@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
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  1061. package/esm/util/stats.js +39 -8
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  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
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  1066. package/esm/util/svAlt.d.ts +145 -0
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  1070. package/esm/util/systemColorScheme.d.ts +12 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
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  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
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  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
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  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
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  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
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  1127. package/esm/util/useFetch.d.ts +55 -0
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  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
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  1137. package/esm/util/usePointerDrag.d.ts +37 -0
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  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
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  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
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  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
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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,105 @@
1
+ import { useRef } from 'react';
2
+ import { usePointerDrag } from './usePointerDrag.js';
3
+ import { useRafCommit } from './useRafCommit.js';
4
+ /**
5
+ * A pointer drag along one axis, reported as a distance per animation frame.
6
+ *
7
+ * This is the whole gesture behind a resize handle with no opinion about how the
8
+ * handle looks. `ui/ResizeHandle` is this hook plus JBrowse's own 4px bar, and an
9
+ * app drawing its own divider spreads the returned props onto it. That is the
10
+ * per-track resize story for an embedder who mounts displays themselves: the
11
+ * track row is the host's box, so the bar has to be theirs, but the gesture and
12
+ * the two model calls are not.
13
+ *
14
+ * ```tsx
15
+ * const handleProps = useResizeDrag({
16
+ * onDrag: distance => {
17
+ * display.resizeHeight(distance)
18
+ * },
19
+ * onDragStart: () => {
20
+ * track.setResizing(true)
21
+ * },
22
+ * onDragEnd: () => {
23
+ * track.setResizing(false)
24
+ * },
25
+ * })
26
+ * return (
27
+ * <div
28
+ * {...handleProps}
29
+ * style={{ height: 4, cursor: 'row-resize', touchAction: 'none' }}
30
+ * />
31
+ * )
32
+ * ```
33
+ *
34
+ * `touchAction: 'none'` is the caller's half of the deal: without it the browser
35
+ * claims a touch drag as a page scroll and the pointer stream never arrives.
36
+ * `usePanZoom` writes the same property itself and this cannot — that one is
37
+ * handed the element as a ref, while this returns props and never sees a node.
38
+ * It stays out of those props because a caller's own `style` would silently
39
+ * replace it.
40
+ *
41
+ * Three things a hand-rolled version gets wrong, none of which fails loudly:
42
+ *
43
+ * - **One commit per frame.** A pointermove stream (plus the browser's own
44
+ * coalesced batches) outruns the frame rate, and each commit reruns whatever
45
+ * the resize drives. Committing per event relayouts a pileup several times a
46
+ * frame and throws all but the last away.
47
+ * - **The distance is measured from the last commit**, not from where the press
48
+ * started, so a dropped intermediate position costs nothing and a drag that
49
+ * runs into a clamp (`resizeHeight` stops at the display's minimum) does not
50
+ * bank a debt the pointer has to pay back on the way out.
51
+ * - **`data-gesture-owner` rides in the props.** It is the marker ancestor
52
+ * gestures test for (`closest('[data-gesture-owner]')`, in the LGV's own pan
53
+ * and in `usePanZoom`) before starting a drag of their own, so without it
54
+ * dragging a resize bar pans the view sideways instead. A `stopPropagation` is
55
+ * not a substitute: those ancestors listen on *mouse* events while this runs
56
+ * on *pointer* events, so there is no shared event to stop, and stopping the
57
+ * mousedown would also cost focus-on-click, whose document-level listener
58
+ * (`useFocusOnInteraction`) React's stopPropagation does block.
59
+ */
60
+ export function useResizeDrag({ onDrag, onDragStart, onDragEnd, vertical = false, gain = 1, }) {
61
+ const prevPosRef = useRef(0);
62
+ const getPos = (event) => vertical ? event.clientX : event.clientY;
63
+ // The scheduled value is the absolute pointer position, last-write-wins, and
64
+ // the delta against the previous commit is derived here.
65
+ //
66
+ // Whole px, and the remainder stays in the baseline rather than in a second
67
+ // ref: a divided delta has a sub-pixel tail, and every consumer rounds (a band
68
+ // height is whole px), so rounding it away each frame instead made a gain-2
69
+ // drag travel 4/3 of the pointer. Leaving the unspent fraction ahead of
70
+ // `prevPos` is the same mechanism that keeps a drag into a clamp from banking
71
+ // debt — the distance is always measured from what was last committed.
72
+ const { schedule, flush } = useRafCommit(pos => {
73
+ const distance = Math.trunc((pos - prevPosRef.current) / gain);
74
+ if (distance !== 0) {
75
+ prevPosRef.current += distance * gain;
76
+ onDrag(distance);
77
+ }
78
+ });
79
+ const handlers = usePointerDrag({
80
+ onDragStart: event => {
81
+ prevPosRef.current = getPos(event);
82
+ onDragStart?.();
83
+ },
84
+ onDrag: event => {
85
+ event.preventDefault();
86
+ // read the position synchronously: the deferred commit runs after React
87
+ // has nulled the event
88
+ schedule(getPos(event));
89
+ },
90
+ onDragEnd: () => {
91
+ // land the resting size exactly, rather than a frame late
92
+ flush();
93
+ onDragEnd?.();
94
+ },
95
+ });
96
+ return {
97
+ ...handlers,
98
+ onPointerDown: (event) => {
99
+ // stops the press from starting a text selection that follows the drag
100
+ event.preventDefault();
101
+ handlers.onPointerDown(event);
102
+ },
103
+ 'data-gesture-owner': 'true',
104
+ };
105
+ }
@@ -0,0 +1,9 @@
1
+ import type { RowResizeTarget } from './applyRowResizeWheel.ts';
2
+ /**
3
+ * Wheel gestures over a **row-stack** panel — the multi-sample variant displays
4
+ * and MAF: `shift`+wheel resizes the rows, keeping the row under the cursor
5
+ * put, and a plain wheel scrolls them unless `scrollZoom` gave it to the view.
6
+ * ctrl/meta is the browser's zoom whatever else is held. The canvas-panel rule,
7
+ * where `shift` scrolls, is `usePanelVirtualScroll` (ADR-027).
8
+ */
9
+ export declare function useRowVirtualScroll(el: HTMLElement | null, model: RowResizeTarget, scrollZoom: boolean): void;
@@ -0,0 +1,22 @@
1
+ import { applyRowResizeWheel } from './applyRowResizeWheel.js';
2
+ import { useVirtualScrollWheel } from './useVirtualScrollWheel.js';
3
+ /**
4
+ * Wheel gestures over a **row-stack** panel — the multi-sample variant displays
5
+ * and MAF: `shift`+wheel resizes the rows, keeping the row under the cursor
6
+ * put, and a plain wheel scrolls them unless `scrollZoom` gave it to the view.
7
+ * ctrl/meta is the browser's zoom whatever else is held. The canvas-panel rule,
8
+ * where `shift` scrolls, is `usePanelVirtualScroll` (ADR-027).
9
+ */
10
+ export function useRowVirtualScroll(el, model, scrollZoom) {
11
+ useVirtualScrollWheel(el, model, (e, scroll, rowsEl) => {
12
+ if (e.ctrlKey || e.metaKey) {
13
+ return;
14
+ }
15
+ if (e.shiftKey) {
16
+ applyRowResizeWheel(e, rowsEl, model);
17
+ }
18
+ else if (!scrollZoom) {
19
+ scroll();
20
+ }
21
+ });
22
+ }
@@ -0,0 +1,23 @@
1
+ /**
2
+ * What a virtually scrolled panel reads and writes. `TrackHeightMixin`
3
+ * implements it, so a display passes itself.
4
+ */
5
+ export interface VirtualScrollModel {
6
+ scrollTop: number;
7
+ /** 0 when the content fits; never sub-pixel */
8
+ scrollableHeight: number;
9
+ scrollViewportHeight: number;
10
+ setScrollTop: (scrollTop: number) => void;
11
+ }
12
+ /**
13
+ * Non-passive wheel wiring for a canvas-backed virtual scroll. Owns the scroll
14
+ * latch (and so `preventDefault`), per-frame coalescing of `setScrollTop`, and
15
+ * the listener lifecycle. `onWheel` decides what the gesture means and calls
16
+ * `scroll` when it means scrolling `model`.
17
+ *
18
+ * **Bind this to the panel, not to the `<canvas>`.** A canvas holds no DOM
19
+ * children, so the clickable overlays drawn over it are siblings, and a wheel
20
+ * over one never reaches a listener on the canvas. Overlays that run their own
21
+ * gestures opt out with `[data-gesture-owner]`.
22
+ */
23
+ export declare function useVirtualScrollWheel(panel: HTMLElement | null, model: VirtualScrollModel, onWheel: (e: WheelEvent, scroll: () => void, panel: HTMLElement) => void): void;
@@ -0,0 +1,74 @@
1
+ import { useEffect, useMemo, useRef } from 'react';
2
+ import { createFrameCoalescer } from './frameCoalescer.js';
3
+ import { trackPointerPresence } from './pointerPresence.js';
4
+ import { createScrollLatch } from './scrollLatch.js';
5
+ import { useEventCallback } from './useEventCallback.js';
6
+ import { normalizeWheelDelta } from './wheelZoom.js';
7
+ // An owner that IS the panel (the scrollbar binds this hook to its own marked
8
+ // track) or sits ABOVE it (`TrackContainer` marks its whole overlay layer) does
9
+ // not count.
10
+ function claimedInside(panel, target) {
11
+ const owner = target instanceof Element ? target.closest('[data-gesture-owner]') : null;
12
+ return owner !== null && owner !== panel && panel.contains(owner);
13
+ }
14
+ /**
15
+ * Non-passive wheel wiring for a canvas-backed virtual scroll. Owns the scroll
16
+ * latch (and so `preventDefault`), per-frame coalescing of `setScrollTop`, and
17
+ * the listener lifecycle. `onWheel` decides what the gesture means and calls
18
+ * `scroll` when it means scrolling `model`.
19
+ *
20
+ * **Bind this to the panel, not to the `<canvas>`.** A canvas holds no DOM
21
+ * children, so the clickable overlays drawn over it are siblings, and a wheel
22
+ * over one never reaches a listener on the canvas. Overlays that run their own
23
+ * gestures opt out with `[data-gesture-owner]`.
24
+ */
25
+ export function useVirtualScrollWheel(panel, model, onWheel) {
26
+ const latch = useMemo(() => createScrollLatch(), []);
27
+ const frame = useMemo(() => createFrameCoalescer(), []);
28
+ // The offset as it advances across one frame's events, so the latch sees
29
+ // every delta before the model has committed any of them.
30
+ const runningRef = useRef(0);
31
+ const handleWheel = useEventCallback((e, el) => {
32
+ onWheel(e, () => {
33
+ // A sideways-dominant gesture is the view's pan unless this panel has
34
+ // already latched it; ties go vertical, as in the view.
35
+ const sideways = Math.abs(e.deltaX) > Math.abs(e.deltaY);
36
+ const { scrollableHeight, scrollViewportHeight } = model;
37
+ if (scrollableHeight <= 0 || (sideways && !latch.holds(e))) {
38
+ return;
39
+ }
40
+ if (!frame.pending) {
41
+ runningRef.current = model.scrollTop;
42
+ }
43
+ const dy = normalizeWheelDelta(e.deltaY, e.deltaMode, scrollViewportHeight);
44
+ const next = latch.scroll(e, runningRef.current, dy, scrollableHeight);
45
+ if (next !== null) {
46
+ runningRef.current = next;
47
+ frame.schedule(() => {
48
+ model.setScrollTop(runningRef.current);
49
+ });
50
+ }
51
+ }, el);
52
+ });
53
+ useEffect(() => {
54
+ if (!panel) {
55
+ return undefined;
56
+ }
57
+ // The browser keeps targeting a gesture at the element it began on after
58
+ // the pointer leaves; release those to the page.
59
+ const presence = trackPointerPresence(panel, () => {
60
+ latch.reset();
61
+ });
62
+ const onWheelNative = (e) => {
63
+ if (presence.isOver && !claimedInside(panel, e.target)) {
64
+ handleWheel(e, panel);
65
+ }
66
+ };
67
+ panel.addEventListener('wheel', onWheelNative, { passive: false });
68
+ return () => {
69
+ panel.removeEventListener('wheel', onWheelNative);
70
+ presence.dispose();
71
+ frame.cancel();
72
+ };
73
+ }, [panel, handleWheel, latch, frame]);
74
+ }
@@ -0,0 +1,3 @@
1
+ import type { HighlightType } from './highlights.ts';
2
+ import type { AssemblyNameResolver } from './tracks.ts';
3
+ export declare function highlightsOnAssemblies(highlights: readonly HighlightType[], assemblyNames: Iterable<string>, assemblyManager: AssemblyNameResolver): HighlightType[];
@@ -0,0 +1,5 @@
1
+ import { isSameAssemblyName } from './tracks.js';
2
+ export function highlightsOnAssemblies(highlights, assemblyNames, assemblyManager) {
3
+ const names = [...assemblyNames];
4
+ return highlights.filter(h => names.some(a => isSameAssemblyName(a, h.assemblyName, assemblyManager)));
5
+ }
@@ -0,0 +1,90 @@
1
+ /**
2
+ * What a view's loading screen says: the label, the determinate fraction when
3
+ * the load reports one, and the URL being fetched when the phase named one.
4
+ */
5
+ export interface ViewLoading {
6
+ message: string;
7
+ progress: number | undefined;
8
+ source?: string;
9
+ }
10
+ interface LoadingAssembly {
11
+ statusMessage?: string;
12
+ statusProgress?: number;
13
+ statusSource?: string;
14
+ }
15
+ /**
16
+ * A view's `loading` getter: undefined unless `showLoading`, and otherwise read
17
+ * off the assembly whose load is the wait. The assembly is a thunk because its
18
+ * status ticks while a file is in flight, and a view that is not loading should
19
+ * not subscribe to it.
20
+ */
21
+ export declare function viewLoading(showLoading: boolean, assembly: () => LoadingAssembly | undefined): ViewLoading | undefined;
22
+ /**
23
+ * The mutually-exclusive lifecycle state of a view, as one value.
24
+ *
25
+ * The payload travels with the branch, so a caller cannot read a loading
26
+ * message out of a failed view or an error out of a healthy one.
27
+ */
28
+ export type ViewStatus = {
29
+ type: 'ready';
30
+ } | {
31
+ type: 'error';
32
+ error: unknown;
33
+ } | ({
34
+ type: 'loading';
35
+ } & ViewLoading) | {
36
+ type: 'noRegions';
37
+ };
38
+ export interface ViewStatusInputs {
39
+ error: unknown;
40
+ /**
41
+ * Whether anything has told the view where to look — displayed regions, or an
42
+ * `init` blob still being applied.
43
+ */
44
+ hasSomethingToShow: boolean;
45
+ /**
46
+ * The view's own loading term, as a thunk: `undefined` when it is not
47
+ * loading, otherwise what the spinner should say.
48
+ *
49
+ * A thunk for the same reason `computeDisplayPhase` takes one. The message
50
+ * and the progress fraction come off the assembly's download status, which
51
+ * ticks continuously while a file is in flight — so evaluating it eagerly
52
+ * would make every reader of a *ready* view subscribe to a churning
53
+ * observable it never displays.
54
+ */
55
+ loading: () => ViewLoading | undefined;
56
+ }
57
+ /**
58
+ * Precedence is `error` > `noRegions` > `loading` > `ready`, in one place,
59
+ * rather than re-encoded by subtraction in each view and again in each host.
60
+ *
61
+ * **`ready` here is strictly narrower than `view.ready`**, which is the point of
62
+ * having it. That getter is true when nothing has told the view where to look —
63
+ * `showLoading` is false in that state and so is `error` — so a host gating on
64
+ * it mounts track components over a view with no regions and gets an empty box
65
+ * with nothing anywhere saying why. `noRegions` is that state, named.
66
+ */
67
+ export declare function computeViewStatus({ error, hasSomethingToShow, loading, }: ViewStatusInputs): ViewStatus;
68
+ /**
69
+ * The slice of `AssemblyManager` this needs, spelled out rather than imported:
70
+ * the real type is an MST model a `PluginManager` built, so naming it here
71
+ * would cost this leaf the whole application's type graph (`util/CLAUDE.md`).
72
+ */
73
+ interface AssemblyErrorSource {
74
+ get: (name: string) => {
75
+ error?: unknown;
76
+ } | undefined;
77
+ }
78
+ /**
79
+ * The assembly failures behind a view's `assemblyNames`, joined, or `undefined`
80
+ * when there are none.
81
+ *
82
+ * **Undefined and not `''`**, which is the whole reason this is shared. Three
83
+ * views spelled it as a bare `.join(', ')`, and a getter that answers the empty
84
+ * string for "nothing failed" reads as an error to every `!== undefined` test —
85
+ * `DotplotView.error` folded it in with `??`, so the view reported a terminal
86
+ * error permanently and jbrowse-img refused to render any dotplot. The in-app
87
+ * readers all happened to be truthiness tests, which is why it stayed invisible.
88
+ */
89
+ export declare function assemblyErrorMessage(assemblyManager: AssemblyErrorSource, assemblyNames: string[]): string | undefined;
90
+ export {};
@@ -0,0 +1,54 @@
1
+ /**
2
+ * A view's `loading` getter: undefined unless `showLoading`, and otherwise read
3
+ * off the assembly whose load is the wait. The assembly is a thunk because its
4
+ * status ticks while a file is in flight, and a view that is not loading should
5
+ * not subscribe to it.
6
+ */
7
+ export function viewLoading(showLoading, assembly) {
8
+ if (!showLoading) {
9
+ return undefined;
10
+ }
11
+ const asm = assembly();
12
+ return {
13
+ message: asm?.statusMessage || 'Loading',
14
+ progress: asm?.statusProgress,
15
+ source: asm?.statusSource,
16
+ };
17
+ }
18
+ /**
19
+ * Precedence is `error` > `noRegions` > `loading` > `ready`, in one place,
20
+ * rather than re-encoded by subtraction in each view and again in each host.
21
+ *
22
+ * **`ready` here is strictly narrower than `view.ready`**, which is the point of
23
+ * having it. That getter is true when nothing has told the view where to look —
24
+ * `showLoading` is false in that state and so is `error` — so a host gating on
25
+ * it mounts track components over a view with no regions and gets an empty box
26
+ * with nothing anywhere saying why. `noRegions` is that state, named.
27
+ */
28
+ export function computeViewStatus({ error, hasSomethingToShow, loading, }) {
29
+ if (error) {
30
+ return { type: 'error', error };
31
+ }
32
+ if (!hasSomethingToShow) {
33
+ return { type: 'noRegions' };
34
+ }
35
+ const pending = loading();
36
+ return pending ? { type: 'loading', ...pending } : { type: 'ready' };
37
+ }
38
+ /**
39
+ * The assembly failures behind a view's `assemblyNames`, joined, or `undefined`
40
+ * when there are none.
41
+ *
42
+ * **Undefined and not `''`**, which is the whole reason this is shared. Three
43
+ * views spelled it as a bare `.join(', ')`, and a getter that answers the empty
44
+ * string for "nothing failed" reads as an error to every `!== undefined` test —
45
+ * `DotplotView.error` folded it in with `??`, so the view reported a terminal
46
+ * error permanently and jbrowse-img refused to render any dotplot. The in-app
47
+ * readers all happened to be truthiness tests, which is why it stayed invisible.
48
+ */
49
+ export function assemblyErrorMessage(assemblyManager, assemblyNames) {
50
+ const errors = assemblyNames
51
+ .map(name => assemblyManager.get(name)?.error)
52
+ .filter(e => !!e);
53
+ return errors.length > 0 ? errors.join(', ') : undefined;
54
+ }
@@ -0,0 +1,36 @@
1
+ /**
2
+ * Index window for a virtualized 1-D axis of uniform cells: the `[start, end)`
3
+ * range covering the visible span plus `overscan` cells of buffer on each side,
4
+ * clamped to `[0, total]`.
5
+ *
6
+ * `end` is anchored to `start` (a fixed cell count) rather than recomputed from
7
+ * `scroll + viewport`. That makes the window **stable across sub-cell scrolling**
8
+ * — it only moves when `start` crosses a cell boundary — which is what lets
9
+ * consumers skip work on most scroll events: a canvas keeps its size and
10
+ * contents, a DOM list keeps its rows mounted. Recomputing `end` independently
11
+ * is tighter by up to `overscan` cells at the origin and costs that stability,
12
+ * which is the wrong trade for both.
13
+ *
14
+ * `start` is clamped to `total`, not just to 0. A list that shrinks while its
15
+ * container keeps its scroll position (a new region or track arriving under a
16
+ * scrolled grid) otherwise yields `start > end` — an inverted range whose
17
+ * consumers compute a negative canvas height and paint nothing until the next
18
+ * scroll event. The faceted selector had already hit that and clamped for it;
19
+ * the MAF sequence grid had the same math without the clamp, which is what
20
+ * brought the two together here.
21
+ */
22
+ export declare function virtualRange({ scroll, cellSize, viewport, overscan, total, }: {
23
+ /** scroll offset of the container, in px */
24
+ scroll: number;
25
+ /** px size of one cell along this axis */
26
+ cellSize: number;
27
+ /** px size of the visible span */
28
+ viewport: number;
29
+ /** cells of buffer to render beyond each edge */
30
+ overscan: number;
31
+ /** total number of cells on this axis */
32
+ total: number;
33
+ }): {
34
+ start: number;
35
+ end: number;
36
+ };
@@ -0,0 +1,26 @@
1
+ /**
2
+ * Index window for a virtualized 1-D axis of uniform cells: the `[start, end)`
3
+ * range covering the visible span plus `overscan` cells of buffer on each side,
4
+ * clamped to `[0, total]`.
5
+ *
6
+ * `end` is anchored to `start` (a fixed cell count) rather than recomputed from
7
+ * `scroll + viewport`. That makes the window **stable across sub-cell scrolling**
8
+ * — it only moves when `start` crosses a cell boundary — which is what lets
9
+ * consumers skip work on most scroll events: a canvas keeps its size and
10
+ * contents, a DOM list keeps its rows mounted. Recomputing `end` independently
11
+ * is tighter by up to `overscan` cells at the origin and costs that stability,
12
+ * which is the wrong trade for both.
13
+ *
14
+ * `start` is clamped to `total`, not just to 0. A list that shrinks while its
15
+ * container keeps its scroll position (a new region or track arriving under a
16
+ * scrolled grid) otherwise yields `start > end` — an inverted range whose
17
+ * consumers compute a negative canvas height and paint nothing until the next
18
+ * scroll event. The faceted selector had already hit that and clamped for it;
19
+ * the MAF sequence grid had the same math without the clamp, which is what
20
+ * brought the two together here.
21
+ */
22
+ export function virtualRange({ scroll, cellSize, viewport, overscan, total, }) {
23
+ const start = Math.min(total, Math.max(0, Math.floor(scroll / cellSize) - overscan));
24
+ const visible = Math.ceil(viewport / cellSize) + overscan * 2;
25
+ return { start, end: Math.min(total, start + visible) };
26
+ }
@@ -0,0 +1,26 @@
1
+ export interface GuardedStorage {
2
+ /**
3
+ * Whether there is a store to persist to at all — the first two failures
4
+ * above, both of which are decided once for the page.
5
+ *
6
+ * Every accessor is safe without asking; what this answers is the different
7
+ * question of whether persistence is *real*. With no store, a write is
8
+ * dropped and the matching read answers the default, so a caller that
9
+ * round-trips a value through a key (rather than merely saving one) has to
10
+ * know, or it reads back its own default and calls it the stored value.
11
+ */
12
+ available: () => boolean;
13
+ /** The raw string stored at `key`, or undefined if absent or unreadable. */
14
+ getItem: (key: string) => string | undefined;
15
+ /**
16
+ * Returns whether the store took the value. Nearly every caller ignores that
17
+ * — a setting that could not be persisted is not worth interrupting anyone
18
+ * over — but a caller that reads the key back to learn the current value
19
+ * needs to know that the read will not reflect this write.
20
+ */
21
+ setItem: (key: string, value: string) => boolean;
22
+ /** Returns whether the store took the removal; see {@link setItem}. */
23
+ removeItem: (key: string) => boolean;
24
+ }
25
+ export declare const guardedLocalStorage: GuardedStorage;
26
+ export declare const guardedSessionStorage: GuardedStorage;
@@ -0,0 +1,92 @@
1
+ // The guard both Web Storage stores need, written once.
2
+ //
3
+ // Every accessor built here is *total*: it falls back rather than throwing.
4
+ // That is not defensiveness for its own sake — the callers are MobX autoruns
5
+ // persisting a setting and state-model actions caching a token, and there a
6
+ // throw is doubly bad. It skips the writes queued behind it in the same autorun
7
+ // body (the LGV persists six keys in a row, the hierarchical track selector
8
+ // seven), and MobX reports it as an uncaught reaction error on every subsequent
9
+ // tick.
10
+ //
11
+ // Three separate ways this can fail, and only the first is the obvious one:
12
+ //
13
+ // - no store global at all — an RPC worker, SSR.
14
+ // - reading the global THROWS rather than being undefined: a cross-origin
15
+ // iframe with third-party storage blocked, or Safari with cookies disabled.
16
+ // `typeof localStorage` invokes the same getter, so even the probe has to be
17
+ // guarded — which is also why a `typeof … === 'undefined'` probe is not a way
18
+ // to ask whether you are in a worker. This is the embedded-product case
19
+ // (`@jbrowse/react-*` on someone else's page), where it is also the least
20
+ // likely to be noticed by us.
21
+ // - the store exists and reads fine, but `setItem` throws: quota exhausted, or
22
+ // Safari private browsing, which refuses every write.
23
+ /**
24
+ * `read` names the global rather than being handed it, so resolving it can be
25
+ * deferred past module load and wrapped in the try that the read itself needs.
26
+ * `label` only ever reaches the one warning below.
27
+ */
28
+ function guardedStorage(read, label) {
29
+ // Resolved once. `null` means "checked, unavailable" — distinct from the
30
+ // `undefined` that means "not checked yet".
31
+ let store;
32
+ function getStore() {
33
+ if (store === undefined) {
34
+ try {
35
+ store = read();
36
+ }
37
+ catch {
38
+ store = null;
39
+ }
40
+ }
41
+ return store ?? undefined;
42
+ }
43
+ // One warning per page per store, not one per failed write: the autoruns that
44
+ // persist settings re-run on every change, so a persistent failure (quota,
45
+ // private browsing) would otherwise fill the console with the same line. Same
46
+ // doctrine as the `savingFailed` latch in jbrowse-web's session autosave.
47
+ let warnedOnWrite = false;
48
+ return {
49
+ available: () => getStore() !== undefined,
50
+ getItem(key) {
51
+ try {
52
+ return getStore()?.getItem(key) ?? undefined;
53
+ }
54
+ catch {
55
+ return undefined;
56
+ }
57
+ },
58
+ setItem(key, value) {
59
+ const s = getStore();
60
+ if (!s) {
61
+ return false;
62
+ }
63
+ try {
64
+ s.setItem(key, value);
65
+ return true;
66
+ }
67
+ catch (e) {
68
+ if (!warnedOnWrite) {
69
+ warnedOnWrite = true;
70
+ console.warn(`Unable to persist to ${label} (key "${key}"); further failures are not reported`, e);
71
+ }
72
+ return false;
73
+ }
74
+ },
75
+ removeItem(key) {
76
+ const s = getStore();
77
+ if (!s) {
78
+ return false;
79
+ }
80
+ try {
81
+ s.removeItem(key);
82
+ return true;
83
+ }
84
+ catch {
85
+ // nothing useful to do: the value we wanted gone is unreachable anyway
86
+ return false;
87
+ }
88
+ },
89
+ };
90
+ }
91
+ export const guardedLocalStorage = guardedStorage(() => localStorage, 'localStorage');
92
+ export const guardedSessionStorage = guardedStorage(() => sessionStorage, 'sessionStorage');
@@ -0,0 +1,65 @@
1
+ export declare const MAX_ZOOM_RATE_PER_MS: number;
2
+ export declare const SCROLL_ZOOM_FACTOR_DIVISOR = 500;
3
+ export declare function wheelZoomAccum(normalizedDeltaY: number, isCtrlZoom: boolean): number;
4
+ export declare function getZoomNormalizer(deltaY: number): 25 | 75 | 150 | 500;
5
+ export declare function normalizeWheelDelta(delta: number, deltaMode: number, pageHeight?: number): number;
6
+ export declare function wheelFrameElapsedMs(now: number, lastRafTime: number | null): number;
7
+ export declare function accumulateScroll(prev: number, deltaX: number): number;
8
+ export declare const ZOOM_ACTIVE_WINDOW_MS = 100;
9
+ export declare function isActivelyZooming(now: number, lastZoomTime: number | null): boolean;
10
+ export declare function applyZoomAccum(bpPerPx: number, zoomAccum: number, elapsedMs: number): number;
11
+ export interface WheelZoomView {
12
+ bpPerPx: number;
13
+ zoomTo: (bpPerPx: number, offset?: number) => void;
14
+ horizontalScroll: (delta: number) => void;
15
+ }
16
+ export interface WheelZoomTarget {
17
+ views: WheelZoomView[];
18
+ scrollZoom: boolean;
19
+ originElement: () => HTMLElement | undefined;
20
+ hold?: <T>(fn: () => T) => T;
21
+ }
22
+ export interface WheelZoomControllerOptions {
23
+ element: HTMLElement;
24
+ resolveTarget: (event: WheelEvent) => WheelZoomTarget | undefined;
25
+ swallowUnhandled?: boolean;
26
+ /**
27
+ * Abandon the gesture once the pointer leaves `element`, rather than following
28
+ * the wheel events the browser keeps latching here (see trackPointerPresence).
29
+ *
30
+ * Only for an element large and stationary enough that "the pointer left" is a
31
+ * real exit. On a small or moving target it isn't: a zoom slides a thin svg
32
+ * ribbon out from under a stationary cursor, the browser fires mouseleave, and
33
+ * the gesture would die halfway through. So this is opt-in, not the default.
34
+ */
35
+ releaseOnPointerLeave?: boolean;
36
+ onEvent?: (event: WheelEvent) => void;
37
+ }
38
+ /**
39
+ * The one wheel gesture handler for linear views. Its decision matrix:
40
+ *
41
+ * - a wheel a nested scroller already consumed → declined, it owns the gesture
42
+ * - ctrl/meta+wheel, or (scrollZoom && |dy| >= |dx|) → zoom about the cursor
43
+ * - shift+wheel while scrollZoom is on → declined, we pass
44
+ * - a sideways delta, unless one arrives mid-zoom → pan by dx
45
+ *
46
+ * Declining shift is what leaves a nested panel its own scroll
47
+ * (`usePanelVirtualScroll`) — it is not a way back to the page. Browsers turn
48
+ * shift+wheel into *horizontal* scrolling, so what a view declines here scrolls
49
+ * the page sideways or not at all. The vertical way out is spatial rather than
50
+ * modal: JBrowse binds this below the view's sticky header, leaving that header
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+ * as a gutter the wheel still scrolls (LinearGenomeViewContainer's tracksRef).
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+ *
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+ * The listener is non-passive so it can preventDefault to suppress native scroll
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+ * during a zoom. To pay for that it only accumulates deltas: every model write
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+ * happens in one requestAnimationFrame, so a burst of events (fast trackpad,
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+ * inertial scroll) collapses to a single update per frame instead of thrashing
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+ * the views once per event.
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+ *
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+ * A zoom lands eased over the frames after its event (`easeZoomBacklog`), and
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+ * all of it lands: how far a gesture zooms depends on the wheel alone, never on
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+ * the frame rate or how the events happened to fall into frames.
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+ *
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+ * Returns its disposer.
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+ */
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+ export declare function createWheelZoomController({ element, resolveTarget, swallowUnhandled, releaseOnPointerLeave, onEvent, }: WheelZoomControllerOptions): () => void;