@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
  1071. package/esm/util/systemColorScheme.js +27 -0
  1072. package/esm/util/tabix.d.ts +125 -0
  1073. package/esm/util/tabix.js +148 -0
  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
  1076. package/esm/util/temporaryAssembly.d.ts +21 -0
  1077. package/esm/util/temporaryAssembly.js +29 -0
  1078. package/esm/util/thresholdScale.d.ts +91 -0
  1079. package/esm/util/thresholdScale.js +166 -0
  1080. package/esm/util/tickLabels.d.ts +36 -0
  1081. package/esm/util/tickLabels.js +45 -0
  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
  1121. package/esm/util/unzip.d.ts +1 -0
  1122. package/esm/util/unzip.js +6 -0
  1123. package/esm/util/useEventCallback.d.ts +1 -0
  1124. package/esm/util/useEventCallback.js +16 -0
  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
  1126. package/esm/util/useFeatureSequence.js +55 -77
  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
  1130. package/esm/util/useFetchPlugins.js +18 -0
  1131. package/esm/util/useMeasure.d.ts +11 -1
  1132. package/esm/util/useMeasure.js +20 -6
  1133. package/esm/util/usePanZoom.d.ts +75 -0
  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
  1136. package/esm/util/usePanelVirtualScroll.js +15 -0
  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
  1144. package/esm/util/useRowVirtualScroll.js +22 -0
  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
  1149. package/esm/util/viewStatus.d.ts +90 -0
  1150. package/esm/util/viewStatus.js +54 -0
  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
  1160. package/esm/util/withFeatureDetails.js +59 -0
  1161. package/esm/util/withLaunchInput.d.ts +174 -0
  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
  1172. package/esm/ReExports/BaseFeatureDetails.js +0 -9
  1173. package/esm/ReExports/DataGrid.d.ts +0 -1
  1174. package/esm/ReExports/DataGrid.js +0 -1
  1175. package/esm/ReExports/index.d.ts +0 -1
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  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
  1181. package/esm/data_adapters/util.js +0 -6
  1182. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1183. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1184. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1185. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1186. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1187. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1188. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1189. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1190. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1191. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1192. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1193. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1195. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1196. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
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  1198. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1199. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1200. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1201. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1202. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1203. package/esm/rpc/baseRpcConfig.js +0 -10
  1204. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
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  1207. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
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  1218. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
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  1220. package/esm/ui/MenuButton.d.ts +0 -1
  1221. package/esm/ui/MenuButton.js +0 -1
  1222. package/esm/ui/MenuItems.d.ts +0 -15
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  1247. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
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  1257. package/esm/util/tss-react/mui/index.d.ts +0 -1
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  1263. /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,51 @@
1
+ import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
2
+ /** what a diagnostic calls the view: its snapshot `type`, or the model name */
3
+ export declare function viewLabel(self: IStateTreeNode): string;
4
+ /**
5
+ * What every surface calls this mistake. A session spec launches a view without
6
+ * ever building a snapshot, so it classifies its own keys and reports them
7
+ * through its own session rather than through the sink below — one wording, so
8
+ * a typo reads the same whether it was written in a config or in a URL.
9
+ */
10
+ export declare function unknownKeysMessage(label: string, keys: string[]): string;
11
+ /** Why a settings key `applyDisplaySettings` was handed wrote nothing. */
12
+ export type UnappliedReason = 'no-slot' | 'setter-only' | 'display-type';
13
+ export interface UnappliedSetting {
14
+ key: string;
15
+ reason: UnappliedReason;
16
+ }
17
+ /** The action `setter-only` names: `height` -> `setHeight`. */
18
+ export declare function displaySetterName(key: string): string;
19
+ /**
20
+ * What a surface calls a key the display has an action for but no slot. Its own
21
+ * sentence rather than `unknownKeysMessage`'s: the display does take the
22
+ * setting, just not written this way, and saying "unknown key" over a key whose
23
+ * setter we name in the same breath contradicts itself.
24
+ */
25
+ export declare function setterOnlyMessage(label: string, keys: string[]): string;
26
+ /**
27
+ * Name the keys a view was handed and could not place, from the partition
28
+ * `withLaunchInput` runs on the snapshot.
29
+ */
30
+ export declare function reportUnknownKeys(self: IStateTreeNode, keys: string[]): void;
31
+ /**
32
+ * Name the row lists a view refused whole. `withLaunchInput` splits an authored
33
+ * array into the recipes a launcher resolves and the built snapshots MST
34
+ * restores, per entry — but a row list is indexed against the view's `levels`
35
+ * and per-level tracks, so a list holding both kinds has no correct split and
36
+ * is refused rather than renumbered.
37
+ */
38
+ export declare function reportMalformedRows(self: IStateTreeNode, keys: string[]): void;
39
+ /**
40
+ * What every surface calls v4's nested `init`. v5 takes every setting directly
41
+ * on the view object and unwraps the nesting on the way in, so the settings
42
+ * still arrive — this names the spelling to fix while they do.
43
+ */
44
+ export declare function legacyInitMessage(label: string): string;
45
+ /**
46
+ * Name a snapshot that still writes v4's nested `init`. The console alone,
47
+ * unlike the two reporters above: the settings were applied, so there is
48
+ * nothing for a visitor to act on and a warning toast over a working view is
49
+ * noise. `jbrowse validate` is where the author of the config hears about it.
50
+ */
51
+ export declare function reportLegacyInit(self: IStateTreeNode): void;
@@ -0,0 +1,82 @@
1
+ import { getType } from '@jbrowse/mobx-state-tree';
2
+ import { getNotificationSink } from './sessionServices.js';
3
+ /** what a diagnostic calls the view: its snapshot `type`, or the model name */
4
+ export function viewLabel(self) {
5
+ return self.type ?? getType(self).name;
6
+ }
7
+ /**
8
+ * What every surface calls this mistake. A session spec launches a view without
9
+ * ever building a snapshot, so it classifies its own keys and reports them
10
+ * through its own session rather than through the sink below — one wording, so
11
+ * a typo reads the same whether it was written in a config or in a URL.
12
+ */
13
+ export function unknownKeysMessage(label, keys) {
14
+ return `${label} ignored unknown key(s): ${keys.join(', ')}`;
15
+ }
16
+ /** The action `setter-only` names: `height` -> `setHeight`. */
17
+ export function displaySetterName(key) {
18
+ return `set${key[0].toUpperCase()}${key.slice(1)}`;
19
+ }
20
+ /**
21
+ * What a surface calls a key the display has an action for but no slot. Its own
22
+ * sentence rather than `unknownKeysMessage`'s: the display does take the
23
+ * setting, just not written this way, and saying "unknown key" over a key whose
24
+ * setter we name in the same breath contradicts itself.
25
+ */
26
+ export function setterOnlyMessage(label, keys) {
27
+ return `${label} did not apply ${keys.join(', ')}: no config slot takes ${keys.length > 1 ? 'them' : 'it'}. Call ${keys.map(displaySetterName).join(', ')} on the display instead.`;
28
+ }
29
+ /**
30
+ * Name the keys a view was handed and could not place, from the partition
31
+ * `withLaunchInput` runs on the snapshot.
32
+ */
33
+ export function reportUnknownKeys(self, keys) {
34
+ if (!keys.length) {
35
+ return;
36
+ }
37
+ const message = unknownKeysMessage(viewLabel(self), keys);
38
+ console.warn(message);
39
+ try {
40
+ getNotificationSink(self).notify(message, 'warning');
41
+ }
42
+ catch {
43
+ // a view built outside a session has nowhere to put it
44
+ }
45
+ }
46
+ /**
47
+ * Name the row lists a view refused whole. `withLaunchInput` splits an authored
48
+ * array into the recipes a launcher resolves and the built snapshots MST
49
+ * restores, per entry — but a row list is indexed against the view's `levels`
50
+ * and per-level tracks, so a list holding both kinds has no correct split and
51
+ * is refused rather than renumbered.
52
+ */
53
+ export function reportMalformedRows(self, keys) {
54
+ if (!keys.length) {
55
+ return;
56
+ }
57
+ const message = `${viewLabel(self)} refused ${keys.join(', ')}: the list mixes built view snapshots with recipes to open one, and the rows index against the levels between them. Write all of them one way.`;
58
+ console.warn(message);
59
+ try {
60
+ getNotificationSink(self).notify(message, 'warning');
61
+ }
62
+ catch {
63
+ // a view built outside a session has nowhere to put it
64
+ }
65
+ }
66
+ /**
67
+ * What every surface calls v4's nested `init`. v5 takes every setting directly
68
+ * on the view object and unwraps the nesting on the way in, so the settings
69
+ * still arrive — this names the spelling to fix while they do.
70
+ */
71
+ export function legacyInitMessage(label) {
72
+ return `${label} nests its settings under "init", which is deprecated: write every setting directly on the view object.`;
73
+ }
74
+ /**
75
+ * Name a snapshot that still writes v4's nested `init`. The console alone,
76
+ * unlike the two reporters above: the settings were applied, so there is
77
+ * nothing for a visitor to act on and a warning toast over a working view is
78
+ * noise. `jbrowse validate` is where the author of the config hears about it.
79
+ */
80
+ export function reportLegacyInit(self) {
81
+ console.warn(legacyInitMessage(viewLabel(self)));
82
+ }
@@ -0,0 +1 @@
1
+ export { unzip } from '@gmod/bgzf-filehandle';
@@ -0,0 +1,6 @@
1
+ // Deliberately its own entry rather than a name on the util barrel:
2
+ // @gmod/bgzf-filehandle declares no `sideEffects`, so webpack cannot tree-shake
3
+ // a re-export of it out of the barrel, and the barrel has ~1090 importers —
4
+ // including eager plugin entries. Re-exporting `unzip` there put bgzf + pako
5
+ // (~180KB) on the startup path of every page load.
6
+ export { unzip } from '@gmod/bgzf-filehandle';
@@ -0,0 +1 @@
1
+ export declare function useEventCallback<Args extends unknown[], Return>(fn: (...args: Args) => Return): (...args: Args) => Return;
@@ -0,0 +1,16 @@
1
+ import { useCallback, useLayoutEffect, useRef } from 'react';
2
+ // Observer-safe replacement for React's useEffectEvent. Returns a stable
3
+ // callback that always invokes the latest `fn`.
4
+ //
5
+ // React's useEffectEvent reads stale state inside mobx-react `observer()`
6
+ // components (its impl swap does not take effect under observer's reactive
7
+ // render), and nearly every JBrowse component is an observer. Here the ref is
8
+ // updated in a layout effect — which runs before paint and before any browser
9
+ // event can fire the stable callback, so it never reads a stale closure.
10
+ export function useEventCallback(fn) {
11
+ const ref = useRef(fn);
12
+ useLayoutEffect(() => {
13
+ ref.current = fn;
14
+ });
15
+ return useCallback((...args) => ref.current(...args), []);
16
+ }
@@ -1,19 +1,25 @@
1
- import type { AbstractSessionModel, Feature } from './index.ts';
2
- export declare function useFeatureSequence({ session, feature, upDownBp, forceLoad, assemblyName, shouldFetch, }: {
3
- assemblyName: string;
1
+ import type { AbstractSessionModel } from './types/index.ts';
2
+ export declare function useFeatureSequence({ session, start, end, refName, upDownBp, forceLoad, assemblyName, }: {
3
+ assemblyName: string | undefined;
4
4
  session?: AbstractSessionModel;
5
- feature: Feature;
5
+ start: number;
6
+ end: number;
7
+ refName: string;
6
8
  upDownBp: number;
7
9
  forceLoad: boolean;
8
- shouldFetch?: boolean;
9
10
  }): {
10
11
  sequence: {
12
+ error: string;
13
+ seq?: undefined;
14
+ upstream?: undefined;
15
+ downstream?: undefined;
16
+ } | {
17
+ error?: undefined;
11
18
  seq: string;
12
19
  upstream: string;
13
20
  downstream: string;
14
- } | {
15
- error: string;
16
21
  } | undefined;
17
22
  loading: boolean;
18
23
  error: unknown;
24
+ status: import("./progress.ts").RpcStatus | undefined;
19
25
  };
@@ -1,87 +1,65 @@
1
- import { useEffect, useMemo, useState } from 'react';
2
- import { fetchSeq } from "./fetchSeq.js";
1
+ import { fetchSeq } from './fetchSeq.js';
2
+ import { createStatusFanOut } from './progress.js';
3
+ import { useFetch } from './useFetch.js';
3
4
  const BPLIMIT = 20_000_000;
4
- export function useFeatureSequence({ session, feature, upDownBp, forceLoad, assemblyName, shouldFetch = true, }) {
5
- const [sequence, setSequence] = useState();
6
- const [error, setError] = useState();
7
- const [loading, setLoading] = useState(false);
8
- const key = useMemo(() => {
9
- if (!session || !shouldFetch) {
10
- return null;
11
- }
12
- const start = feature.get('start');
13
- const end = feature.get('end');
14
- const refName = feature.get('refName');
15
- return {
5
+ export function useFeatureSequence({ session, start, end, refName, upDownBp, forceLoad, assemblyName, }) {
6
+ const guard = session && assemblyName ? { session, assemblyName } : null;
7
+ const { data: sequence, error, isLoading: loading, status, } = useFetch(guard
8
+ ? [
9
+ 'featureSequence',
10
+ guard.assemblyName,
11
+ refName,
16
12
  start,
17
13
  end,
18
- refName,
19
- assemblyName,
20
14
  upDownBp,
21
15
  forceLoad,
22
- sessionId: session.id || 'default',
23
- };
24
- }, [session, feature, assemblyName, upDownBp, forceLoad, shouldFetch]);
25
- useEffect(() => {
26
- if (!key) {
27
- setSequence(undefined);
28
- setError(undefined);
29
- return;
30
- }
31
- ;
32
- (async () => {
33
- try {
34
- setLoading(true);
35
- setError(undefined);
36
- const { start, end, refName, assemblyName, upDownBp, forceLoad } = key;
37
- if (!forceLoad && end - start > BPLIMIT) {
38
- setSequence({
39
- error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
40
- });
41
- return;
42
- }
43
- const b = start - upDownBp;
44
- const e = end + upDownBp;
45
- const [seq, upstream, downstream] = await Promise.all([
46
- fetchSeq({
47
- start,
48
- end,
49
- refName,
50
- assemblyName,
51
- session: session,
52
- }),
53
- fetchSeq({
54
- start: Math.max(0, b),
16
+ ]
17
+ : null, guard
18
+ ? async (_name, _asm, _ref, _start, _end, _upDown, _force, signal, statusCallback) => {
19
+ const { session: s, assemblyName: asmName } = guard;
20
+ if (!forceLoad && end - start > BPLIMIT) {
21
+ return {
22
+ error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
23
+ };
24
+ }
25
+ // three concurrent reads sharing one status field, so each gets its
26
+ // own slot and they aggregate into one bar
27
+ const slot = createStatusFanOut(statusCallback);
28
+ const [seq, upstream, downstream] = await Promise.all([
29
+ fetchSeq({
30
+ start,
31
+ end,
32
+ refName,
33
+ assemblyName: asmName,
34
+ session: s,
35
+ signal,
36
+ statusCallback: slot(),
37
+ }),
38
+ upDownBp > 0
39
+ ? fetchSeq({
40
+ start: Math.max(0, start - upDownBp),
55
41
  end: start,
56
42
  refName,
57
- assemblyName,
58
- session: session,
59
- }),
60
- fetchSeq({
43
+ assemblyName: asmName,
44
+ session: s,
45
+ signal,
46
+ statusCallback: slot(),
47
+ })
48
+ : Promise.resolve(''),
49
+ upDownBp > 0
50
+ ? fetchSeq({
61
51
  start: end,
62
- end: e,
52
+ end: end + upDownBp,
63
53
  refName,
64
- assemblyName,
65
- session: session,
66
- }),
67
- ]);
68
- setSequence({
69
- seq,
70
- upstream,
71
- downstream,
72
- });
73
- }
74
- catch (err) {
75
- setError(err);
76
- }
77
- finally {
78
- setLoading(false);
79
- }
80
- })();
81
- }, [key, session]);
82
- return {
83
- sequence,
84
- loading,
85
- error,
86
- };
54
+ assemblyName: asmName,
55
+ session: s,
56
+ signal,
57
+ statusCallback: slot(),
58
+ })
59
+ : Promise.resolve(''),
60
+ ]);
61
+ return { seq, upstream, downstream };
62
+ }
63
+ : null);
64
+ return { sequence, loading, error, status };
87
65
  }
@@ -0,0 +1,55 @@
1
+ import type { RpcStatus, StatusCallback } from './progress.ts';
2
+ export type FetchKey = string | readonly unknown[] | null | undefined | false;
3
+ type FetchingKey<Key> = Exclude<Key, null | undefined | false>;
4
+ /**
5
+ * The fetcher's parameter list, derived from the key. An array key is spread
6
+ * into the parameters, so a tuple key gives the fetcher one typed parameter per
7
+ * element (`MafSequenceWidget` destructures its key that way, to reuse the
8
+ * narrowing the null-key ternary already did); a string key arrives as the
9
+ * single argument (`useGenomesData`). Most fetchers close over what they need
10
+ * and declare no parameters at all, which stays assignable either way.
11
+ *
12
+ * A signal and a status callback follow the key arguments. The signal is
13
+ * created per fetch and aborted when the key changes or the component unmounts,
14
+ * so a fetcher that forwards it to an RPC cancels the worker instead of leaving
15
+ * it grinding on an answer nobody is waiting for. The callback is what the RPC's
16
+ * own progress comes back through, and it surfaces on the hook's `status` — a
17
+ * dialog that forwards both gets "Downloading features 42%" and a cancel that
18
+ * works, instead of a bare spinner over an uninterruptible whole-chromosome
19
+ * read. Fetchers that take neither are unaffected.
20
+ */
21
+ type FetcherArgs<Key> = FetchingKey<Key> extends readonly unknown[] ? [...FetchingKey<Key>, AbortSignal, StatusCallback] : [FetchingKey<Key>, AbortSignal, StatusCallback];
22
+ interface FetchState<Data> {
23
+ data: Data | undefined;
24
+ error: unknown;
25
+ isLoading: boolean;
26
+ }
27
+ interface UseFetchOptions<Data> {
28
+ onError?: (error: unknown) => void;
29
+ onSuccess?: (data: Data) => void;
30
+ }
31
+ interface UseFetchResponse<Data> extends FetchState<Data> {
32
+ /**
33
+ * Trigger a refetch. Returns nothing: the result arrives through
34
+ * `data`/`error`/`isLoading` like the initial fetch, and a promise here could
35
+ * only resolve before the refetch it schedules had run.
36
+ */
37
+ mutate: () => void;
38
+ isValidating: boolean;
39
+ /**
40
+ * Latest progress the in-flight fetcher reported through its status callback,
41
+ * or undefined when it reported none or the fetch has settled. Render it with
42
+ * `statusProgressLabel` (and `statusFraction` for a bar); a fetcher that never
43
+ * calls its callback leaves this undefined and the consumer shows whatever it
44
+ * showed before.
45
+ */
46
+ status: RpcStatus | undefined;
47
+ }
48
+ /**
49
+ * Revalidate every mounted `useFetch` on this key. Synchronous for the same
50
+ * reason the per-hook `mutate` is: it schedules the refetches, and each hook
51
+ * reports its own result through the state it already exposes.
52
+ */
53
+ export declare function mutate(key: FetchKey): void;
54
+ export declare function useFetch<Data = unknown, Key extends FetchKey = FetchKey>(key: Key, fetcher: ((...args: FetcherArgs<Key>) => Promise<Data>) | null, options?: UseFetchOptions<Data>): UseFetchResponse<Data>;
55
+ export {};
@@ -0,0 +1,197 @@
1
+ import { useCallback, useEffect, useRef, useState } from 'react';
2
+ import { createStatusWindow } from './progress.js';
3
+ // The whole key as the "don't fetch" sentinel: `cond && [...]`, `cond ? [...] :
4
+ // null`. `false` belongs here and NOT in the element check below, which is what
5
+ // this used to share with it.
6
+ const isNoKey = (k) => k === null || k === undefined || k === false;
7
+ // An element that has not resolved yet — an offset still being computed, an
8
+ // assembly still loading. **`false` is not one of them**: it is a resolved
9
+ // boolean, and a caller with a `false`-valued setting in its key meant to fetch
10
+ // under that setting. Sharing one predicate with the sentinel above made every
11
+ // such key unfetchable, which the MAF sequence widget shipped — its
12
+ // `includeInsertions` defaults to `false`, so the widget sat on its loading
13
+ // animation forever and issued no RPC at all. `SaveTrackData` hit the same
14
+ // thing and encoded its boolean as a string rather than fixing it here.
15
+ const isUnresolved = (k) => k === null || k === undefined;
16
+ function serializeKey(key) {
17
+ return isNoKey(key) || (Array.isArray(key) && key.some(isUnresolved))
18
+ ? null
19
+ : JSON.stringify(key);
20
+ }
21
+ // Cross-component refetch coordination, keyed by serialized key. Holds only
22
+ // refetch callbacks (never data), so there is no global cache to go stale —
23
+ // this is the one SWR feature we relied on: mutate(key) revalidates every
24
+ // mounted useFetch sharing that key.
25
+ const listeners = new Map();
26
+ /**
27
+ * Revalidate every mounted `useFetch` on this key. Synchronous for the same
28
+ * reason the per-hook `mutate` is: it schedules the refetches, and each hook
29
+ * reports its own result through the state it already exposes.
30
+ */
31
+ export function mutate(key) {
32
+ const serialized = serializeKey(key);
33
+ if (serialized) {
34
+ for (const refetch of listeners.get(serialized) ?? []) {
35
+ refetch();
36
+ }
37
+ }
38
+ }
39
+ export function useFetch(key, fetcher, options = {}) {
40
+ const serialized = serializeKey(key);
41
+ // A null fetcher is the second way to say "don't fetch", so its nullness is a
42
+ // fetch input exactly like the key is — the effect below has to re-run when it
43
+ // flips. Only the boolean can go in the dependency list: the fetcher itself is
44
+ // usually an inline closure, so depending on its identity would refetch every
45
+ // render. Tracked separately from the key because the two are independent —
46
+ // gating on the key alone leaves a `fetcher` that resolves from null to a real
47
+ // function (an adapter/config arriving late) permanently stuck not fetching.
48
+ const hasFetcher = fetcher !== null;
49
+ const [state, setState] = useState(() => ({
50
+ data: undefined,
51
+ error: undefined,
52
+ // seeded from the key rather than starting false: the effect below runs
53
+ // after the first paint, so a false seed showed the resolved-and-empty state
54
+ // for a frame before the spinner (an empty attribute table, an empty list)
55
+ isLoading: serialized !== null && hasFetcher,
56
+ }));
57
+ // bumped to force a refetch (local mutate() or a cross-component mutate(key))
58
+ const [nonce, setNonce] = useState(0);
59
+ // separate from `state` because it moves on its own cadence: the RPC status
60
+ // stream ticks throughout one fetch, while data/error/isLoading move once
61
+ const [status, setStatus] = useState(undefined);
62
+ // refs let the fetch effect depend only on the serialized key + nonce without
63
+ // re-running when the (often inline) fetcher/options/key identities change
64
+ const optionsRef = useRef(options);
65
+ optionsRef.current = options;
66
+ const fetcherRef = useRef(fetcher);
67
+ fetcherRef.current = fetcher;
68
+ const keyRef = useRef(key);
69
+ keyRef.current = key;
70
+ // the key the last fetch ran under, to tell a mutate()-driven refetch from a
71
+ // key change — see the setState below
72
+ const fetchedKeyRef = useRef(null);
73
+ useEffect(() => {
74
+ const key = keyRef.current;
75
+ const fetcher = fetcherRef.current;
76
+ if (serialized === null || !fetcher) {
77
+ // when the key becomes null, callers see undefined data again rather
78
+ // than the prior fetch's result
79
+ fetchedKeyRef.current = null;
80
+ setState({ data: undefined, error: undefined, isLoading: false });
81
+ // and the same for the progress, which otherwise sticks: a key going nil
82
+ // *during* a fetch runs this branch's cleanup first, so the `alive` guard
83
+ // on the settle below has already closed and nothing else clears it
84
+ setStatus(undefined);
85
+ return undefined;
86
+ }
87
+ else {
88
+ let alive = true;
89
+ // `alive` is about this effect run; `settled` is about this fetch. They
90
+ // differ for exactly one thing, the status stream below: an RPC resolves
91
+ // its status channel asynchronously, so a status can arrive after the
92
+ // fetch it describes has resolved — and without a second term it lands on
93
+ // top of the clear and sticks. (The trailing write queued *before* the
94
+ // fetch resolved is a different case, and the stream's own `clear` drops
95
+ // that one.)
96
+ let settled = false;
97
+ const controller = new AbortController();
98
+ // A refetch under the same key — mutate(), or the cross-component
99
+ // mutate(key) — is the same question asked again, so what is on screen is
100
+ // a stale answer to it rather than an answer to something else: leave it
101
+ // up and let `isLoading` say it is being rechecked. A key *change* still
102
+ // clears, because the old data describes a different question.
103
+ //
104
+ // Blanking on every refetch is what made the desktop start screen flash
105
+ // "No sessions available" after each rename, delete, or cancelled dialog.
106
+ // Consumers that want the old view gone during a revalidate already have
107
+ // it: they gate on `isLoading`, which is unchanged.
108
+ const sameKey = fetchedKeyRef.current === serialized;
109
+ fetchedKeyRef.current = serialized;
110
+ setState(prev => ({
111
+ data: sameKey ? prev.data : undefined,
112
+ error: undefined,
113
+ isLoading: true,
114
+ }));
115
+ // the previous fetch's last progress describes work that is over
116
+ setStatus(undefined);
117
+ // The runtime counterpart of FetcherArgs: an array key becomes one
118
+ // argument per element, anything else a single argument, then the stop
119
+ // signal and the status callback. A conditional type over an unresolved
120
+ // `Key` can't be discharged
121
+ // inside the function body, so the parameter list is erased for this one
122
+ // call — callers still get the precise arity, and the looseness stops
123
+ // here.
124
+ const keyArgs = Array.isArray(key) ? key : [key];
125
+ // guarded and throttled for the same reason every other owner of a
126
+ // progress stream is: an RPC emits ~40 of these a second, and each one
127
+ // re-renders the dialog holding this hook
128
+ // one fetch is one stream, so the window is this effect run's
129
+ // the one writer, so the settle below clears through the same guard its
130
+ // statuses pass
131
+ const statusWindow = createStatusWindow(status => {
132
+ if (alive) {
133
+ setStatus(status);
134
+ }
135
+ });
136
+ const { statusCallback, clear: clearStatus } = statusWindow.open({
137
+ isCurrent: () => alive && !settled,
138
+ });
139
+ const args = [...keyArgs, controller.signal, statusCallback];
140
+ const call = fetcher;
141
+ Promise.resolve()
142
+ .then(() => call(...args))
143
+ .then(data => {
144
+ if (alive) {
145
+ setState({ data, error: undefined, isLoading: false });
146
+ optionsRef.current.onSuccess?.(data);
147
+ }
148
+ })
149
+ .catch((error) => {
150
+ if (alive) {
151
+ setState({ data: undefined, error, isLoading: false });
152
+ optionsRef.current.onError?.(error);
153
+ }
154
+ })
155
+ .finally(() => {
156
+ // however it settled, the progress it reported describes work that is
157
+ // over
158
+ settled = true;
159
+ clearStatus();
160
+ });
161
+ return () => {
162
+ alive = false;
163
+ // the signal's lifetime is this fetch's. An abort rejection lands in the
164
+ // catch above with alive already false, so it never surfaces as an error
165
+ controller.abort();
166
+ // and the window's lifetime is too: `alive` already makes a queued
167
+ // trailing write a no-op, but the timer behind it would otherwise stand
168
+ // for up to a window past unmount
169
+ statusWindow.reset();
170
+ };
171
+ }
172
+ }, [serialized, hasFetcher, nonce]);
173
+ // register this instance so a cross-component mutate(key) can refetch it
174
+ useEffect(() => {
175
+ if (serialized === null) {
176
+ return undefined;
177
+ }
178
+ else {
179
+ const refetch = () => {
180
+ setNonce(n => n + 1);
181
+ };
182
+ const set = listeners.get(serialized) ?? new Set();
183
+ set.add(refetch);
184
+ listeners.set(serialized, set);
185
+ return () => {
186
+ set.delete(refetch);
187
+ if (set.size === 0) {
188
+ listeners.delete(serialized);
189
+ }
190
+ };
191
+ }
192
+ }, [serialized]);
193
+ const mutate = useCallback(() => {
194
+ setNonce(n => n + 1);
195
+ }, []);
196
+ return { ...state, mutate, isValidating: state.isLoading, status };
197
+ }
@@ -0,0 +1,16 @@
1
+ /**
2
+ * The plugin store listing. Shared by every surface that installs plugins (the
3
+ * in-session plugin store widget, Desktop's global plugins dialog) so they read
4
+ * the same manifest version and get the same integrity hashes and compatibility
5
+ * ranges — a second copy of this fetch is how one of them silently ends up on
6
+ * the unhashed v1 list.
7
+ *
8
+ * Through `fetchPlugins`, which memoizes its request, rather than fetching the
9
+ * url directly: `useFetch` holds no data cache, so every open of the store
10
+ * widget was a fresh round trip beside whatever the boot path had already
11
+ * asked for.
12
+ */
13
+ export declare function useFetchPlugins(): {
14
+ plugins: import("./index.ts").JBrowsePlugin[] | undefined;
15
+ error: unknown;
16
+ };
@@ -0,0 +1,18 @@
1
+ import { fetchPlugins } from '../checkPlugins.js';
2
+ import { useFetch } from './useFetch.js';
3
+ /**
4
+ * The plugin store listing. Shared by every surface that installs plugins (the
5
+ * in-session plugin store widget, Desktop's global plugins dialog) so they read
6
+ * the same manifest version and get the same integrity hashes and compatibility
7
+ * ranges — a second copy of this fetch is how one of them silently ends up on
8
+ * the unhashed v1 list.
9
+ *
10
+ * Through `fetchPlugins`, which memoizes its request, rather than fetching the
11
+ * url directly: `useFetch` holds no data cache, so every open of the store
12
+ * widget was a fresh round trip beside whatever the boot path had already
13
+ * asked for.
14
+ */
15
+ export function useFetchPlugins() {
16
+ const { data, error } = useFetch('jbrowse-plugin-store-v2', fetchPlugins);
17
+ return { plugins: data?.plugins, error };
18
+ }
@@ -1,4 +1,14 @@
1
- export default function useMeasure(): readonly [import("react").RefObject<HTMLDivElement | null>, {
1
+ /**
2
+ * Element size, via ResizeObserver.
3
+ *
4
+ * `track` names the axes the caller actually uses, and it is a performance knob
5
+ * as much as an API one: the observer fires for a change on *either* axis, so a
6
+ * width-only caller re-rendered every time its content grew taller. That is the
7
+ * common case in a view container, whose height follows its tracks. Naming the
8
+ * axis lets those updates be dropped instead. The unnamed axis is reported as
9
+ * `undefined` rather than a stale number, so nothing can quietly read it.
10
+ */
11
+ export default function useMeasure(track?: 'both' | 'width' | 'height'): readonly [import("react").RefObject<HTMLDivElement | null>, {
2
12
  width?: number;
3
13
  height?: number;
4
14
  }];