would silently
129
+ // swallow clicks/hovers over the top-center of every track it overlays. There
130
+ // is no fade transition, so mount/unmount is visually identical to toggling
131
+ // opacity anyway.
132
+ // `loading-overlay` is a readiness selector meaning work in flight, so the
133
+ // canceled state, which is finished, publishes its own
134
+ return shown ? (_jsx("span", { className: classes.overlay, "data-testid": canceled ? 'loading-overlay-canceled' : 'loading-overlay', children: _jsx("span", { className: classes.content, children: canceled ? (_jsxs("span", { className: classes.row, children: [_jsx("span", { className: classes.text, children: "Loading canceled" }), onRetry ? (_jsx(Tooltip, { title: "Retry", children: _jsx(IconButton, { size: "small", "data-testid": "loading-overlay-retry", onClick: () => {
135
+ onRetry();
136
+ }, children: _jsx(RefreshIcon, { fontSize: "inherit" }) }) })) : null] })) : (_jsxs(_Fragment, { children: [_jsxs("span", { className: classes.row, children: [_jsxs("span", { className: classes.text, children: [progressLabel(statusMessage || 'Loading', progress), hasProgress ? null : _jsx(LoadingDots, {})] }), onCancel && cancelable ? (_jsx(Tooltip, { title: "Cancel", children: _jsx(IconButton, { size: "small", "data-testid": "loading-overlay-cancel", onClick: () => {
137
+ onCancel();
138
+ }, children: _jsx(CloseIcon, { fontSize: "inherit" }) }) })) : null] }), hasProgress ? (_jsx(StatusProgressBar, { className: classes.bar, fraction: progress })) : null] })) }) })) : null;
139
+ }
@@ -0,0 +1,16 @@
1
+ import type { TypographyProps } from '@mui/material';
2
+ /**
3
+ * The shared "labelled ellipses + optional determinate bar" body used by the
4
+ * loading/refetch indicators. Renders a {@link LoadingEllipses} label — with the
5
+ * rounded percent appended via {@link progressLabel} when `fraction` is
6
+ * determinate — and a determinate {@link StatusProgressBar} only when a
7
+ * `fraction` is present (an indeterminate phase shows just the animated label,
8
+ * no bar). Callers own the surrounding layout and supply `barClassName` for the
9
+ * bar width.
10
+ */
11
+ export default function LoadingProgress({ message, fraction, variant, barClassName, }: {
12
+ message?: string;
13
+ fraction?: number;
14
+ variant?: TypographyProps['variant'];
15
+ barClassName?: string;
16
+ }): import("react").JSX.Element;