@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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  1024. package/esm/util/rpc.d.ts +16 -1
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1088. package/esm/util/translateTranscript.d.ts +44 -0
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  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
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  1106. package/esm/util/types/isAny.d.ts +11 -0
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  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
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  1118. package/esm/util/types/util.d.ts +8 -2
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  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,183 +1,742 @@
1
- import type React from 'react';
1
+ import type { AnyConfigurationModel } from '../../configuration/index.ts';
2
2
  import type { MenuItem } from '../../ui/index.ts';
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+ import type { RpcStatus } from '../../util/progress.ts';
4
+ import type { UnappliedSetting } from '../../util/unknownSnapshotKeys.ts';
3
5
  import type { Instance } from '@jbrowse/mobx-state-tree';
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+ import type React from 'react';
4
7
  export declare const BaseDisplay: import("@jbrowse/mobx-state-tree").IModelType<{
8
+ /**
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+ * #property
10
+ */
5
11
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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+ /**
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+ * #property
14
+ */
6
15
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
7
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
8
16
  }, {
9
- rendererTypeName: string;
10
17
  error: unknown;
11
18
  statusMessage: string | undefined;
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+ /**
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+ * #volatile
21
+ * determinate progress fraction [0,1] for the current status, or
22
+ * undefined when the in-flight phase is indeterminate. Set alongside
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+ * `statusMessage` by `setStatusMessage`; a display that never shows a
24
+ * bar simply leaves it undefined.
25
+ */
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+ statusProgress: number | undefined;
12
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  } & {
28
+ /**
29
+ * #getter
30
+ */
31
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
32
+ } & {
33
+ /**
34
+ * #getter
35
+ */
13
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  readonly RenderingComponent: React.FC<{
14
- model: {
15
- id: string;
16
- type: string;
17
- rpcDriverName: string | undefined;
18
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
19
- rendererTypeName: string;
37
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
38
+ /**
39
+ * #property
40
+ */
41
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
42
+ /**
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+ * #property
44
+ */
45
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
46
+ }> & {
20
47
  error: unknown;
21
48
  statusMessage: string | undefined;
49
+ /**
50
+ * #volatile
51
+ * determinate progress fraction [0,1] for the current status, or
52
+ * undefined when the in-flight phase is indeterminate. Set alongside
53
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
54
+ * bar simply leaves it undefined.
55
+ */
56
+ statusProgress: number | undefined;
57
+ } & {
58
+ /**
59
+ * #getter
60
+ */
61
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
22
62
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
63
+ /**
64
+ * #property
65
+ */
23
66
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
67
+ /**
68
+ * #property
69
+ */
24
70
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
25
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
26
71
  }, {
27
- rendererTypeName: string;
28
72
  error: unknown;
29
73
  statusMessage: string | undefined;
74
+ /**
75
+ * #volatile
76
+ * determinate progress fraction [0,1] for the current status, or
77
+ * undefined when the in-flight phase is indeterminate. Set alongside
78
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
79
+ * bar simply leaves it undefined.
80
+ */
81
+ statusProgress: number | undefined;
82
+ } & {
83
+ /**
84
+ * #getter
85
+ */
86
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
30
87
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
31
- onHorizontalScroll?: () => void;
32
- blockState?: Record<string, any>;
88
+ onHorizontalScroll?: (distance: number) => void;
89
+ blockState?: Record<string, unknown>;
33
90
  }>;
91
+ /**
92
+ * #getter
93
+ */
34
94
  readonly DisplayBlurb: React.FC<{
35
- model: {
36
- id: string;
37
- type: string;
38
- rpcDriverName: string | undefined;
39
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
40
- rendererTypeName: string;
95
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
96
+ /**
97
+ * #property
98
+ */
99
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
100
+ /**
101
+ * #property
102
+ */
103
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
104
+ }> & {
41
105
  error: unknown;
42
106
  statusMessage: string | undefined;
107
+ /**
108
+ * #volatile
109
+ * determinate progress fraction [0,1] for the current status, or
110
+ * undefined when the in-flight phase is indeterminate. Set alongside
111
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
112
+ * bar simply leaves it undefined.
113
+ */
114
+ statusProgress: number | undefined;
115
+ } & {
116
+ /**
117
+ * #getter
118
+ */
119
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
43
120
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
121
+ /**
122
+ * #property
123
+ */
44
124
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
125
+ /**
126
+ * #property
127
+ */
45
128
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
46
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
47
129
  }, {
48
- rendererTypeName: string;
49
130
  error: unknown;
50
131
  statusMessage: string | undefined;
132
+ /**
133
+ * #volatile
134
+ * determinate progress fraction [0,1] for the current status, or
135
+ * undefined when the in-flight phase is indeterminate. Set alongside
136
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
137
+ * bar simply leaves it undefined.
138
+ */
139
+ statusProgress: number | undefined;
140
+ } & {
141
+ /**
142
+ * #getter
143
+ */
144
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
51
145
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
52
146
  }> | null;
53
- readonly adapterConfig: any;
54
- readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
147
+ /**
148
+ * #getter
149
+ */
150
+ readonly adapterConfig: Record<string, unknown>;
151
+ /**
152
+ * #getter
153
+ * Returns true if the parent track is minimized. Used to skip
154
+ * expensive operations like autoruns when track is not visible.
155
+ */
55
156
  readonly isMinimized: boolean;
56
- readonly parentDisplay: any;
57
- readonly effectiveRpcDriverName: any;
157
+ /**
158
+ * #getter
159
+ * Overridable hook (default `undefined`): what the pointer is currently
160
+ * over, for readers **outside** the display. `LinearGenomeViewContainer`
161
+ * publishes it to `session.hovered`, the view-wide "what is the user
162
+ * pointing at" channel a plugin can subscribe to.
163
+ *
164
+ * Declared here because a cross-display consumer can only read a name the
165
+ * base declares — the same reason `FetchMixin.fetchInert` is a
166
+ * hook rather than a getter each display invents. The container used to
167
+ * read `featureUnderMouse`, which only the wiggle, alignments and
168
+ * Manhattan families spelled that way — canvas said `hoveredFeature`,
169
+ * variants `hoveredGenotype` — so the channel carried a hover from a third
170
+ * of the display types and nothing said which. It also asked only
171
+ * `displays[0]` of each track.
172
+ *
173
+ * `unknown` because the payload genuinely differs — a read, a wiggle bin,
174
+ * a SNP, a genotype cell — and `session.hovered` is typed to match ("can
175
+ * be anything; code that wants to deal with this should examine it").
176
+ * Narrow it in the override.
177
+ */
178
+ readonly hoveredFeature: unknown;
179
+ /**
180
+ * #getter
181
+ * Overridable hook (default `'feature'`): the SINGULAR word for one of
182
+ * the things this display draws, as a menu row or a chip says it —
183
+ * "Hide this read", "Showing 3 variants".
184
+ *
185
+ * Declared here for the same reason as `hoveredFeature` above: it is read
186
+ * across the display boundary, by chrome that has no idea which display
187
+ * it is drawing for (`SoloSelectionChip`, alignments' group-label
188
+ * overlay), and a name only the base declares is a name every such
189
+ * consumer can rely on. Two displays declared it independently and one of
190
+ * those declarations WAS this default.
191
+ *
192
+ * **A control keeps the generic word; content takes this one.** "Variant
193
+ * height" reads as a different setting from "Feature height" when it is
194
+ * the same one, so the shared menus stay on "feature" however the display
195
+ * answers here, and the noun varies where it names what the user is
196
+ * looking at — "Showing 3 variants", "Hide this read". A display drawing
197
+ * something the generic word already fits is right to leave this alone.
198
+ *
199
+ * Distinct from the per-hit noun a context menu takes off the clicked
200
+ * item's own `type` ("mRNA", "gene"); that names one annotation, this
201
+ * names what the track holds. The hit noun falls back to this.
202
+ */
203
+ readonly featureNoun: string;
204
+ /**
205
+ * #getter
206
+ * The widget `openFeatureWidget` opens for one of this display's
207
+ * features. Displays may override it. The default is the generic feature
208
+ * widget, for displays drawing plain features.
209
+ *
210
+ * Displays whose features are a specific kind (a read, a variant, a
211
+ * synteny block) override it, including the `id`: two displays naming
212
+ * one id share the drawer panel, which suits two displays showing the
213
+ * same kind of feature.
214
+ */
215
+ readonly featureWidgetType: {
216
+ type: string;
217
+ id: string;
218
+ };
58
219
  } & {
59
- renderProps(): any;
220
+ /**
221
+ * #method
222
+ * props passed to the renderer's React "Rendering" component.
223
+ * these are client-side only and never sent to the worker.
224
+ * includes displayModel and callbacks
225
+ */
60
226
  renderingProps(): {
61
- displayModel: {
62
- id: string;
63
- type: string;
64
- rpcDriverName: string | undefined;
65
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
66
- rendererTypeName: string;
227
+ displayModel: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
228
+ /**
229
+ * #property
230
+ */
231
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
232
+ /**
233
+ * #property
234
+ */
235
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
236
+ }> & {
67
237
  error: unknown;
68
238
  statusMessage: string | undefined;
239
+ /**
240
+ * #volatile
241
+ * determinate progress fraction [0,1] for the current status, or
242
+ * undefined when the in-flight phase is indeterminate. Set alongside
243
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
244
+ * bar simply leaves it undefined.
245
+ */
246
+ statusProgress: number | undefined;
69
247
  } & {
248
+ /**
249
+ * #getter
250
+ */
251
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
252
+ } & {
253
+ /**
254
+ * #getter
255
+ */
70
256
  readonly RenderingComponent: React.FC<{
71
- model: {
72
- id: string;
73
- type: string;
74
- rpcDriverName: string | undefined;
75
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
76
- rendererTypeName: string;
257
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
258
+ /**
259
+ * #property
260
+ */
261
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
262
+ /**
263
+ * #property
264
+ */
265
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
266
+ }> & {
77
267
  error: unknown;
78
268
  statusMessage: string | undefined;
269
+ /**
270
+ * #volatile
271
+ * determinate progress fraction [0,1] for the current status, or
272
+ * undefined when the in-flight phase is indeterminate. Set alongside
273
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
274
+ * bar simply leaves it undefined.
275
+ */
276
+ statusProgress: number | undefined;
277
+ } & {
278
+ /**
279
+ * #getter
280
+ */
281
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
79
282
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
283
+ /**
284
+ * #property
285
+ */
80
286
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
287
+ /**
288
+ * #property
289
+ */
81
290
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
82
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
83
291
  }, {
84
- rendererTypeName: string;
85
292
  error: unknown;
86
293
  statusMessage: string | undefined;
294
+ /**
295
+ * #volatile
296
+ * determinate progress fraction [0,1] for the current status, or
297
+ * undefined when the in-flight phase is indeterminate. Set alongside
298
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
299
+ * bar simply leaves it undefined.
300
+ */
301
+ statusProgress: number | undefined;
302
+ } & {
303
+ /**
304
+ * #getter
305
+ */
306
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
87
307
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
88
- onHorizontalScroll?: () => void;
89
- blockState?: Record<string, any>;
308
+ onHorizontalScroll?: (distance: number) => void;
309
+ blockState?: Record<string, unknown>;
90
310
  }>;
311
+ /**
312
+ * #getter
313
+ */
91
314
  readonly DisplayBlurb: React.FC<{
92
- model: {
93
- id: string;
94
- type: string;
95
- rpcDriverName: string | undefined;
96
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
97
- rendererTypeName: string;
315
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
316
+ /**
317
+ * #property
318
+ */
319
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
320
+ /**
321
+ * #property
322
+ */
323
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
324
+ }> & {
98
325
  error: unknown;
99
326
  statusMessage: string | undefined;
327
+ /**
328
+ * #volatile
329
+ * determinate progress fraction [0,1] for the current status, or
330
+ * undefined when the in-flight phase is indeterminate. Set alongside
331
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
332
+ * bar simply leaves it undefined.
333
+ */
334
+ statusProgress: number | undefined;
335
+ } & {
336
+ /**
337
+ * #getter
338
+ */
339
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
100
340
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
341
+ /**
342
+ * #property
343
+ */
101
344
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
345
+ /**
346
+ * #property
347
+ */
102
348
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
103
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
104
349
  }, {
105
- rendererTypeName: string;
106
350
  error: unknown;
107
351
  statusMessage: string | undefined;
352
+ /**
353
+ * #volatile
354
+ * determinate progress fraction [0,1] for the current status, or
355
+ * undefined when the in-flight phase is indeterminate. Set alongside
356
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
357
+ * bar simply leaves it undefined.
358
+ */
359
+ statusProgress: number | undefined;
360
+ } & {
361
+ /**
362
+ * #getter
363
+ */
364
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
108
365
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
109
366
  }> | null;
110
- readonly adapterConfig: any;
111
- readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
367
+ /**
368
+ * #getter
369
+ */
370
+ readonly adapterConfig: Record<string, unknown>;
371
+ /**
372
+ * #getter
373
+ * Returns true if the parent track is minimized. Used to skip
374
+ * expensive operations like autoruns when track is not visible.
375
+ */
112
376
  readonly isMinimized: boolean;
113
- readonly parentDisplay: any;
114
- readonly effectiveRpcDriverName: any;
377
+ /**
378
+ * #getter
379
+ * Overridable hook (default `undefined`): what the pointer is currently
380
+ * over, for readers **outside** the display. `LinearGenomeViewContainer`
381
+ * publishes it to `session.hovered`, the view-wide "what is the user
382
+ * pointing at" channel a plugin can subscribe to.
383
+ *
384
+ * Declared here because a cross-display consumer can only read a name the
385
+ * base declares — the same reason `FetchMixin.fetchInert` is a
386
+ * hook rather than a getter each display invents. The container used to
387
+ * read `featureUnderMouse`, which only the wiggle, alignments and
388
+ * Manhattan families spelled that way — canvas said `hoveredFeature`,
389
+ * variants `hoveredGenotype` — so the channel carried a hover from a third
390
+ * of the display types and nothing said which. It also asked only
391
+ * `displays[0]` of each track.
392
+ *
393
+ * `unknown` because the payload genuinely differs — a read, a wiggle bin,
394
+ * a SNP, a genotype cell — and `session.hovered` is typed to match ("can
395
+ * be anything; code that wants to deal with this should examine it").
396
+ * Narrow it in the override.
397
+ */
398
+ readonly hoveredFeature: unknown;
399
+ /**
400
+ * #getter
401
+ * Overridable hook (default `'feature'`): the SINGULAR word for one of
402
+ * the things this display draws, as a menu row or a chip says it —
403
+ * "Hide this read", "Showing 3 variants".
404
+ *
405
+ * Declared here for the same reason as `hoveredFeature` above: it is read
406
+ * across the display boundary, by chrome that has no idea which display
407
+ * it is drawing for (`SoloSelectionChip`, alignments' group-label
408
+ * overlay), and a name only the base declares is a name every such
409
+ * consumer can rely on. Two displays declared it independently and one of
410
+ * those declarations WAS this default.
411
+ *
412
+ * **A control keeps the generic word; content takes this one.** "Variant
413
+ * height" reads as a different setting from "Feature height" when it is
414
+ * the same one, so the shared menus stay on "feature" however the display
415
+ * answers here, and the noun varies where it names what the user is
416
+ * looking at — "Showing 3 variants", "Hide this read". A display drawing
417
+ * something the generic word already fits is right to leave this alone.
418
+ *
419
+ * Distinct from the per-hit noun a context menu takes off the clicked
420
+ * item's own `type` ("mRNA", "gene"); that names one annotation, this
421
+ * names what the track holds. The hit noun falls back to this.
422
+ */
423
+ readonly featureNoun: string;
424
+ /**
425
+ * #getter
426
+ * The widget `openFeatureWidget` opens for one of this display's
427
+ * features. Displays may override it. The default is the generic feature
428
+ * widget, for displays drawing plain features.
429
+ *
430
+ * Displays whose features are a specific kind (a read, a variant, a
431
+ * synteny block) override it, including the `id`: two displays naming
432
+ * one id share the drawer panel, which suits two displays showing the
433
+ * same kind of feature.
434
+ */
435
+ readonly featureWidgetType: {
436
+ type: string;
437
+ id: string;
438
+ };
115
439
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
440
+ /**
441
+ * #property
442
+ */
116
443
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
444
+ /**
445
+ * #property
446
+ */
117
447
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
118
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
119
448
  }, {
120
- rendererTypeName: string;
121
449
  error: unknown;
122
450
  statusMessage: string | undefined;
451
+ /**
452
+ * #volatile
453
+ * determinate progress fraction [0,1] for the current status, or
454
+ * undefined when the in-flight phase is indeterminate. Set alongside
455
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
456
+ * bar simply leaves it undefined.
457
+ */
458
+ statusProgress: number | undefined;
123
459
  } & {
460
+ /**
461
+ * #getter
462
+ */
463
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
464
+ } & {
465
+ /**
466
+ * #getter
467
+ */
124
468
  readonly RenderingComponent: React.FC<{
125
- model: {
126
- id: string;
127
- type: string;
128
- rpcDriverName: string | undefined;
129
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
130
- rendererTypeName: string;
469
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
470
+ /**
471
+ * #property
472
+ */
473
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
474
+ /**
475
+ * #property
476
+ */
477
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
478
+ }> & {
131
479
  error: unknown;
132
480
  statusMessage: string | undefined;
481
+ /**
482
+ * #volatile
483
+ * determinate progress fraction [0,1] for the current status, or
484
+ * undefined when the in-flight phase is indeterminate. Set alongside
485
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
486
+ * bar simply leaves it undefined.
487
+ */
488
+ statusProgress: number | undefined;
489
+ } & {
490
+ /**
491
+ * #getter
492
+ */
493
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
133
494
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
495
+ /**
496
+ * #property
497
+ */
134
498
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
499
+ /**
500
+ * #property
501
+ */
135
502
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
136
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
137
503
  }, {
138
- rendererTypeName: string;
139
504
  error: unknown;
140
505
  statusMessage: string | undefined;
506
+ /**
507
+ * #volatile
508
+ * determinate progress fraction [0,1] for the current status, or
509
+ * undefined when the in-flight phase is indeterminate. Set alongside
510
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
511
+ * bar simply leaves it undefined.
512
+ */
513
+ statusProgress: number | undefined;
514
+ } & {
515
+ /**
516
+ * #getter
517
+ */
518
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
141
519
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
142
- onHorizontalScroll?: () => void;
143
- blockState?: Record<string, any>;
520
+ onHorizontalScroll?: (distance: number) => void;
521
+ blockState?: Record<string, unknown>;
144
522
  }>;
523
+ /**
524
+ * #getter
525
+ */
145
526
  readonly DisplayBlurb: React.FC<{
146
- model: {
147
- id: string;
148
- type: string;
149
- rpcDriverName: string | undefined;
150
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
151
- rendererTypeName: string;
527
+ model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
528
+ /**
529
+ * #property
530
+ */
531
+ id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
532
+ /**
533
+ * #property
534
+ */
535
+ type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
536
+ }> & {
152
537
  error: unknown;
153
538
  statusMessage: string | undefined;
539
+ /**
540
+ * #volatile
541
+ * determinate progress fraction [0,1] for the current status, or
542
+ * undefined when the in-flight phase is indeterminate. Set alongside
543
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
544
+ * bar simply leaves it undefined.
545
+ */
546
+ statusProgress: number | undefined;
547
+ } & {
548
+ /**
549
+ * #getter
550
+ */
551
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
154
552
  } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
553
+ /**
554
+ * #property
555
+ */
155
556
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
557
+ /**
558
+ * #property
559
+ */
156
560
  type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
157
- rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
158
561
  }, {
159
- rendererTypeName: string;
160
562
  error: unknown;
161
563
  statusMessage: string | undefined;
564
+ /**
565
+ * #volatile
566
+ * determinate progress fraction [0,1] for the current status, or
567
+ * undefined when the in-flight phase is indeterminate. Set alongside
568
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
569
+ * bar simply leaves it undefined.
570
+ */
571
+ statusProgress: number | undefined;
572
+ } & {
573
+ /**
574
+ * #getter
575
+ */
576
+ readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
162
577
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
163
578
  }> | null;
164
- readonly adapterConfig: any;
165
- readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
579
+ /**
580
+ * #getter
581
+ */
582
+ readonly adapterConfig: Record<string, unknown>;
583
+ /**
584
+ * #getter
585
+ * Returns true if the parent track is minimized. Used to skip
586
+ * expensive operations like autoruns when track is not visible.
587
+ */
166
588
  readonly isMinimized: boolean;
167
- readonly parentDisplay: any;
168
- readonly effectiveRpcDriverName: any;
589
+ /**
590
+ * #getter
591
+ * Overridable hook (default `undefined`): what the pointer is currently
592
+ * over, for readers **outside** the display. `LinearGenomeViewContainer`
593
+ * publishes it to `session.hovered`, the view-wide "what is the user
594
+ * pointing at" channel a plugin can subscribe to.
595
+ *
596
+ * Declared here because a cross-display consumer can only read a name the
597
+ * base declares — the same reason `FetchMixin.fetchInert` is a
598
+ * hook rather than a getter each display invents. The container used to
599
+ * read `featureUnderMouse`, which only the wiggle, alignments and
600
+ * Manhattan families spelled that way — canvas said `hoveredFeature`,
601
+ * variants `hoveredGenotype` — so the channel carried a hover from a third
602
+ * of the display types and nothing said which. It also asked only
603
+ * `displays[0]` of each track.
604
+ *
605
+ * `unknown` because the payload genuinely differs — a read, a wiggle bin,
606
+ * a SNP, a genotype cell — and `session.hovered` is typed to match ("can
607
+ * be anything; code that wants to deal with this should examine it").
608
+ * Narrow it in the override.
609
+ */
610
+ readonly hoveredFeature: unknown;
611
+ /**
612
+ * #getter
613
+ * Overridable hook (default `'feature'`): the SINGULAR word for one of
614
+ * the things this display draws, as a menu row or a chip says it —
615
+ * "Hide this read", "Showing 3 variants".
616
+ *
617
+ * Declared here for the same reason as `hoveredFeature` above: it is read
618
+ * across the display boundary, by chrome that has no idea which display
619
+ * it is drawing for (`SoloSelectionChip`, alignments' group-label
620
+ * overlay), and a name only the base declares is a name every such
621
+ * consumer can rely on. Two displays declared it independently and one of
622
+ * those declarations WAS this default.
623
+ *
624
+ * **A control keeps the generic word; content takes this one.** "Variant
625
+ * height" reads as a different setting from "Feature height" when it is
626
+ * the same one, so the shared menus stay on "feature" however the display
627
+ * answers here, and the noun varies where it names what the user is
628
+ * looking at — "Showing 3 variants", "Hide this read". A display drawing
629
+ * something the generic word already fits is right to leave this alone.
630
+ *
631
+ * Distinct from the per-hit noun a context menu takes off the clicked
632
+ * item's own `type` ("mRNA", "gene"); that names one annotation, this
633
+ * names what the track holds. The hit noun falls back to this.
634
+ */
635
+ readonly featureNoun: string;
636
+ /**
637
+ * #getter
638
+ * The widget `openFeatureWidget` opens for one of this display's
639
+ * features. Displays may override it. The default is the generic feature
640
+ * widget, for displays drawing plain features.
641
+ *
642
+ * Displays whose features are a specific kind (a read, a variant, a
643
+ * synteny block) override it, including the `id`: two displays naming
644
+ * one id share the drawer panel, which suits two displays showing the
645
+ * same kind of feature.
646
+ */
647
+ readonly featureWidgetType: {
648
+ type: string;
649
+ id: string;
650
+ };
169
651
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
170
652
  };
171
- readonly rendererType: import("../index.ts").RendererType;
172
- readonly DisplayMessageComponent: undefined | React.FC<any>;
653
+ /**
654
+ * #method
655
+ */
173
656
  trackMenuItems(): MenuItem[];
174
- readonly viewMenuActions: MenuItem[];
175
- regionCannotBeRendered(): null;
176
657
  } & {
177
- setStatusMessage(arg?: string): void;
658
+ /**
659
+ * #action
660
+ */
661
+ setStatusMessage(status?: RpcStatus): void;
662
+ /**
663
+ * #action
664
+ */
178
665
  setError(error?: unknown): void;
179
- setRpcDriverName(rpcDriverName: string): void;
666
+ /**
667
+ * #action
668
+ * Overridable hook (default no-op): drop whatever `hoveredFeature`
669
+ * reports. The writing twin of that getter, and what
670
+ * `installClearHoverOnViewportChange` calls.
671
+ *
672
+ * A display that STORES its hover owes an override; one that derives it
673
+ * from the live pointer (MAF, Hi-C, LD) owes nothing, and the default
674
+ * costs it nothing. Declared here so the clear can be installed for every
675
+ * display rather than remembered per display — forgetting it is the
676
+ * failure ARCHITECTURE.md's stored-hover section is about, and it used to
677
+ * be six closures at six call sites, which is six chances to omit one.
678
+ */
679
+ clearHoveredFeature(): void;
680
+ /**
681
+ * #action
682
+ * base display reload does nothing, see specialized displays for details
683
+ */
180
684
  reload(): void;
685
+ /**
686
+ * #action
687
+ * Apply a set of display settings to the live display, and report which
688
+ * were applied. Each key runs through the display config schema's
689
+ * `preProcessSnapshot` (shorthand expansions and legacy-key migrations,
690
+ * as `showTrackGeneric` applies to a session spec's inline track keys),
691
+ * then writes the matching config slot. A key naming a sub-schema
692
+ * (`facet`, `color`) replaces the whole object, its string shorthand
693
+ * lifted by that schema, and `null` clears it. Keys that are not slots
694
+ * come back in `unapplied` as `{ key, reason }`, so a caller can tell a
695
+ * misspelling from a key that has an action instead of a slot.
696
+ *
697
+ * `allowSetters` also routes a non-slot key to a single-argument action
698
+ * named `set<Key>`. It is off by default because session specs, share
699
+ * links and embeds pass untyped JSON here, and a default fallback would
700
+ * let them call internal setters (`setError`, `setScrollTop`, ...) and
701
+ * call multi-argument setters with one argument. A caller that wants a
702
+ * specific action can call it directly.
703
+ *
704
+ * A key whose write threw is reported in `failed`. Only `failed` means
705
+ * the caller passed a bad value. `unapplied` needs the caller's own
706
+ * context to read: `showTrackGeneric` spreads the same settings into the
707
+ * display's snapshot, so a declared prop (`resolution`) has already
708
+ * landed by the time it reports here, while the restyle path spreads
709
+ * nothing and every entry there did nothing.
710
+ *
711
+ * A per-key error does not abort the remaining keys. A caller
712
+ * mid-`showTrack` has already pushed the track, and one rejected value
713
+ * should not leave it half-configured.
714
+ */
715
+ applyDisplaySettings(settings: Record<string, unknown>, options?: {
716
+ allowSetters?: boolean;
717
+ }): {
718
+ applied: string[];
719
+ unapplied: UnappliedSetting[];
720
+ failed: {
721
+ key: string;
722
+ error: string;
723
+ }[];
724
+ };
181
725
  }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
182
726
  export type BaseDisplayStateModel = typeof BaseDisplay;
183
727
  export type BaseDisplayModel = Instance<BaseDisplayStateModel>;
728
+ /**
729
+ * The shape every display instance held in a track's `displays` array
730
+ * satisfies: the composed `BaseDisplay` state model (RenderingComponent,
731
+ * DisplayBlurb, trackMenuItems, ...) plus the `configuration`
732
+ * reference every display gains at instantiation. `getPortableSettings` is
733
+ * optional — only display types that support switching type via the track menu
734
+ * implement it. This is the concrete element type behind
735
+ * `BaseTrackModel.displays`, which the runtime plugin union erases to `any`.
736
+ */
737
+ export interface DisplayModel extends BaseDisplayModel {
738
+ configuration: AnyConfigurationModel & {
739
+ displayId: string;
740
+ };
741
+ getPortableSettings?: (newDisplayId?: string) => Record<string, unknown> | undefined;
742
+ }