@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
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  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
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  1028. package/esm/util/sameStrings.d.ts +16 -0
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  1044. package/esm/util/sessionSharing.d.ts +40 -0
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  1046. package/esm/util/sessionStorage.d.ts +1 -0
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  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
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  1099. package/esm/util/tss-react/types.d.ts +1 -1
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  1110. package/esm/util/types/predicate.d.ts +9 -0
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  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
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@@ -0,0 +1,297 @@
1
+ // Shared wheel-zoom math and event handling for linear genome views. The LGV
2
+ // wheel handler, the breakpoint-split overlay and the synteny canvas all zoom on
3
+ // ctrl/scroll-zoom wheel gestures and must behave identically, so the normalizer,
4
+ // the rate limit and the whole gesture decision matrix live here —
5
+ // createWheelZoomController below is what each of those three actually runs.
6
+ import { transaction } from 'mobx';
7
+ import { createFrameCoalescer } from './frameCoalescer.js';
8
+ import { trackPointerPresence } from './pointerPresence.js';
9
+ // max zoom delta per millisecond — equivalent to 0.2 per frame at 60fps
10
+ export const MAX_ZOOM_RATE_PER_MS = 0.2 / 16.67;
11
+ // Scroll-zoom (plain wheel with the scrollZoom preference on) divides by a fixed
12
+ // amount for a smooth proportional feel, rather than the adaptive
13
+ // getZoomNormalizer used for ctrl/pinch zoom where device deltas vary wildly.
14
+ export const SCROLL_ZOOM_FACTOR_DIVISOR = 500;
15
+ // The per-event contribution to the zoom accumulator, given a wheel delta
16
+ // already normalized to pixels via normalizeWheelDelta. ctrl/pinch zoom uses the
17
+ // adaptive normalizer; scroll-zoom uses the fixed divisor. Single source of the
18
+ // zoom-step feel so every wheel handler (LGV, breakpoint overlay, synteny)
19
+ // zooms identically for the same gesture.
20
+ export function wheelZoomAccum(normalizedDeltaY, isCtrlZoom) {
21
+ return (normalizedDeltaY /
22
+ (isCtrlZoom
23
+ ? getZoomNormalizer(normalizedDeltaY)
24
+ : SCROLL_ZOOM_FACTOR_DIVISOR));
25
+ }
26
+ // larger wheel deltas (e.g. mouse wheel notches) divide by more so a single
27
+ // notch produces a consistent zoom step regardless of device delta magnitude
28
+ export function getZoomNormalizer(deltaY) {
29
+ const abs = Math.abs(deltaY);
30
+ if (abs < 6) {
31
+ return 25;
32
+ }
33
+ if (abs > 150) {
34
+ return 500;
35
+ }
36
+ if (abs > 30) {
37
+ return 150;
38
+ }
39
+ return 75;
40
+ }
41
+ // One wheel notch in line mode (deltaMode 1) is roughly this many pixels, and a
42
+ // page (deltaMode 2) roughly WHEEL_PAGE_HEIGHT — the values Facebook's
43
+ // normalize-wheel uses, the de-facto cross-browser convention. Pixel mode (0),
44
+ // which trackpads and modern mice report, passes through untouched.
45
+ const WHEEL_LINE_HEIGHT = 40;
46
+ const WHEEL_PAGE_HEIGHT = 800;
47
+ // Convert a WheelEvent delta from its deltaMode units to pixels. Panel-scroll
48
+ // callers pass the viewport height as `pageHeight` so a page maps to exactly one
49
+ // screen; the zoom path omits it and takes the default. Single normalizer for
50
+ // both the zoom math here and the vertical-scroll handlers so a notch means the
51
+ // same thing everywhere.
52
+ export function normalizeWheelDelta(delta, deltaMode, pageHeight = WHEEL_PAGE_HEIGHT) {
53
+ return deltaMode === 1
54
+ ? delta * WHEEL_LINE_HEIGHT
55
+ : deltaMode === 2
56
+ ? delta * pageHeight
57
+ : delta;
58
+ }
59
+ // elapsed since the previous animation frame, clamped to 100ms and defaulting
60
+ // to one 60fps frame when there is no prior frame (first event or post-resume)
61
+ export function wheelFrameElapsedMs(now, lastRafTime) {
62
+ return Math.min(100, lastRafTime !== null ? now - lastRafTime : 16.67);
63
+ }
64
+ // Accumulate horizontal scroll across a frame, restarting from zero when the
65
+ // gesture reverses direction so a flick the opposite way isn't cancelled out by
66
+ // leftover momentum.
67
+ export function accumulateScroll(prev, deltaX) {
68
+ const reversed = prev !== 0 && Math.sign(deltaX) !== Math.sign(prev);
69
+ return (reversed ? 0 : prev) + deltaX;
70
+ }
71
+ // A pinch/scroll-zoom gesture fires a continuous stream of wheel events, so we
72
+ // treat the view as "actively zooming" until this many ms pass with no zoom
73
+ // event. While actively zooming, callers ignore horizontal deltas: trackpads
74
+ // emit an unintentional side-scroll mid-gesture that would otherwise pan the
75
+ // view out from under the user.
76
+ export const ZOOM_ACTIVE_WINDOW_MS = 100;
77
+ // `now` and `lastZoomTime` are both wheel-event timeStamps (same clock).
78
+ // lastZoomTime is null before any zoom has occurred.
79
+ export function isActivelyZooming(now, lastZoomTime) {
80
+ return lastZoomTime !== null && now - lastZoomTime < ZOOM_ACTIVE_WINDOW_MS;
81
+ }
82
+ // apply an accumulated zoom amount to bpPerPx, rate-limited so a burst of wheel
83
+ // events can't zoom faster than MAX_ZOOM_RATE_PER_MS over the frame's elapsed
84
+ export function applyZoomAccum(bpPerPx, zoomAccum, elapsedMs) {
85
+ const max = MAX_ZOOM_RATE_PER_MS * elapsedMs;
86
+ const d = Math.max(-max, Math.min(max, zoomAccum));
87
+ return d > 0 ? bpPerPx * (1 + d) : bpPerPx / (1 - d);
88
+ }
89
+ // A mouse notch lands as ~80ms of eased motion instead of one frame's jump, and
90
+ // a trackpad whose events fall two or three to a frame zooms at an even pace
91
+ const ZOOM_EASE_MS = 24;
92
+ // in log(bpPerPx): a free-spinning wheel can't bank a zoom that runs on after
93
+ // the hand stops
94
+ const MAX_ZOOM_BACKLOG = Math.log(16);
95
+ const ZOOM_SETTLE = 1e-3;
96
+ function zoomAccumToLog(zoomAccum) {
97
+ return zoomAccum > 0 ? Math.log1p(zoomAccum) : -Math.log1p(-zoomAccum);
98
+ }
99
+ function addToZoomBacklog(backlog, zoomAccum) {
100
+ return Math.max(-MAX_ZOOM_BACKLOG, Math.min(MAX_ZOOM_BACKLOG, backlog + zoomAccumToLog(zoomAccum)));
101
+ }
102
+ // the rate limit bounds how fast the owed zoom lands, never how much of it
103
+ function easeZoomBacklog(backlog, elapsedMs) {
104
+ const rest = backlog * Math.exp(-elapsedMs / ZOOM_EASE_MS);
105
+ const step = Math.abs(rest) < ZOOM_SETTLE ? backlog : backlog - rest;
106
+ const max = Math.log1p(MAX_ZOOM_RATE_PER_MS * elapsedMs);
107
+ return Math.max(-max, Math.min(max, step));
108
+ }
109
+ /**
110
+ * The one wheel gesture handler for linear views. Its decision matrix:
111
+ *
112
+ * - a wheel a nested scroller already consumed → declined, it owns the gesture
113
+ * - ctrl/meta+wheel, or (scrollZoom && |dy| >= |dx|) → zoom about the cursor
114
+ * - shift+wheel while scrollZoom is on → declined, we pass
115
+ * - a sideways delta, unless one arrives mid-zoom → pan by dx
116
+ *
117
+ * Declining shift is what leaves a nested panel its own scroll
118
+ * (`usePanelVirtualScroll`) — it is not a way back to the page. Browsers turn
119
+ * shift+wheel into *horizontal* scrolling, so what a view declines here scrolls
120
+ * the page sideways or not at all. The vertical way out is spatial rather than
121
+ * modal: JBrowse binds this below the view's sticky header, leaving that header
122
+ * as a gutter the wheel still scrolls (LinearGenomeViewContainer's tracksRef).
123
+ *
124
+ * The listener is non-passive so it can preventDefault to suppress native scroll
125
+ * during a zoom. To pay for that it only accumulates deltas: every model write
126
+ * happens in one requestAnimationFrame, so a burst of events (fast trackpad,
127
+ * inertial scroll) collapses to a single update per frame instead of thrashing
128
+ * the views once per event.
129
+ *
130
+ * A zoom lands eased over the frames after its event (`easeZoomBacklog`), and
131
+ * all of it lands: how far a gesture zooms depends on the wheel alone, never on
132
+ * the frame rate or how the events happened to fall into frames.
133
+ *
134
+ * Returns its disposer.
135
+ */
136
+ export function createWheelZoomController({ element, resolveTarget, swallowUnhandled = false, releaseOnPointerLeave = false, onEvent, }) {
137
+ const frame = createFrameCoalescer();
138
+ const s = {
139
+ scrollDelta: 0,
140
+ zoomBacklog: 0,
141
+ target: undefined,
142
+ lastClientX: 0,
143
+ originLeft: undefined,
144
+ lastRafTime: null,
145
+ lastZoomTime: null,
146
+ lastEventTime: null,
147
+ warnedNonCancelable: false,
148
+ };
149
+ // see releaseOnPointerLeave: drop any in-flight accumulation and stop consuming
150
+ // latched wheel events, so a continued gesture pans/zooms nothing and chains to
151
+ // the page instead of staying stuck to this element
152
+ const presence = releaseOnPointerLeave
153
+ ? trackPointerPresence(element, () => {
154
+ s.scrollDelta = 0;
155
+ s.zoomBacklog = 0;
156
+ s.originLeft = undefined;
157
+ })
158
+ : undefined;
159
+ function flush(now) {
160
+ const elapsed = wheelFrameElapsedMs(now, s.lastRafTime);
161
+ s.lastRafTime = now;
162
+ const { target } = s;
163
+ if (target) {
164
+ const origin = target.originElement();
165
+ if (s.zoomBacklog !== 0 && origin && s.originLeft === undefined) {
166
+ s.originLeft = origin.getBoundingClientRect().left;
167
+ }
168
+ const originLeft = s.originLeft;
169
+ if (originLeft === undefined) {
170
+ s.zoomBacklog = 0;
171
+ }
172
+ const step = easeZoomBacklog(s.zoomBacklog, elapsed);
173
+ const apply = () => {
174
+ transaction(() => {
175
+ if (step !== 0 && originLeft !== undefined) {
176
+ const offset = s.lastClientX - originLeft;
177
+ let moved = false;
178
+ for (const view of target.views) {
179
+ const before = view.bpPerPx;
180
+ view.zoomTo(before * Math.exp(step), offset);
181
+ moved ||= view.bpPerPx !== before;
182
+ }
183
+ // pinned at a zoom limit, the rest can never land
184
+ s.zoomBacklog = moved ? s.zoomBacklog - step : 0;
185
+ }
186
+ if (s.scrollDelta !== 0) {
187
+ for (const view of target.views) {
188
+ view.horizontalScroll(s.scrollDelta);
189
+ }
190
+ }
191
+ });
192
+ };
193
+ if (target.hold) {
194
+ target.hold(apply);
195
+ }
196
+ else {
197
+ apply();
198
+ }
199
+ }
200
+ else {
201
+ s.zoomBacklog = 0;
202
+ }
203
+ s.scrollDelta = 0;
204
+ if (s.zoomBacklog !== 0) {
205
+ frame.schedule(flush);
206
+ }
207
+ else {
208
+ s.lastRafTime = null;
209
+ }
210
+ }
211
+ function onWheel(event) {
212
+ onEvent?.(event);
213
+ // A nested vertical scroller preventDefaults exactly what it consumed, and
214
+ // that flag is still readable on the way up, so the view declines what a
215
+ // panel is already scrolling: a trackpad emits a small deltaX alongside
216
+ // every vertical swipe, which used to pan the genome sideways under someone
217
+ // who was only scrolling reads. No timer of our own — the scroll latch
218
+ // holds the whole continuous gesture, boundary included, and releasing it
219
+ // is the pause that ends the gesture.
220
+ const gated = event.defaultPrevented || (presence !== undefined && !presence.isOver);
221
+ const target = gated ? undefined : resolveTarget(event);
222
+ if (target && !(event.shiftKey && target.scrollZoom)) {
223
+ // a gap longer than the frame-elapsed clamp means this event starts a new
224
+ // gesture, so the previous frame time is meaningless — including when it
225
+ // predates a spell in a backgrounded tab, where a huge elapsed would
226
+ // otherwise lift the zoom rate limit on the first frame back
227
+ if (!isActivelyZooming(event.timeStamp, s.lastEventTime)) {
228
+ s.lastRafTime = null;
229
+ s.originLeft = undefined;
230
+ }
231
+ s.lastEventTime = event.timeStamp;
232
+ s.target = target;
233
+ const deltaY = normalizeWheelDelta(event.deltaY, event.deltaMode);
234
+ const deltaX = normalizeWheelDelta(event.deltaX, event.deltaMode);
235
+ const isCtrlZoom = event.ctrlKey || event.metaKey;
236
+ const isZoom = isCtrlZoom ||
237
+ (target.scrollZoom && Math.abs(deltaY) >= Math.abs(deltaX));
238
+ if (isZoom) {
239
+ // warn once per latched run, not once per event — a non-cancelable
240
+ // sequence fires ~100 events/sec and console.warn is not free
241
+ if (event.cancelable) {
242
+ s.warnedNonCancelable = false;
243
+ }
244
+ else if (!s.warnedNonCancelable) {
245
+ s.warnedNonCancelable = true;
246
+ console.warn('[wheelZoom] wheel event not cancelable — scroll sequence already in progress');
247
+ }
248
+ event.preventDefault();
249
+ s.zoomBacklog = addToZoomBacklog(s.zoomBacklog, wheelZoomAccum(deltaY, isCtrlZoom));
250
+ s.lastClientX = event.clientX;
251
+ s.lastZoomTime = event.timeStamp;
252
+ // drop any side-scroll accumulated earlier this frame — we're zooming,
253
+ // and a deltaX that arrived just before the zoom is part of the same
254
+ // noisy gesture
255
+ s.scrollDelta = 0;
256
+ }
257
+ else if (isActivelyZooming(event.timeStamp, s.lastZoomTime)) {
258
+ // ignore stray horizontal deltas that arrive mid-zoom — trackpads emit
259
+ // an unintentional side-scroll during a pinch/scroll-zoom gesture that
260
+ // would otherwise pan the view away from where the user is zooming.
261
+ // preventDefault anyway so the page itself doesn't scroll instead.
262
+ event.preventDefault();
263
+ }
264
+ else {
265
+ // With scrollZoom on, swallow the gesture even though it fell outside
266
+ // the zoom threshold: without this, a diagonal trackpad gesture whose
267
+ // |deltaX| slightly exceeds |deltaY| slips through and scrolls the page
268
+ // (shift+wheel above is the deliberate exception). With scrollZoom
269
+ // off, only swallow what we are about to pan with, so a plain vertical
270
+ // wheel isn't silently eaten.
271
+ if (swallowUnhandled ||
272
+ target.scrollZoom ||
273
+ Math.abs(deltaX) > Math.abs(2 * deltaY)) {
274
+ event.preventDefault();
275
+ }
276
+ // Pan on a gesture that is actually sideways. A trackpad puts a small
277
+ // deltaX on every vertical swipe, and panning on it drifted the genome
278
+ // under anyone scrolling a track — including where no panel handler
279
+ // reports the scroll for us to decline, as with the natively-scrolling
280
+ // pinned-tracks block. Ties go vertical, the same way the zoom test
281
+ // above resolves them. With scrollZoom on this changes nothing: a
282
+ // vertical-dominant wheel was already taken as a zoom.
283
+ if (Math.abs(deltaX) > Math.abs(deltaY)) {
284
+ s.scrollDelta = accumulateScroll(s.scrollDelta, deltaX);
285
+ }
286
+ }
287
+ frame.schedule(flush);
288
+ }
289
+ }
290
+ element.addEventListener('wheel', onWheel, { passive: false });
291
+ return () => {
292
+ element.removeEventListener('wheel', onWheel);
293
+ presence?.dispose();
294
+ // so a flush can't fire against a detached view
295
+ frame.cancel();
296
+ };
297
+ }
@@ -0,0 +1,74 @@
1
+ export interface SettleableView {
2
+ initialized: boolean;
3
+ error: unknown;
4
+ pendingLaunch?: unknown;
5
+ }
6
+ /**
7
+ * A view that is up AND has finished applying whatever launched it.
8
+ *
9
+ * Both terms, for the reason spelled out on {@link whenViewSettled} below.
10
+ * Exported because AppReadyMarker decides the same thing from the same model
11
+ * for the whole app, the two drifted on exactly this second term, and
12
+ * `readinessTerms.test.tsx` in app-core now holds them together.
13
+ */
14
+ export declare const viewSettled: (view: SettleableView) => boolean;
15
+ /**
16
+ * Wait until a view has either initialized — launch blob consumed and all — or
17
+ * failed, and report which.
18
+ *
19
+ * `initialized` folds in a view's assemblies, so an assembly that fails to load
20
+ * leaves it false **forever**. A bare `when(() => view.initialized)` therefore
21
+ * does not fail — it never settles at all, and whatever the caller meant to do
22
+ * next simply never happens, with no error, no toast and a pending promise left
23
+ * behind. That has surfaced twice now as two different-looking bugs: an SVG
24
+ * export hung behind its dialog's spinner, and a launched breakpoint split view
25
+ * that opened but was never navigated or zoomed.
26
+ *
27
+ * `pendingLaunch` is the other half, and it matters because `initialized` can
28
+ * go true MID-launch: LGV's flips the moment displayedRegions land, while the
29
+ * same apply pass still has tracks to attach — so a caller acting there reads a
30
+ * positioned view with its tracks missing (an SVG export saves it that way).
31
+ * A launch failure cannot hang this: the state machine either clears the blob
32
+ * (materialized, reported as a snackbar) or sets the view's `error`
33
+ * (installInitAutorun's failure policy). A view with no launch machinery has no
34
+ * `pendingLaunch` and the term is vacuously satisfied.
35
+ *
36
+ * Every view exposes a resolved `error` beside `initialized`, so waiting on the
37
+ * pair turns the hang into something reportable. What to report is the caller's,
38
+ * because the vocabularies genuinely differ — an export says "cannot export"
39
+ * and attaches its failures for `awaitSvgRenders` to collect, while a launcher
40
+ * says the launch failed — which is why this returns the answer instead of
41
+ * throwing one wording at both.
42
+ *
43
+ * No time bound, deliberately: `(initialized && launch consumed) || error` is a
44
+ * terminal set, so a slow-but-healthy remote assembly is waited out rather than
45
+ * guessed at. `escape` is how a caller adds the one term that is not the view's
46
+ * own — a session-level render failure for an export, `superseded` for a view
47
+ * an `installInitAutorun` apply is waiting on — which is what keeps a caller
48
+ * from re-spelling the whole predicate around it.
49
+ *
50
+ * **Not for the view whose `apply` you are inside.** `applyInitOnce` clears the
51
+ * launch blob only after awaiting `apply`, so `pendingLaunch` is held for the
52
+ * whole of it and this can end only on `escape` or `error`, never on success.
53
+ * A wait on `self` stays hand-rolled; `reference/VIEW_INIT.md` has the shape.
54
+ *
55
+ * @returns true if the view initialized (and consumed any launch), false if it
56
+ * settled on an error
57
+ */
58
+ export declare function whenViewSettled(view: SettleableView, escape?: () => boolean): Promise<boolean>;
59
+ /**
60
+ * The same wait over several views at once — a synteny view's genome rows. An
61
+ * SVG export of a split view keeps its own per-panel loop instead: the split
62
+ * view's `initialized` folds in `views.every(v => v.initialized)` but not each
63
+ * panel's own `pendingLaunch`, so that loop is waiting on a different question
64
+ * by the time it runs.
65
+ *
66
+ * One predicate over `every`, never `Promise.all` of the single form: `when`
67
+ * returns a cancellable promise, so racing N of them against an escape leaves
68
+ * N-1 live reactions behind on the path that escapes. This is one reaction with
69
+ * nothing to cancel.
70
+ *
71
+ * @returns true if every view initialized, false if any settled on an error or
72
+ * the escape fired
73
+ */
74
+ export declare function whenViewsSettled(views: SettleableView[], escape?: () => boolean): Promise<boolean>;
@@ -0,0 +1,77 @@
1
+ import { when } from 'mobx';
2
+ /**
3
+ * A view that is up AND has finished applying whatever launched it.
4
+ *
5
+ * Both terms, for the reason spelled out on {@link whenViewSettled} below.
6
+ * Exported because AppReadyMarker decides the same thing from the same model
7
+ * for the whole app, the two drifted on exactly this second term, and
8
+ * `readinessTerms.test.tsx` in app-core now holds them together.
9
+ */
10
+ export const viewSettled = (view) => view.initialized && view.pendingLaunch === undefined;
11
+ const done = (view) => viewSettled(view) || !!view.error;
12
+ /**
13
+ * Wait until a view has either initialized — launch blob consumed and all — or
14
+ * failed, and report which.
15
+ *
16
+ * `initialized` folds in a view's assemblies, so an assembly that fails to load
17
+ * leaves it false **forever**. A bare `when(() => view.initialized)` therefore
18
+ * does not fail — it never settles at all, and whatever the caller meant to do
19
+ * next simply never happens, with no error, no toast and a pending promise left
20
+ * behind. That has surfaced twice now as two different-looking bugs: an SVG
21
+ * export hung behind its dialog's spinner, and a launched breakpoint split view
22
+ * that opened but was never navigated or zoomed.
23
+ *
24
+ * `pendingLaunch` is the other half, and it matters because `initialized` can
25
+ * go true MID-launch: LGV's flips the moment displayedRegions land, while the
26
+ * same apply pass still has tracks to attach — so a caller acting there reads a
27
+ * positioned view with its tracks missing (an SVG export saves it that way).
28
+ * A launch failure cannot hang this: the state machine either clears the blob
29
+ * (materialized, reported as a snackbar) or sets the view's `error`
30
+ * (installInitAutorun's failure policy). A view with no launch machinery has no
31
+ * `pendingLaunch` and the term is vacuously satisfied.
32
+ *
33
+ * Every view exposes a resolved `error` beside `initialized`, so waiting on the
34
+ * pair turns the hang into something reportable. What to report is the caller's,
35
+ * because the vocabularies genuinely differ — an export says "cannot export"
36
+ * and attaches its failures for `awaitSvgRenders` to collect, while a launcher
37
+ * says the launch failed — which is why this returns the answer instead of
38
+ * throwing one wording at both.
39
+ *
40
+ * No time bound, deliberately: `(initialized && launch consumed) || error` is a
41
+ * terminal set, so a slow-but-healthy remote assembly is waited out rather than
42
+ * guessed at. `escape` is how a caller adds the one term that is not the view's
43
+ * own — a session-level render failure for an export, `superseded` for a view
44
+ * an `installInitAutorun` apply is waiting on — which is what keeps a caller
45
+ * from re-spelling the whole predicate around it.
46
+ *
47
+ * **Not for the view whose `apply` you are inside.** `applyInitOnce` clears the
48
+ * launch blob only after awaiting `apply`, so `pendingLaunch` is held for the
49
+ * whole of it and this can end only on `escape` or `error`, never on success.
50
+ * A wait on `self` stays hand-rolled; `reference/VIEW_INIT.md` has the shape.
51
+ *
52
+ * @returns true if the view initialized (and consumed any launch), false if it
53
+ * settled on an error
54
+ */
55
+ export async function whenViewSettled(view, escape = () => false) {
56
+ await when(() => escape() || done(view));
57
+ return viewSettled(view);
58
+ }
59
+ /**
60
+ * The same wait over several views at once — a synteny view's genome rows. An
61
+ * SVG export of a split view keeps its own per-panel loop instead: the split
62
+ * view's `initialized` folds in `views.every(v => v.initialized)` but not each
63
+ * panel's own `pendingLaunch`, so that loop is waiting on a different question
64
+ * by the time it runs.
65
+ *
66
+ * One predicate over `every`, never `Promise.all` of the single form: `when`
67
+ * returns a cancellable promise, so racing N of them against an escape leaves
68
+ * N-1 live reactions behind on the path that escapes. This is one reaction with
69
+ * nothing to cancel.
70
+ *
71
+ * @returns true if every view initialized, false if any settled on an error or
72
+ * the escape fired
73
+ */
74
+ export async function whenViewsSettled(views, escape = () => false) {
75
+ await when(() => escape() || views.every(done));
76
+ return views.every(viewSettled);
77
+ }
@@ -0,0 +1,34 @@
1
+ import type { Feature } from './simpleFeature.ts';
2
+ import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
3
+ /**
4
+ * Run `onFeat` on the feature a details lookup answers with, and say something
5
+ * when it answers with nothing.
6
+ *
7
+ * Every display paints from slim render arrays and re-fetches the whole feature
8
+ * on demand, so "click a feature, open its details" is always a round trip that
9
+ * can come back empty. Six call sites across three plugins had written that
10
+ * round trip out, and the shape they shared was
11
+ * `if (feature && isAlive(self)) { … }` — a guard that reads as defensive and is
12
+ * really the whole of what a click does when the lookup fails. Five of the six
13
+ * did nothing at all, which is the worst answer to a click: the user cannot tell
14
+ * a missing feature from a dead menu item.
15
+ *
16
+ * **The three outcomes are separated here because only here can they be told
17
+ * apart**, and conflating any two of them is a bug this replaces:
18
+ *
19
+ * - **threw** — reported with its own reason, through `notifyError`. A `fetch`
20
+ * passed in must therefore let its errors out; one that catches and answers
21
+ * `undefined` turns its failure into the miss below, and the user is told off
22
+ * twice for one click, the second time less usefully.
23
+ * - **answered nothing** — `onMiss`, which defaults to the shared sentence.
24
+ * - **the node died mid-flight** — nothing but the console. A track can be
25
+ * unticked while the fetch is in flight, and every branch below reaches
26
+ * `getSession(self)`, which throws on a detached node — inside a floating
27
+ * promise, where nothing catches it.
28
+ *
29
+ * `onMiss` is a parameter rather than fixed because one caller legitimately
30
+ * stays quiet: the pileup pre-warms the read behind a context menu before the
31
+ * user has asked for anything, so a miss there just leaves the menu without its
32
+ * feature items. Passing `() => {}` is how a call site says it is speculative.
33
+ */
34
+ export declare function withFeatureDetails(self: IStateTreeNode, fetch: () => Promise<Feature | undefined>, onFeat: (feat: Feature) => void, onMiss?: () => void): Promise<void>;
@@ -0,0 +1,59 @@
1
+ import { isAlive } from '@jbrowse/mobx-state-tree';
2
+ import { notifyFeatureDetailsMiss } from './openFeatureWidget.js';
3
+ import { getNotificationSink } from './sessionServices.js';
4
+ /**
5
+ * Run `onFeat` on the feature a details lookup answers with, and say something
6
+ * when it answers with nothing.
7
+ *
8
+ * Every display paints from slim render arrays and re-fetches the whole feature
9
+ * on demand, so "click a feature, open its details" is always a round trip that
10
+ * can come back empty. Six call sites across three plugins had written that
11
+ * round trip out, and the shape they shared was
12
+ * `if (feature && isAlive(self)) { … }` — a guard that reads as defensive and is
13
+ * really the whole of what a click does when the lookup fails. Five of the six
14
+ * did nothing at all, which is the worst answer to a click: the user cannot tell
15
+ * a missing feature from a dead menu item.
16
+ *
17
+ * **The three outcomes are separated here because only here can they be told
18
+ * apart**, and conflating any two of them is a bug this replaces:
19
+ *
20
+ * - **threw** — reported with its own reason, through `notifyError`. A `fetch`
21
+ * passed in must therefore let its errors out; one that catches and answers
22
+ * `undefined` turns its failure into the miss below, and the user is told off
23
+ * twice for one click, the second time less usefully.
24
+ * - **answered nothing** — `onMiss`, which defaults to the shared sentence.
25
+ * - **the node died mid-flight** — nothing but the console. A track can be
26
+ * unticked while the fetch is in flight, and every branch below reaches
27
+ * `getSession(self)`, which throws on a detached node — inside a floating
28
+ * promise, where nothing catches it.
29
+ *
30
+ * `onMiss` is a parameter rather than fixed because one caller legitimately
31
+ * stays quiet: the pileup pre-warms the read behind a context menu before the
32
+ * user has asked for anything, so a miss there just leaves the menu without its
33
+ * feature items. Passing `() => {}` is how a call site says it is speculative.
34
+ */
35
+ export async function withFeatureDetails(self, fetch, onFeat, onMiss = () => {
36
+ notifyFeatureDetailsMiss(self);
37
+ }) {
38
+ try {
39
+ const feature = await fetch();
40
+ if (!isAlive(self)) {
41
+ return;
42
+ }
43
+ if (feature) {
44
+ onFeat(feature);
45
+ }
46
+ else {
47
+ onMiss();
48
+ }
49
+ }
50
+ catch (e) {
51
+ // Logged whatever happened, and only toasted while the display is still
52
+ // there: `getSession` throws on a detached node, and a message naming a
53
+ // track the user has already closed is noise they cannot act on.
54
+ console.error(e);
55
+ if (isAlive(self)) {
56
+ getNotificationSink(self).notifyError(`${e}`, e);
57
+ }
58
+ }
59
+ }