@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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@@ -0,0 +1,189 @@
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+ import type { RefObject } from 'react';
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+ export declare function useFocusOnInteraction(ref: RefObject<HTMLElement | null>, onInteract: () => void): void;
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+ /**
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+ * Has `key` stayed the same for five seconds? A loading screen passes
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+ * everything it is showing, so any status at all — a new phase, another chunk
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+ * of bytes — restarts the wait, and only a load that has stopped saying
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+ * anything gets there. `ViewLoadingScreen` and the embed `ViewStatus` use it to
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+ * name the file a stalled load is waiting on.
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+ *
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+ * The timeout stores the key it fired for rather than a boolean, so a key that
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+ * has moved on is not stalled and the notice goes away with no write to undo.
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+ */
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+ export declare function useStalled(key: string): boolean;
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+ /**
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+ * Has the loading screen been up for two seconds? Until then it says only
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+ * "Loading": a fast load flashes its phase labels too briefly to read, and a
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+ * label glimpsed for a frame reads as a claim about what the app is doing.
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+ */
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+ export declare function useSlowLoad(): boolean;
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+ export declare function useDebounce<T>(value: T, delay: number): T;
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+ export declare function useWidthSetter(view: {
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+ setWidth: (arg: number) => void;
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+ id?: string;
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+ }): RefObject<HTMLDivElement | null>;
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+ /**
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+ * Build a value exactly once per mount — including under React StrictMode,
27
+ * which `useState(() => build())` does not.
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+ *
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+ * StrictMode double-invokes a state initializer in development and throws the
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+ * SECOND result away. For an ordinary value that is the intended lint: it
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+ * surfaces impure initializers and costs nothing. For anything that owns
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+ * something — an MST tree, a worker pool, a subscription — it stands up a second
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+ * one and then drops the only reference to it, so nothing can ever tear it down,
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+ * and it is invisible because the one React kept behaves perfectly.
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+ *
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+ * A ref is written once and survives the double render; this is React's own
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+ * "avoiding recreating the ref contents" pattern.
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+ */
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+ export declare function useCreateOnce<T>(create: () => T): T;
40
+ /**
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+ * `useCreateOnce` for an asynchronous factory: returns undefined until
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+ * `create` resolves, and rethrows a rejection from render. The value can
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+ * resolve after the component is gone — a caller whose value is expensive to
44
+ * leak should use product-core's `useAsyncEngineLifecycle`, which discards
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+ * that late arrival.
46
+ */
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+ export declare function useCreateOnceAsync<T>(create: () => Promise<T>): T | undefined;
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+ /**
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+ * Run `cleanup` when the component *really* unmounts.
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+ *
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+ * "Really" is the whole difficulty, because React does not distinguish a final
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+ * unmount from a simulated one. The obvious spelling —
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+ * `useEffect(() => () => cleanup(), [])` — is wrong in exactly the environment
54
+ * most hosts develop in, jbrowse-web included: StrictMode runs
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+ * setup → cleanup → setup on a live component, so a cleanup that destroys
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+ * something leaves the component holding the destroyed thing for the rest of its
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+ * life, with the second setup having nothing to rebuild from. For an MST tree
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+ * that is not a quiet degradation — the next read throws `[mobx-state-tree] …
59
+ * [dead]`.
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+ *
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+ * So the teardown is deferred by a microtask and cancelled if setup runs again.
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+ * StrictMode's cleanup and re-setup are one synchronous block, so the cancel
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+ * always wins there; a real unmount never runs setup again, so the microtask
64
+ * fires.
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+ *
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+ * This owns a *component's* teardown, not a per-value one: `cleanup` always sees
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+ * the latest render's closure, and swapping the thing being torn down mid-life
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+ * is not supported. Pair it with {@link useCreateOnce}, which is the shape that
69
+ * makes that true.
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+ *
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+ * Deliberately not covered: a subtree hidden with `<Activity>`, which destroys
72
+ * effects and re-creates them a TASK later rather than synchronously, so the
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+ * cancel below cannot reach it. Measured, not assumed — `useFinalUnmount.test.tsx`
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+ * pins that hiding tears the value down and showing does not rebuild it, since
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+ * `useCreateOnce`'s ref survives the hide. A host that needs a view to survive
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+ * being hidden owns the engine itself and keeps it outside the hidden tree.
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+ */
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+ export declare function useFinalUnmount(cleanup: () => void): void;
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+ /**
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+ * `useState` backed by a localStorage key.
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+ *
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+ * Originally https://usehooks.com/useLocalStorage/, which is per-instance: two
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+ * components on the same key each kept their own copy of it, so toggling a
84
+ * setting in one BreakpointSplitView header left a second one open beside it
85
+ * showing the old value until it remounted. Instances on a key now subscribe to
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+ * each other's writes, and to other tabs' — `subscribeToLocalStorageKey`.
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+ *
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+ * The store is read on every notify rather than cached, so nothing here can go
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+ * stale against a `localStorage.clear()`. Which also means a functional update
90
+ * resolves against what is actually stored: two `setValue(v => …)` calls in one
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+ * handler used to keep only the second, because both resolved against the value
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+ * captured by the render that produced the setter.
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+ *
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+ * `enabled: false` keeps the value in component state only: nothing is read,
95
+ * written or shared. Callers use it for a key that isn't meaningful yet (no
96
+ * assembly chosen, so nothing to scope the key to). A page with no usable store
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+ * at all — an RPC worker, SSR, a cross-origin iframe with third-party storage
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+ * blocked, which is the embedded products on someone else's page — runs in that
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+ * same mode, because reading a key back through a store that dropped the write
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+ * answers the default and would report it as the stored value: the control
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+ * would revert the instant the user moved it.
102
+ */
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+ export declare function useLocalStorage<T>(key: string, initialValue: T, enabled?: boolean): readonly [T, (value: T | ((val: T) => T)) => void];
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+ /**
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+ * The CSS custom property a scroll port publishes its own visible height as, for
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+ * descendants that have to size against the surface they actually scroll in.
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+ *
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+ * `100vh` is the wrong answer for all three of JBrowse's scroll ports and looks
109
+ * right in the one place it is least wrong: the classic view stack sits under a
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+ * 48px AppBar (measured 852 against a 900px window), a workspace panel is an
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+ * arbitrary dockview cell, and a bounded embedded view is whatever box the host
112
+ * gave it. A sticky element's offsets are relative to its scroll port, so a
113
+ * `max-height` that bounds one has to be too.
114
+ */
115
+ export declare const SCROLL_PORT_HEIGHT_VAR = "--jbrowse-scrollport-height";
116
+ /**
117
+ * Publishes {@link SCROLL_PORT_HEIGHT_VAR} on the element the returned ref is
118
+ * attached to. Put it on the element that actually scrolls; the property
119
+ * inherits, so anything inside can read it with a `100vh` fallback for hosts
120
+ * that never mount one.
121
+ *
122
+ * Written straight to the node instead of through state on purpose. This sits on
123
+ * a container wrapping every view, so a re-render per resize frame would
124
+ * re-render all of them to produce a number only CSS reads.
125
+ */
126
+ export declare function useScrollPortHeightVar(): RefObject<HTMLDivElement | null>;
127
+ /**
128
+ * The nearest ancestor that actually scrolls `el`, or undefined if nothing
129
+ * above it does.
130
+ */
131
+ export declare function scrollPortOf(el: HTMLElement): HTMLElement | undefined;
132
+ /**
133
+ * Whether the element the ref is on is taller than the scroll port it sits in —
134
+ * i.e. whether there is content a user could actually scroll to.
135
+ *
136
+ * Not the same question as "does the port overflow": a port can overflow by
137
+ * trailing space it renders for its own reasons, and a scrollbar offering only
138
+ * that is worse than none, since it says the page has more to show when it does
139
+ * not. So this measures the *content* box and leaves the trailing space out of
140
+ * the comparison, which means the caller has to keep that space outside the
141
+ * measured element.
142
+ *
143
+ * Stable rather than oscillating, and not by luck: turning the answer true adds
144
+ * a scrollbar, which narrows the content, and narrowing can only make content
145
+ * taller — so a true answer stays true and a false one stays false.
146
+ *
147
+ * `useLayoutEffect`, so the first measurement and the re-render it causes both
148
+ * land before paint. A view added to the stack scrolls itself into view from a
149
+ * passive effect, and passive effects run after every layout effect in the tree:
150
+ * measuring here means the trailing space this gates is already in the DOM by
151
+ * the time that scroll is computed against it.
152
+ */
153
+ export declare function useScrollPortOverflow(ref: React.RefObject<HTMLElement | null>): boolean;
154
+ /**
155
+ * Heights of the chrome boxes a sticky element below them has to clear. Each is
156
+ * published from a measurement rather than assumed, because the constants they
157
+ * default to are nominal: `VIEW_HEADER_HEIGHT` and the LGV header bar's height
158
+ * were written into the CSS by the pin-elements work (#4237) so that the sticky
159
+ * offsets summing them would be true, and a box pinned to a constant clips its
160
+ * own content once the root font size grows — measured on the stock theme, the
161
+ * view header overflows at a 18px root and the LGV controls row at 24px.
162
+ *
163
+ * So those CSS heights are minimums and these carry the truth. The fallbacks
164
+ * keep the nominal answer for the frame before the first measurement, and for a
165
+ * host that mounts no publisher. A box that stays fixed still publishes — see
166
+ * the embedded `ViewTitle`, which is a density choice rather than a constraint
167
+ * now that nothing below it re-derives its height.
168
+ *
169
+ * Cheap enough to put on every view: measured across a jbrowse-web session, the
170
+ * observers behind these fired 0 times over 60 pan frames and 10 zooms, and ~5
171
+ * times per window resize.
172
+ */
173
+ export declare const VIEW_HEADER_HEIGHT_VAR = "--jbrowse-view-header-height";
174
+ export declare const LGV_HEADER_HEIGHT_VAR = "--jbrowse-lgv-header-height";
175
+ /**
176
+ * Publishes the measured height of `ref`'s element as `varName`, set on its
177
+ * **parent**. The parent, not the element itself: what reads these is a sticky
178
+ * sibling *below* the measured box, so publishing on the box would put the
179
+ * property out of the reader's inheritance chain.
180
+ *
181
+ * Takes the ref rather than returning one — the boxes being measured are also
182
+ * the ones a view scrolls into view or hangs a gesture on, so they tend to
183
+ * already have one.
184
+ *
185
+ * Written straight to the node rather than through state, for the reason
186
+ * {@link useScrollPortHeightVar} gives — and here with the extra one that a
187
+ * header re-rendering on its own resize is a loop waiting for a rounding error.
188
+ */
189
+ export declare function useChromeHeightVar(ref: React.RefObject<HTMLElement | null>, varName: string): void;
@@ -0,0 +1,485 @@
1
+ import { useEffect, useLayoutEffect, useRef, useState } from 'react';
2
+ // The package names itself here on purpose, and this import must not be made
3
+ // relative: `jest.config.js` maps `@jbrowse/core/util/useMeasure` to a mock,
4
+ // and `moduleNameMapper` matches the request string rather than the file it
5
+ // resolves to. jsdom has no layout, so the real hook reports 0×0 — a relative
6
+ // path reaches the same file, misses the mock, and every view then measures
7
+ // zero and never initializes. Which fails as a suite of timeouts nowhere near
8
+ // this line. The three plugins importing it do so for the same reason.
9
+ import { useEventCallback } from '@jbrowse/core/util/useEventCallback';
10
+ import useMeasure from '@jbrowse/core/util/useMeasure';
11
+ import { isAlive } from '@jbrowse/mobx-state-tree';
12
+ // relative, not through the `util` barrel: that barrel re-exports this file
13
+ import { localStorageAvailable, localStorageGetJSON, localStorageRemoveItem, localStorageSetItem, notifyLocalStorageKey, subscribeToLocalStorageKey, } from './localStorage.js';
14
+ // Fires `onInteract` when a mousedown/keydown/focusin lands inside `ref`; used
15
+ // to set the focused view on click and on Tab. Listens at the document level
16
+ // rather than through React handlers so one listener covers the whole subtree,
17
+ // but bubble-phase: a child calling stopPropagation DOES suppress it, which is
18
+ // why `ResizeHandle` claims its press with a `data-gesture-owner` marker instead
19
+ // of stopping the mousedown. Registering with `{ capture: true }` would make
20
+ // focus survive those, at the cost of focusing the view for menus and error bars
21
+ // that currently do not — a behavior change, not a bug fix.
22
+ //
23
+ // **`focusin` is the one that makes keyboard entry work**, and it is not
24
+ // redundant with `keydown`. A Tab that moves focus INTO the container fires its
25
+ // keydown on the element being left, which is outside `ref` — so with keydown
26
+ // alone the assignment lagged a keystroke, and the first shortcut a keyboard
27
+ // user pressed after arriving went to whichever view they came from.
28
+ // `focusin` (unlike `focus`) bubbles, so one document listener sees it, and its
29
+ // target is the element that just RECEIVED focus. A mouse press on a focusable
30
+ // node fires both; `onInteract` is idempotent for every caller (it assigns an
31
+ // id), so the double call costs nothing.
32
+ //
33
+ // `onInteract` is wrapped in a stable callback so callers can pass an inline
34
+ // closure without re-subscribing the listeners every render (we don't rely on
35
+ // the React Compiler memoizing it, since library consumers may not run it).
36
+ export function useFocusOnInteraction(ref, onInteract) {
37
+ const stableOnInteract = useEventCallback(onInteract);
38
+ useEffect(() => {
39
+ function handleSelectView(e) {
40
+ if (e.target instanceof Element && ref.current?.contains(e.target)) {
41
+ stableOnInteract();
42
+ }
43
+ }
44
+ document.addEventListener('mousedown', handleSelectView);
45
+ document.addEventListener('keydown', handleSelectView);
46
+ document.addEventListener('focusin', handleSelectView);
47
+ return () => {
48
+ document.removeEventListener('mousedown', handleSelectView);
49
+ document.removeEventListener('keydown', handleSelectView);
50
+ document.removeEventListener('focusin', handleSelectView);
51
+ };
52
+ }, [ref, stableOnInteract]);
53
+ }
54
+ // Long enough that a load which is merely slow never says it, short enough to
55
+ // beat the point where someone decides the app is broken
56
+ const STALL_MS = 5000;
57
+ /**
58
+ * Has `key` stayed the same for five seconds? A loading screen passes
59
+ * everything it is showing, so any status at all — a new phase, another chunk
60
+ * of bytes — restarts the wait, and only a load that has stopped saying
61
+ * anything gets there. `ViewLoadingScreen` and the embed `ViewStatus` use it to
62
+ * name the file a stalled load is waiting on.
63
+ *
64
+ * The timeout stores the key it fired for rather than a boolean, so a key that
65
+ * has moved on is not stalled and the notice goes away with no write to undo.
66
+ */
67
+ export function useStalled(key) {
68
+ const [stalledKey, setStalledKey] = useState();
69
+ useEffect(() => {
70
+ const timer = setTimeout(() => {
71
+ setStalledKey(key);
72
+ }, STALL_MS);
73
+ return () => {
74
+ clearTimeout(timer);
75
+ };
76
+ }, [key]);
77
+ return stalledKey === key;
78
+ }
79
+ const SLOW_LOAD_MS = 2000;
80
+ /**
81
+ * Has the loading screen been up for two seconds? Until then it says only
82
+ * "Loading": a fast load flashes its phase labels too briefly to read, and a
83
+ * label glimpsed for a frame reads as a claim about what the app is doing.
84
+ */
85
+ export function useSlowLoad() {
86
+ const [slow, setSlow] = useState(false);
87
+ useEffect(() => {
88
+ const timer = setTimeout(() => {
89
+ setSlow(true);
90
+ }, SLOW_LOAD_MS);
91
+ return () => {
92
+ clearTimeout(timer);
93
+ };
94
+ }, []);
95
+ return slow;
96
+ }
97
+ export function useDebounce(value, delay) {
98
+ const [debouncedValue, setDebouncedValue] = useState(value);
99
+ useEffect(() => {
100
+ const handle = setTimeout(() => {
101
+ setDebouncedValue(value);
102
+ }, delay);
103
+ return () => {
104
+ clearTimeout(handle);
105
+ };
106
+ }, [value, delay]);
107
+ return debouncedValue;
108
+ }
109
+ // used in ViewContainer files to get the width. useMeasure reports the content
110
+ // box, so padding is already excluded from the measured width.
111
+ //
112
+ // Width-only on purpose: the observed element is the whole view container, so
113
+ // its height moves whenever a track is added, resized or grows with its data.
114
+ // Measuring both axes turned every one of those into a re-render of the view
115
+ // chrome (two MUI Papers, the header and its buttons) for a number this hook
116
+ // never reads.
117
+ export function useWidthSetter(view) {
118
+ const [ref, { width }] = useMeasure('width');
119
+ useEffect(() => {
120
+ let token;
121
+ if (width && isAlive(view)) {
122
+ // sets after a requestAnimationFrame
123
+ // https://stackoverflow.com/a/58701523/2129219
124
+ // avoids ResizeObserver loop error being shown during development
125
+ token = requestAnimationFrame(() => {
126
+ view.setWidth(width);
127
+ });
128
+ }
129
+ return () => {
130
+ if (token) {
131
+ cancelAnimationFrame(token);
132
+ }
133
+ };
134
+ }, [view, width]);
135
+ return ref;
136
+ }
137
+ /**
138
+ * Build a value exactly once per mount — including under React StrictMode,
139
+ * which `useState(() => build())` does not.
140
+ *
141
+ * StrictMode double-invokes a state initializer in development and throws the
142
+ * SECOND result away. For an ordinary value that is the intended lint: it
143
+ * surfaces impure initializers and costs nothing. For anything that owns
144
+ * something — an MST tree, a worker pool, a subscription — it stands up a second
145
+ * one and then drops the only reference to it, so nothing can ever tear it down,
146
+ * and it is invisible because the one React kept behaves perfectly.
147
+ *
148
+ * A ref is written once and survives the double render; this is React's own
149
+ * "avoiding recreating the ref contents" pattern.
150
+ */
151
+ export function useCreateOnce(create) {
152
+ // boxed, so a `create` that legitimately returns undefined isn't re-run every
153
+ // render by the nullish assignment
154
+ const ref = useRef(undefined);
155
+ ref.current ??= { value: create() };
156
+ return ref.current.value;
157
+ }
158
+ /**
159
+ * `useCreateOnce` for an asynchronous factory: returns undefined until
160
+ * `create` resolves, and rethrows a rejection from render. The value can
161
+ * resolve after the component is gone — a caller whose value is expensive to
162
+ * leak should use product-core's `useAsyncEngineLifecycle`, which discards
163
+ * that late arrival.
164
+ */
165
+ export function useCreateOnceAsync(create) {
166
+ const started = useRef(false);
167
+ const [state, setState] = useState();
168
+ useEffect(() => {
169
+ if (!started.current) {
170
+ started.current = true;
171
+ create().then(value => {
172
+ setState({ value });
173
+ }, (error) => {
174
+ setState({ error });
175
+ });
176
+ }
177
+ // create is read on the first effect only, as in useCreateOnce
178
+ // eslint-disable-next-line @eslint-react/exhaustive-deps
179
+ }, []);
180
+ if (state && 'error' in state) {
181
+ throw state.error;
182
+ }
183
+ return state?.value;
184
+ }
185
+ /**
186
+ * Run `cleanup` when the component *really* unmounts.
187
+ *
188
+ * "Really" is the whole difficulty, because React does not distinguish a final
189
+ * unmount from a simulated one. The obvious spelling —
190
+ * `useEffect(() => () => cleanup(), [])` — is wrong in exactly the environment
191
+ * most hosts develop in, jbrowse-web included: StrictMode runs
192
+ * setup → cleanup → setup on a live component, so a cleanup that destroys
193
+ * something leaves the component holding the destroyed thing for the rest of its
194
+ * life, with the second setup having nothing to rebuild from. For an MST tree
195
+ * that is not a quiet degradation — the next read throws `[mobx-state-tree] …
196
+ * [dead]`.
197
+ *
198
+ * So the teardown is deferred by a microtask and cancelled if setup runs again.
199
+ * StrictMode's cleanup and re-setup are one synchronous block, so the cancel
200
+ * always wins there; a real unmount never runs setup again, so the microtask
201
+ * fires.
202
+ *
203
+ * This owns a *component's* teardown, not a per-value one: `cleanup` always sees
204
+ * the latest render's closure, and swapping the thing being torn down mid-life
205
+ * is not supported. Pair it with {@link useCreateOnce}, which is the shape that
206
+ * makes that true.
207
+ *
208
+ * Deliberately not covered: a subtree hidden with `<Activity>`, which destroys
209
+ * effects and re-creates them a TASK later rather than synchronously, so the
210
+ * cancel below cannot reach it. Measured, not assumed — `useFinalUnmount.test.tsx`
211
+ * pins that hiding tears the value down and showing does not rebuild it, since
212
+ * `useCreateOnce`'s ref survives the hide. A host that needs a view to survive
213
+ * being hidden owns the engine itself and keeps it outside the hidden tree.
214
+ */
215
+ export function useFinalUnmount(cleanup) {
216
+ const stableCleanup = useEventCallback(cleanup);
217
+ const teardownPending = useRef(false);
218
+ useEffect(() => {
219
+ // this setup owns the value: cancel a teardown a preceding cleanup queued
220
+ teardownPending.current = false;
221
+ return () => {
222
+ teardownPending.current = true;
223
+ queueMicrotask(() => {
224
+ if (teardownPending.current) {
225
+ // cleared BEFORE running, so the teardown happens once however many
226
+ // microtasks are in flight. A StrictMode mount queues one that its
227
+ // own re-setup cancels — but only if that microtask has drained
228
+ // before the next cleanup. Unmount inside the same synchronous block
229
+ // as the mount (a test, a route that redirects on its first effect)
230
+ // and it has not: the stale microtask finds the flag set again by the
231
+ // real cleanup and fires, then the real one fires too. Idempotent
232
+ // teardowns hid it, which is every caller in the tree today.
233
+ teardownPending.current = false;
234
+ stableCleanup();
235
+ }
236
+ });
237
+ };
238
+ }, [stableCleanup]);
239
+ }
240
+ function resolveUpdate(value, prev) {
241
+ return typeof value === 'function' ? value(prev) : value;
242
+ }
243
+ /**
244
+ * `useState` backed by a localStorage key.
245
+ *
246
+ * Originally https://usehooks.com/useLocalStorage/, which is per-instance: two
247
+ * components on the same key each kept their own copy of it, so toggling a
248
+ * setting in one BreakpointSplitView header left a second one open beside it
249
+ * showing the old value until it remounted. Instances on a key now subscribe to
250
+ * each other's writes, and to other tabs' — `subscribeToLocalStorageKey`.
251
+ *
252
+ * The store is read on every notify rather than cached, so nothing here can go
253
+ * stale against a `localStorage.clear()`. Which also means a functional update
254
+ * resolves against what is actually stored: two `setValue(v => …)` calls in one
255
+ * handler used to keep only the second, because both resolved against the value
256
+ * captured by the render that produced the setter.
257
+ *
258
+ * `enabled: false` keeps the value in component state only: nothing is read,
259
+ * written or shared. Callers use it for a key that isn't meaningful yet (no
260
+ * assembly chosen, so nothing to scope the key to). A page with no usable store
261
+ * at all — an RPC worker, SSR, a cross-origin iframe with third-party storage
262
+ * blocked, which is the embedded products on someone else's page — runs in that
263
+ * same mode, because reading a key back through a store that dropped the write
264
+ * answers the default and would report it as the stored value: the control
265
+ * would revert the instant the user moved it.
266
+ */
267
+ export function useLocalStorage(key, initialValue, enabled = true) {
268
+ // one concept, not two: `persists` is "this key is really backed by the
269
+ // store", and everything below branches on it rather than on `enabled`
270
+ const persists = enabled && localStorageAvailable();
271
+ const [storedValue, setStoredValue] = useState(() => persists ? localStorageGetJSON(key, initialValue) : initialValue);
272
+ // re-read when the key or `persists` changes at runtime (the useState
273
+ // initializer only runs once); render-phase reset rather than an effect
274
+ const [prev, setPrev] = useState({ key, persists });
275
+ // Latched when the store refuses a write. Until then the store is the base
276
+ // every update resolves against, which is what makes two `setValue(v => …)`
277
+ // calls in one handler both land. Afterwards it cannot be: the store still
278
+ // holds the value the user changed away from, so every later update would
279
+ // recompute the same `next` from it and the control would move once and then
280
+ // stick. Reset with the key, since the refusal was about this one.
281
+ const storeRefusedRef = useRef(false);
282
+ if (key !== prev.key || persists !== prev.persists) {
283
+ setPrev({ key, persists });
284
+ storeRefusedRef.current = false;
285
+ setStoredValue(persists ? localStorageGetJSON(key, initialValue) : initialValue);
286
+ }
287
+ // initialValue is deliberately not a dependency: callers pass inline literals
288
+ // (`[]`, `{}`), and it only ever decides what an absent key reads as
289
+ const initialRef = useRef(initialValue);
290
+ initialRef.current = initialValue;
291
+ useEffect(() => {
292
+ if (!persists) {
293
+ return;
294
+ }
295
+ return subscribeToLocalStorageKey(key, () => {
296
+ setStoredValue(localStorageGetJSON(key, initialRef.current));
297
+ });
298
+ }, [key, persists]);
299
+ const setValue = useEventCallback((value) => {
300
+ if (!persists || storeRefusedRef.current) {
301
+ setStoredValue(prevValue => resolveUpdate(value, prevValue));
302
+ return;
303
+ }
304
+ const next = resolveUpdate(value, localStorageGetJSON(key, initialRef.current));
305
+ const wrote = next === undefined
306
+ ? // clearing the key, not storing the string "undefined" — which is what
307
+ // `setItem(key, JSON.stringify(undefined))` writes, and which then
308
+ // throws on the way back in. `useAssemblySelection` holds a
309
+ // `string | undefined`
310
+ localStorageRemoveItem(key)
311
+ : localStorageSetItem(key, JSON.stringify(next));
312
+ if (wrote) {
313
+ notifyLocalStorageKey(key);
314
+ }
315
+ else {
316
+ // The store read fine and then refused the write: quota exhausted, or
317
+ // Safari private browsing. Notifying would hand every instance what the
318
+ // store still holds — the value the user just changed away from — so the
319
+ // control would snap back. Fall to the same component-local mode
320
+ // `enabled: false` runs in.
321
+ storeRefusedRef.current = true;
322
+ setStoredValue(next);
323
+ }
324
+ });
325
+ return [storedValue, setValue];
326
+ }
327
+ /**
328
+ * The CSS custom property a scroll port publishes its own visible height as, for
329
+ * descendants that have to size against the surface they actually scroll in.
330
+ *
331
+ * `100vh` is the wrong answer for all three of JBrowse's scroll ports and looks
332
+ * right in the one place it is least wrong: the classic view stack sits under a
333
+ * 48px AppBar (measured 852 against a 900px window), a workspace panel is an
334
+ * arbitrary dockview cell, and a bounded embedded view is whatever box the host
335
+ * gave it. A sticky element's offsets are relative to its scroll port, so a
336
+ * `max-height` that bounds one has to be too.
337
+ */
338
+ export const SCROLL_PORT_HEIGHT_VAR = '--jbrowse-scrollport-height';
339
+ /**
340
+ * Publishes {@link SCROLL_PORT_HEIGHT_VAR} on the element the returned ref is
341
+ * attached to. Put it on the element that actually scrolls; the property
342
+ * inherits, so anything inside can read it with a `100vh` fallback for hosts
343
+ * that never mount one.
344
+ *
345
+ * Written straight to the node instead of through state on purpose. This sits on
346
+ * a container wrapping every view, so a re-render per resize frame would
347
+ * re-render all of them to produce a number only CSS reads.
348
+ */
349
+ export function useScrollPortHeightVar() {
350
+ const ref = useRef(null);
351
+ useEffect(() => {
352
+ const el = ref.current;
353
+ if (!el || !('ResizeObserver' in window)) {
354
+ return;
355
+ }
356
+ // clientHeight, not the border box: it is the visible content area net of a
357
+ // horizontal scrollbar, which is the box a sticky child is bounded by
358
+ const publish = () => {
359
+ el.style.setProperty(SCROLL_PORT_HEIGHT_VAR, `${el.clientHeight}px`);
360
+ };
361
+ publish();
362
+ const observer = new ResizeObserver(publish);
363
+ observer.observe(el);
364
+ return () => {
365
+ observer.disconnect();
366
+ };
367
+ }, []);
368
+ return ref;
369
+ }
370
+ /**
371
+ * The nearest ancestor that actually scrolls `el`, or undefined if nothing
372
+ * above it does.
373
+ */
374
+ export function scrollPortOf(el) {
375
+ let node = el.parentElement;
376
+ while (node) {
377
+ const { overflowY } = getComputedStyle(node);
378
+ if (overflowY === 'auto' || overflowY === 'scroll') {
379
+ return node;
380
+ }
381
+ node = node.parentElement;
382
+ }
383
+ return undefined;
384
+ }
385
+ /**
386
+ * Whether the element the ref is on is taller than the scroll port it sits in —
387
+ * i.e. whether there is content a user could actually scroll to.
388
+ *
389
+ * Not the same question as "does the port overflow": a port can overflow by
390
+ * trailing space it renders for its own reasons, and a scrollbar offering only
391
+ * that is worse than none, since it says the page has more to show when it does
392
+ * not. So this measures the *content* box and leaves the trailing space out of
393
+ * the comparison, which means the caller has to keep that space outside the
394
+ * measured element.
395
+ *
396
+ * Stable rather than oscillating, and not by luck: turning the answer true adds
397
+ * a scrollbar, which narrows the content, and narrowing can only make content
398
+ * taller — so a true answer stays true and a false one stays false.
399
+ *
400
+ * `useLayoutEffect`, so the first measurement and the re-render it causes both
401
+ * land before paint. A view added to the stack scrolls itself into view from a
402
+ * passive effect, and passive effects run after every layout effect in the tree:
403
+ * measuring here means the trailing space this gates is already in the DOM by
404
+ * the time that scroll is computed against it.
405
+ */
406
+ export function useScrollPortOverflow(ref) {
407
+ const [overflowing, setOverflowing] = useState(false);
408
+ useLayoutEffect(() => {
409
+ const el = ref.current;
410
+ const port = el ? scrollPortOf(el) : undefined;
411
+ if (!el || !port || !('ResizeObserver' in window)) {
412
+ return;
413
+ }
414
+ const check = () => {
415
+ setOverflowing(el.getBoundingClientRect().height > port.clientHeight);
416
+ };
417
+ check();
418
+ const observer = new ResizeObserver(check);
419
+ observer.observe(el);
420
+ observer.observe(port);
421
+ return () => {
422
+ observer.disconnect();
423
+ };
424
+ }, [ref]);
425
+ return overflowing;
426
+ }
427
+ /**
428
+ * Heights of the chrome boxes a sticky element below them has to clear. Each is
429
+ * published from a measurement rather than assumed, because the constants they
430
+ * default to are nominal: `VIEW_HEADER_HEIGHT` and the LGV header bar's height
431
+ * were written into the CSS by the pin-elements work (#4237) so that the sticky
432
+ * offsets summing them would be true, and a box pinned to a constant clips its
433
+ * own content once the root font size grows — measured on the stock theme, the
434
+ * view header overflows at a 18px root and the LGV controls row at 24px.
435
+ *
436
+ * So those CSS heights are minimums and these carry the truth. The fallbacks
437
+ * keep the nominal answer for the frame before the first measurement, and for a
438
+ * host that mounts no publisher. A box that stays fixed still publishes — see
439
+ * the embedded `ViewTitle`, which is a density choice rather than a constraint
440
+ * now that nothing below it re-derives its height.
441
+ *
442
+ * Cheap enough to put on every view: measured across a jbrowse-web session, the
443
+ * observers behind these fired 0 times over 60 pan frames and 10 zooms, and ~5
444
+ * times per window resize.
445
+ */
446
+ export const VIEW_HEADER_HEIGHT_VAR = '--jbrowse-view-header-height';
447
+ export const LGV_HEADER_HEIGHT_VAR = '--jbrowse-lgv-header-height';
448
+ /**
449
+ * Publishes the measured height of `ref`'s element as `varName`, set on its
450
+ * **parent**. The parent, not the element itself: what reads these is a sticky
451
+ * sibling *below* the measured box, so publishing on the box would put the
452
+ * property out of the reader's inheritance chain.
453
+ *
454
+ * Takes the ref rather than returning one — the boxes being measured are also
455
+ * the ones a view scrolls into view or hangs a gesture on, so they tend to
456
+ * already have one.
457
+ *
458
+ * Written straight to the node rather than through state, for the reason
459
+ * {@link useScrollPortHeightVar} gives — and here with the extra one that a
460
+ * header re-rendering on its own resize is a loop waiting for a rounding error.
461
+ */
462
+ export function useChromeHeightVar(ref, varName) {
463
+ useEffect(() => {
464
+ const el = ref.current;
465
+ const parent = el?.parentElement;
466
+ if (!el || !parent || !('ResizeObserver' in window)) {
467
+ return;
468
+ }
469
+ // the border box, since this is a distance a sibling below has to clear
470
+ // rather than a content area — and read off the rect, not `offsetHeight`,
471
+ // which rounds to whole pixels and so left the box below up to half a pixel
472
+ // off a header that had grown to 29.28
473
+ const publish = () => {
474
+ const { height } = el.getBoundingClientRect();
475
+ parent.style.setProperty(varName, `${height}px`);
476
+ };
477
+ publish();
478
+ const observer = new ResizeObserver(publish);
479
+ observer.observe(el);
480
+ return () => {
481
+ observer.disconnect();
482
+ parent.style.removeProperty(varName);
483
+ };
484
+ }, [ref, varName]);
485
+ }