@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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  1099. package/esm/util/tss-react/types.d.ts +1 -1
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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,81 +1,401 @@
1
1
  import PhasedScheduler from './PhasedScheduler.ts';
2
- import ReExports from './ReExports/index.ts';
3
- import AdapterType from './pluggableElementTypes/AdapterType.ts';
4
- import AddTrackWorkflowType from './pluggableElementTypes/AddTrackWorkflowType.ts';
5
- import ConnectionType from './pluggableElementTypes/ConnectionType.ts';
6
- import DisplayType from './pluggableElementTypes/DisplayType.ts';
7
- import GlyphType from './pluggableElementTypes/GlyphType.ts';
8
- import InternetAccountType from './pluggableElementTypes/InternetAccountType.ts';
9
- import RpcMethodType from './pluggableElementTypes/RpcMethodType.ts';
10
- import TextSearchAdapterType from './pluggableElementTypes/TextSearchAdapterType.ts';
11
- import TrackType from './pluggableElementTypes/TrackType.ts';
12
- import ViewType from './pluggableElementTypes/ViewType.ts';
13
- import WidgetType from './pluggableElementTypes/WidgetType.ts';
14
- import RendererType from './pluggableElementTypes/renderers/RendererType.tsx';
2
+ import './util/tracks.ts';
15
3
  import type Plugin from './Plugin.ts';
16
- import type { PluginDefinition } from './PluginLoader.ts';
4
+ import type { PluginConstructor } from './Plugin.ts';
5
+ import type { PluggableConfigNode } from './configuration/index.ts';
6
+ import type AdapterType from './pluggableElementTypes/AdapterType.ts';
7
+ import type AddTrackWorkflowType from './pluggableElementTypes/AddTrackWorkflowType.ts';
8
+ import type ConnectionType from './pluggableElementTypes/ConnectionType.ts';
9
+ import type DisplayType from './pluggableElementTypes/DisplayType.ts';
10
+ import type InternetAccountType from './pluggableElementTypes/InternetAccountType.ts';
17
11
  import type PluggableElementBase from './pluggableElementTypes/PluggableElementBase.ts';
12
+ import type RpcMethodType from './pluggableElementTypes/RpcMethodType.ts';
13
+ import type TextSearchAdapterType from './pluggableElementTypes/TextSearchAdapterType.ts';
14
+ import type TrackType from './pluggableElementTypes/TrackType.ts';
15
+ import type ViewType from './pluggableElementTypes/ViewType.ts';
16
+ import type WidgetType from './pluggableElementTypes/WidgetType.ts';
18
17
  import type { PluggableElementType } from './pluggableElementTypes/index.ts';
19
- import type { AbstractRootModel } from './util/index.ts';
20
- import type { IAnyModelType, IAnyType } from '@jbrowse/mobx-state-tree';
21
- type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' | 'connection' | 'view' | 'widget' | 'rpc method' | 'internet account' | 'text search adapter' | 'add track workflow' | 'glyph';
18
+ import './pluggableElementTypes/models/migrateTrackConfig.ts';
19
+ import type { PluginDefinition } from './pluginDefinitions.ts';
20
+ import './rpc/WebWorkerRpcDriver.ts';
21
+ import './ui/buildExtraTrackMenuItems.ts';
22
+ import './ui/multiTrackMenuItems.ts';
23
+ import './util/addTrackComponent.ts';
24
+ import type { AbstractRootModel, AbstractSessionModel, SimpleFeatureSerialized } from './util/index.ts';
25
+ import type { IAnyModelType, IAnyType, IStateTreeNode, IType, SnapshotIn } from '@jbrowse/mobx-state-tree';
26
+ import type { ComponentType, ReactNode } from 'react';
27
+ /**
28
+ * What `pluggableConfigSchemaType` builds: a union whose members are checked
29
+ * at runtime, read as a config node carrying the `type` every member names
30
+ * itself by; a member's other slots read through `getConf`.
31
+ */
32
+ export type PluggableConfigSchemaType = IType<any, any, PluggableConfigNode>;
33
+ /**
34
+ * Every pluggable element group, in the order `elementCreationSchedule` builds
35
+ * them. The array is the declaration and the union is derived from it, so a
36
+ * consumer that has to visit every group — `pruneUnbuildableNodes` walking a
37
+ * session snapshot for containers of a pluggable union — enumerates them at
38
+ * runtime instead of keeping a second hand-written list that goes stale.
39
+ */
40
+ export declare const pluggableElementTypeGroups: readonly ['adapter', 'text search adapter', 'display', 'track', 'connection', 'view', 'widget', 'rpc method', 'internet account', 'add track workflow'];
41
+ export type PluggableElementTypeGroup = (typeof pluggableElementTypeGroups)[number];
42
+ /**
43
+ * The group a `pluggableMstType(group, 'stateModel')` union holds, read off
44
+ * its name: with every member a lazy model not yet loaded, the union has no
45
+ * members to recognise it by.
46
+ */
47
+ export declare function pluggableStateModelGroup(type: IAnyType): "adapter" | "add track workflow" | "connection" | "display" | "internet account" | "rpc method" | "text search adapter" | "track" | "view" | "widget" | undefined;
48
+ /** internal class that holds the info for a certain element type */
22
49
  declare class TypeRecord<ElementClass extends PluggableElementBase> {
23
- typeName: string;
24
- baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
25
- prototype: ElementClass;
26
- });
27
50
  registeredTypes: Record<string, ElementClass>;
28
- constructor(typeName: string, baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
29
- prototype: ElementClass;
30
- }));
51
+ typeName: string;
52
+ constructor(typeName: string);
31
53
  add(name: string, t: ElementClass): void;
32
54
  has(name: string): boolean;
33
- get(name: string): ElementClass | undefined;
55
+ get(name: string): ElementClass;
56
+ registeredNames(): string;
34
57
  all(): ElementClass[];
35
58
  }
36
59
  type AnyFunction = (...args: any) => any;
37
- export type PluginMetadata = Record<string, unknown>;
60
+ type ExtensionPointCallback = (extendee: unknown, props?: Record<string, unknown>) => unknown;
61
+ /**
62
+ * Marks a component built by wrapping the one the extension point accumulated
63
+ * so far, so {@link PluginManager.evaluateComponentExtensionPoint} can tell
64
+ * composition (two plugins each wrapping, both still visible) from a genuine
65
+ * clobber (a second plugin discarding the first). Set by `wrapComponent`.
66
+ */
67
+ export declare const wrappedComponent: unique symbol;
68
+ /**
69
+ * A point that resolves to one component — a slot with a default, which a
70
+ * plugin wraps or replaces. Declared as
71
+ * `'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>`, produced by
72
+ * {@link PluggableComponent}, registered on with `wrapComponent`.
73
+ */
74
+ export interface ComponentSlot<P> {
75
+ args: ComponentType<P>;
76
+ result: ComponentType<P>;
77
+ props: P;
78
+ /**
79
+ * Type-only: never present at runtime, and what makes the shape *declared*
80
+ * rather than guessed. Reading it off the value cannot work — a
81
+ * `TrackTypeGuesser` takes an argument and returns a string, which is also
82
+ * what a function component does, so a structural test admits it as a slot.
83
+ */
84
+ kind: 'componentSlot';
85
+ }
86
+ /**
87
+ * A point that accumulates an array of components — the panel points. Produced
88
+ * by {@link PluggableComponents}, registered on with
89
+ * {@link PluginManager.contributeToExtensionPoint}; each panel scopes itself
90
+ * and draws its own chrome.
91
+ */
92
+ export interface ComponentList<P> {
93
+ args: ComponentType<P>[];
94
+ result: ComponentType<P>[];
95
+ props: P;
96
+ /** type-only, see {@link ComponentSlot.kind} */
97
+ kind: 'componentList';
98
+ }
99
+ /**
100
+ * A point that accumulates already-rendered elements — the overlay points.
101
+ * Produced by {@link PluggableElements}, registered on with
102
+ * `addExtensionElement`, which fixes the React key at registration time.
103
+ */
104
+ export interface ElementList<P> {
105
+ args: ReactNode[];
106
+ result: ReactNode[];
107
+ props: P;
108
+ /** type-only, see {@link ComponentSlot.kind} */
109
+ kind: 'elementList';
110
+ }
111
+ /** The names of the points declared as `K`. */
112
+ export type PointsOfKind<K extends string> = {
113
+ [N in ExtensionPointName]: ExtensionPointRegistry[N] extends {
114
+ kind: K;
115
+ } ? N : never;
116
+ }[ExtensionPointName];
117
+ type FeatureWidgetModel = IStateTreeNode & {
118
+ trackId?: string;
119
+ trackType?: string;
120
+ };
121
+ type WidgetModel = FeatureWidgetModel & {
122
+ type: string;
123
+ };
124
+ export interface FeaturePanelProps {
125
+ /** has `trackId` and `trackType` */
126
+ model: FeatureWidgetModel;
127
+ /** snapshot of the feature being shown, as `formatDetails` reshaped it */
128
+ feature: SimpleFeatureSerialized;
129
+ /** the same feature before `formatDetails` ran */
130
+ unformatted?: SimpleFeatureSerialized;
131
+ /**
132
+ * how far down the subfeature tree this card is: 0 is the feature the user
133
+ * clicked, 1 its subfeatures, and so on. The point fires for every card, so a
134
+ * panel that belongs only on the clicked feature selects on `depth === 0`
135
+ */
136
+ depth: number;
137
+ }
138
+ export interface ReplaceWidgetProps {
139
+ session: AbstractSessionModel;
140
+ /** has `type`; feature detail widgets also have `trackId` and `trackType` */
141
+ model: WidgetModel;
142
+ toolbarHeight?: number;
143
+ }
144
+ /**
145
+ * Typed registries of the view and display types a plugin can extend, in the
146
+ * same shape as {@link ExtensionPointRegistry} and augmented the same way:
147
+ *
148
+ * declare module '@jbrowse/core/PluginManager' {
149
+ * interface ViewTypeRegistry {
150
+ * LinearGenomeView: LinearGenomeViewStateModel
151
+ * }
152
+ * }
153
+ *
154
+ * That is what makes `extendViewType(pm, 'LinearGenomeView', …)` hand back a
155
+ * typed state model, and a misspelled or renamed name a compile error rather
156
+ * than an extension that quietly never applies. `getViewType` reads it too, so
157
+ * a caller composing another view's model into its own gets the real type
158
+ * instead of `IAnyModelType`.
159
+ *
160
+ * AN AUGMENTATION IS HAND-WRITTEN, so each registration annotates the model it
161
+ * passes to `ViewType` against its own entry here (`const stateModel:
162
+ * ViewTypeRegistry['CircularView'] = …`). That one line is what makes the
163
+ * registry earn what `getViewType` promises: without it a drifted entry is
164
+ * worse than the `IAnyModelType` it replaced, since a caller would get a
165
+ * confidently wrong type rather than an unchecked one. It cannot live on
166
+ * `ViewType`'s constructor — TypeScript forbids type parameters there, and a
167
+ * class parameter widens `name` to `string`, so the conditional never fires. Declaring them here rather than
168
+ * beside the helpers is load-bearing: an interface can only be augmented
169
+ * through the module that declares it, and a barrel re-exporting the type would
170
+ * give every augmentation its own unrelated copy.
171
+ */
172
+ export interface ViewTypeRegistry {
173
+ }
174
+ export interface DisplayTypeRegistry {
175
+ }
176
+ export type ViewTypeName = keyof ViewTypeRegistry;
177
+ export type DisplayTypeName = keyof DisplayTypeRegistry;
178
+ /**
179
+ * What `addView(name, snapshot)` takes for a view type name. A registered name
180
+ * gets the view's authored shape — the snapshot type `withLaunchInput` widened
181
+ * to accept the launch keys beside the declared properties — so a misspelled
182
+ * key is a compile error at the literal site. `type` is optional because
183
+ * `addView` writes it. An unregistered name stays `Record<string, unknown>`,
184
+ * which is what an out-of-tree view's `addView` has always been.
185
+ *
186
+ * Read off `ViewTypeRegistry` rather than registered a second time, so the
187
+ * snapshot type cannot drift from the model: a view that augments the registry
188
+ * has typed `addView`, `replaceView` and `addOrReplaceView` for free.
189
+ */
190
+ export type ViewSnapshotInput<N extends string> = N extends ViewTypeName ? Omit<SnapshotIn<ViewTypeRegistry[N]>, 'type'> & {
191
+ type?: N;
192
+ } : Record<string, unknown>;
193
+ /**
194
+ * what a plugin knows of an assembly the session does not hold, answered
195
+ * without connecting anything: its assembly config as the config holding it
196
+ * writes it, a relative uri carrying the `baseUri` it resolves against, and
197
+ * the adapter of its gene track. A multi-way synteny display holds the
198
+ * assembly as a temporary one while it draws that genome's lane, so renaming
199
+ * reaches its sequence and aliases the way it reaches any assembly's
200
+ */
201
+ export interface AssemblyDescription {
202
+ assembly?: Record<string, unknown>;
203
+ geneAdapter?: Record<string, unknown>;
204
+ }
205
+ export interface ExtensionPointRegistry {
206
+ 'Core-extendSession': {
207
+ args: IAnyModelType;
208
+ result: IAnyModelType;
209
+ };
210
+ 'Core-handleUnrecognizedAssembly': {
211
+ args: undefined;
212
+ result: undefined | Promise<void>;
213
+ props: {
214
+ assemblyName: string;
215
+ /**
216
+ * the session the lookup came from. `unknown` because the assembly
217
+ * manager holds it as the narrow shape it needs rather than the whole
218
+ * session model, and nothing in tree reads it — narrow it yourself if you
219
+ * do
220
+ */
221
+ session?: unknown;
222
+ };
223
+ };
224
+ 'Core-describeAssemblies': {
225
+ args: Record<string, AssemblyDescription>;
226
+ result: Record<string, AssemblyDescription>;
227
+ props: {
228
+ assemblyNames: string[];
229
+ session?: unknown;
230
+ };
231
+ };
232
+ 'Core-extendPluggableElement': {
233
+ args: PluggableElementType;
234
+ result: PluggableElementType;
235
+ props: {
236
+ group: PluggableElementTypeGroup;
237
+ };
238
+ };
239
+ 'Core-extraFeaturePanel': ComponentList<FeaturePanelProps>;
240
+ /** #extensionPoint Core-replaceWidget | sync | Replace or wrap the component that renders a widget */
241
+ 'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>;
242
+ }
243
+ export type ExtensionPointName = keyof ExtensionPointRegistry;
244
+ export type ExtensionPointArgs<N extends ExtensionPointName> = ExtensionPointRegistry[N]['args'];
245
+ export type ExtensionPointResult<N extends ExtensionPointName> = ExtensionPointRegistry[N]['result'];
246
+ export type ExtensionPointProps<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? ExtensionPointRegistry[N]['props'] : Record<string, unknown>;
247
+ /**
248
+ * Points that carry their whole payload in `props` and whose return value
249
+ * nothing reads — a notification rather than a fold. Registered with
250
+ * {@link PluginManager.listenToExtensionPoint}.
251
+ */
252
+ export type NotificationPointName = {
253
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends undefined ? N : never;
254
+ }[ExtensionPointName];
255
+ /**
256
+ * Points whose `args` are an array accumulate: the value threaded through the
257
+ * fold is every plugin's entries so far. They are registered with
258
+ * {@link PluginManager.contributeToExtensionPoint}, never
259
+ * {@link PluginManager.addToExtensionPoint} — see the entry type below for why.
260
+ */
261
+ export type AccumulatingPointName = {
262
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends readonly unknown[] ? N : never;
263
+ }[ExtensionPointName];
264
+ /** One element of an accumulating point's array — what a plugin contributes. */
265
+ export type ExtensionPointEntry<N extends AccumulatingPointName> = ExtensionPointArgs<N> extends readonly (infer E)[] ? E : never;
266
+ /**
267
+ * The trailing `props` parameter of the evaluate methods, required exactly when
268
+ * the point declares one. Omitting it there used to typecheck and then hand
269
+ * `undefined` to every callback, so each one threw on destructuring the props
270
+ * it was promised.
271
+ */
272
+ export type ExtensionPointPropsArgs<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? [props: ExtensionPointProps<N>] : [props?: Record<string, unknown>];
273
+ /**
274
+ * A point name that is *not* in the registry, which is what the loose evaluate
275
+ * overloads accept. Keeping a registered name out of them is what makes the
276
+ * typed overload binding: they otherwise match whenever it doesn't, so a call
277
+ * that omitted a required `props` or passed the wrong `extendee` fell through
278
+ * and compiled. Plugin-defined points, and any name that isn't a literal, are
279
+ * unaffected.
280
+ *
281
+ * A registered name resolves to a message-shaped type rather than `never`
282
+ * because this overload is the last one tried, so its error is the one TS
283
+ * reports: `not assignable to never` says nothing about what to fix.
284
+ */
285
+ export type UnregisteredPointName<S extends string> = S extends ExtensionPointName ? {
286
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the extendee type, and pass props if it declares them';
287
+ } : S;
288
+ /**
289
+ * The same guard for `addToExtensionPoint`'s loose overload. Each excluded kind
290
+ * needs its own message, because the useful thing to say is which method the
291
+ * point does belong to.
292
+ *
293
+ * Excluding those names from the *typed* overload is not enough on its own. The
294
+ * loose overload matches whenever the typed one doesn't, so
295
+ * `addToExtensionPoint('Core-extraFeaturePanel', panels => [MyPanel])` — the one
296
+ * call `contributeToExtensionPoint` exists to make impossible — fell through and
297
+ * compiled, with `T` inferred from whatever the callback returned, dropping every
298
+ * other plugin's panels exactly as if the exclusion weren't there.
299
+ *
300
+ * `S` is inferred from the name, so this binds on the ordinary call. It does not
301
+ * bind when a caller writes the type argument out — `addToExtensionPoint<T>(…)`
302
+ * pins `T` and leaves `S` on its default — which is the price of keeping that
303
+ * arity working for plugins compiled against the older signature.
304
+ */
305
+ export type FoldPointName<S extends string> = S extends AccumulatingPointName ? {
306
+ ERROR: 'this extension point accumulates a list; register with contributeToExtensionPoint, whose callback returns only its own entries';
307
+ } : S extends NotificationPointName ? {
308
+ ERROR: 'this extension point is a notification; register with listenToExtensionPoint, which joins async handlers rather than letting the last one registered replace the rest';
309
+ } : S extends ExtensionPointName ? {
310
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the callback against its args/result types';
311
+ } : S;
312
+ /**
313
+ * metadata related to the instance of this plugin. `isCore` is set when the
314
+ * plugin was loaded as part of the "core" set of plugins for this application,
315
+ * and `url` records the resolved location it was loaded from. The index
316
+ * signature keeps it free-form so other things about why the plugin is loaded
317
+ * (where it came from, what depends on it, etc.) can be stashed too.
318
+ */
319
+ export interface PluginMetadata {
320
+ isCore?: boolean;
321
+ isGlobal?: boolean;
322
+ url?: string;
323
+ [key: string]: unknown;
324
+ }
38
325
  export interface PluginLoadRecord {
39
326
  metadata?: PluginMetadata;
40
327
  plugin: Plugin;
41
328
  }
329
+ /**
330
+ * Instantiate an application's bundled plugin list as `isCore` load records —
331
+ * what tells the plugin store these came with the bundle rather than being
332
+ * installed by the user, so `InstalledPluginsList` filters them out and the
333
+ * About widget lists them. Every product and every test harness builds its
334
+ * manager from one of these lists, and a harness that passed bare instances
335
+ * silently disagreed with the app it was testing.
336
+ */
337
+ export declare function corePluginRecords(plugins: PluginConstructor[]): PluginLoadRecord[];
42
338
  export interface RuntimePluginLoadRecord extends PluginLoadRecord {
43
339
  definition: PluginDefinition;
44
340
  }
45
341
  export default class PluginManager {
342
+ #private;
46
343
  plugins: Plugin[];
47
344
  jexl: import("@jbrowse/jexl").Jexl;
48
345
  pluginMetadata: Record<string, PluginMetadata>;
49
346
  runtimePluginDefinitions: PluginDefinition[];
50
- elementCreationSchedule: PhasedScheduler<PluggableElementTypeGroup> | undefined;
51
- glyphTypes: TypeRecord<GlyphType>;
52
- rendererTypes: TypeRecord<RendererType>;
53
- adapterTypes: TypeRecord<AdapterType>;
54
- textSearchAdapterTypes: TypeRecord<TextSearchAdapterType>;
347
+ elementCreationSchedule: PhasedScheduler<"adapter" | "add track workflow" | "connection" | "display" | "internet account" | "rpc method" | "text search adapter" | "track" | "view" | "widget">;
348
+ pluggableElementsCreated: boolean;
349
+ adapterTypes: TypeRecord<AdapterType<any>>;
350
+ textSearchAdapterTypes: TypeRecord<TextSearchAdapterType<any>>;
55
351
  trackTypes: TypeRecord<TrackType>;
56
352
  displayTypes: TypeRecord<DisplayType>;
57
353
  connectionTypes: TypeRecord<ConnectionType>;
58
354
  viewTypes: TypeRecord<ViewType>;
59
355
  widgetTypes: TypeRecord<WidgetType>;
60
- rpcMethods: TypeRecord<RpcMethodType>;
356
+ rpcMethods: TypeRecord<RpcMethodType<string>>;
61
357
  addTrackWidgets: TypeRecord<AddTrackWorkflowType>;
62
358
  internetAccountTypes: TypeRecord<InternetAccountType>;
63
359
  configured: boolean;
64
360
  rootModel?: AbstractRootModel;
65
- extensionPoints: Map<string, Function[]>;
66
- constructor(initialPlugins?: (Plugin | PluginLoadRecord)[]);
361
+ extensionPoints: Map<string, ExtensionPointCallback[]>;
362
+ warnedClobber: Set<string>;
363
+ /**
364
+ * The lazily-hydrated MST config node for one frozen track config, built by
365
+ * `build` on first ask and returned by identity after that.
366
+ * `configuration/configurationSchema.ts` is the only caller.
367
+ *
368
+ * `jbrowse.tracks` is `types.frozen` for large-tracklist performance, so a
369
+ * track config is a plain JS object until first referenced; hydrating it into
370
+ * an MST node is deferred to that read. MST's custom-reference `getValue` has
371
+ * no memoization of its own — it reruns on every property access — so without
372
+ * this, every read of `track.configuration` would fabricate a fresh,
373
+ * non-identical node. Keyed by schemaType (each track type's config schema is
374
+ * rebuilt fresh per PluginManager instance, see addTrackType) then by the
375
+ * frozen object, so a hit can only ever come from this same instance and this
376
+ * same track type. See ADR-031.
377
+ *
378
+ * The node is never mutated: admin edits replace the frozen entry (new
379
+ * identity drops the WeakMap entry), and a non-admin's edits go to a private
380
+ * session working copy, not here (ADR-032). Both levels are `WeakMap`s so
381
+ * entries collect normally — no manual invalidation needed, which is why this
382
+ * is a memo and not a cache with a lifecycle to expose.
383
+ */
384
+ hydratedTrackConfig(schemaType: IAnyType, frozen: object, build: () => unknown): unknown;
385
+ constructor(initialPlugins?: (Plugin | PluginLoadRecord | RuntimePluginLoadRecord)[]);
67
386
  pluginConfigurationNamespacedSchemas(): Record<string, unknown>;
68
387
  pluginConfigurationUnnamespacedSchemas(): Record<string, unknown>;
69
388
  pluginConfigurationRootSchemas(): Record<string, unknown>;
70
389
  addPlugin(load: Plugin | PluginLoadRecord | RuntimePluginLoadRecord): this;
71
390
  getPlugin(name: string): Plugin | undefined;
72
391
  hasPlugin(name: string): boolean;
392
+ removePlugin(pluginName: string): this;
73
393
  createPluggableElements(): this;
74
394
  setRootModel(rootModel: AbstractRootModel): this;
75
395
  configure(): this;
76
396
  getElementTypeRecord(groupName: PluggableElementTypeGroup): TypeRecord<PluggableElementBase>;
77
397
  addElementType(groupName: PluggableElementTypeGroup, creationCallback: (pluginManager: PluginManager) => PluggableElementType): this;
78
- getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase | undefined;
398
+ getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase;
79
399
  getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
80
400
  getViewElements(): ViewType[];
81
401
  getTrackElements(): TrackType[];
@@ -84,27 +404,71 @@ export default class PluginManager {
84
404
  getRpcElements(): RpcMethodType[];
85
405
  getDisplayElements(): DisplayType[];
86
406
  getAdapterElements(): AdapterType[];
407
+ /**
408
+ * get a MST type for the union of all specified pluggable MST types.
409
+ * Membership is late-bound, so a lazily registered state model joins when
410
+ * its loader resolves; a snapshot naming one cannot be cast until then.
411
+ */
87
412
  pluggableMstType(groupName: PluggableElementTypeGroup, fieldName: string, fallback?: IAnyType): IAnyType;
88
- pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): IAnyModelType;
413
+ /**
414
+ * The union of every registered config schema of a pluggable element group,
415
+ * whose instance reads as a config node naming its `type`.
416
+ */
417
+ pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): PluggableConfigSchemaType;
89
418
  jbrequireCache: Map<any, any>;
90
- lib: any;
419
+ get lib(): Record<string, unknown>;
91
420
  load: <FTYPE extends AnyFunction>(lib: FTYPE) => ReturnType<FTYPE>;
92
- jbrequire: (lib: keyof typeof ReExports | AnyFunction | {
421
+ /**
422
+ * Get the re-exported version of the given package name.
423
+ * Throws an error if the package is not re-exported by the plugin manager.
424
+ *
425
+ * @returns the library's default export
426
+ */
427
+ jbrequire: (lib: string | AnyFunction | {
93
428
  default: AnyFunction;
94
429
  }) => any;
95
- getRendererType(typeName: string): RendererType | undefined;
96
- getRendererTypes(): RendererType[];
97
- getAdapterType(typeName: string): AdapterType | undefined;
98
- getTextSearchAdapterType(typeName: string): TextSearchAdapterType | undefined;
99
- getTrackType(typeName: string): TrackType | undefined;
100
- getDisplayType(typeName: string): DisplayType | undefined;
101
- getViewType(typeName: string): ViewType | undefined;
102
- getAddTrackWorkflow(typeName: string): AddTrackWorkflowType | undefined;
103
- getWidgetType(typeName: string): WidgetType | undefined;
104
- getConnectionType(typeName: string): ConnectionType | undefined;
105
- getRpcMethodType(methodName: string): RpcMethodType | undefined;
106
- getInternetAccountType(name: string): InternetAccountType | undefined;
107
- addRendererType(cb: (pm: PluginManager) => RendererType): this;
430
+ getAdapterType(typeName: string): AdapterType<any>;
431
+ /**
432
+ * Whether an adapter type is registered, for a caller walking a config where
433
+ * `type` names a track, a display and an adapter alike — `getAdapterType`
434
+ * throws on a miss, which is right when the name came from a config that
435
+ * claims to be an adapter and wrong when you are asking whether it is one.
436
+ */
437
+ hasAdapterType(typeName: string): boolean;
438
+ getTextSearchAdapterType(typeName: string): TextSearchAdapterType<any>;
439
+ getTrackType(typeName: string): TrackType;
440
+ getDisplayType(typeName: string): DisplayType;
441
+ getViewType<N extends ViewTypeName>(typeName: N): Omit<ViewType, 'stateModel'> & {
442
+ stateModel: ViewTypeRegistry[N];
443
+ };
444
+ getViewType(typeName: string): ViewType;
445
+ /**
446
+ * The registered view and display types a snapshot names, from every `type`
447
+ * string anywhere in it — `heldForMissingPlugins` included. Over-collection
448
+ * is harmless: a name that resolves to neither is dropped here.
449
+ */
450
+ private sessionElementTypes;
451
+ /**
452
+ * Every async code path that hands a snapshot to a synchronous session
453
+ * instantiation (`setSession`, `cast`) must await this first.
454
+ */
455
+ preloadSessionTypes(sessionSnapshot: unknown): Promise<void>;
456
+ unloadedSessionTypes(sessionSnapshot: unknown): string[];
457
+ /**
458
+ * Without this, a snapshot naming an unloaded lazy type fails inside MST as
459
+ * a union mismatch that reads like a corrupt snapshot.
460
+ */
461
+ assertSessionTypesLoaded(sessionSnapshot: unknown): void;
462
+ /**
463
+ * Aliases resolve here because a legacy session names the alias, and the
464
+ * model that remaps it cannot be consulted before it is loaded.
465
+ */
466
+ resolveDisplayTypeRecord(name: string): DisplayType | undefined;
467
+ getAddTrackWorkflow(typeName: string): AddTrackWorkflowType;
468
+ getWidgetType(typeName: string): WidgetType;
469
+ getConnectionType(typeName: string): ConnectionType;
470
+ getRpcMethodType(methodName: string): RpcMethodType<string>;
471
+ getInternetAccountType(name: string): InternetAccountType;
108
472
  addAdapterType(cb: (pm: PluginManager) => AdapterType): this;
109
473
  addTextSearchAdapterType(cb: (pm: PluginManager) => TextSearchAdapterType): this;
110
474
  addTrackType(cb: (pm: PluginManager) => TrackType): this;
@@ -115,11 +479,66 @@ export default class PluginManager {
115
479
  addRpcMethod(cb: (pm: PluginManager) => RpcMethodType): this;
116
480
  addInternetAccountType(cb: (pm: PluginManager) => InternetAccountType): this;
117
481
  addAddTrackWorkflowType(cb: (pm: PluginManager) => AddTrackWorkflowType): this;
118
- addGlyphType(cb: (pm: PluginManager) => GlyphType): this;
119
- getGlyphType(typeName: string): GlyphType | undefined;
120
- getGlyphTypes(): GlyphType[];
121
- addToExtensionPoint<T>(extensionPointName: string, callback: (extendee: T, props: Record<string, unknown>) => T): void;
122
- evaluateExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): unknown;
123
- evaluateAsyncExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
482
+ /**
483
+ * Contribute entries to an accumulating point.
484
+ *
485
+ * The callback is handed only the props and returns what it wants to add —
486
+ * one entry, several, or `undefined` to add nothing. It never receives the
487
+ * array, which is the whole point: the concatenation happens here, once, so
488
+ * no plugin can write the `[MyEntry]` that silently drops every other
489
+ * plugin's entries. That mistake looked correct to whoever made it, because
490
+ * with one plugin registered there is nothing to drop.
491
+ */
492
+ contributeToExtensionPoint<N extends AccumulatingPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => ExtensionPointEntry<N> | ExtensionPointEntry<N>[] | undefined): void;
493
+ /**
494
+ * Listen to a notification point — one that carries its payload in `props`
495
+ * and whose return value nothing reads. The callback returns nothing;
496
+ * `addToExtensionPoint` rejects these names, so this is the only way in.
497
+ *
498
+ * The reason it is the only way in is the async join below, not the shorter
499
+ * callback. A handler that works asynchronously states so by returning a
500
+ * promise, and the producer waits on the folded value; written by hand
501
+ * through `addToExtensionPoint`, the second async handler's promise silently
502
+ * replaced the first's, so the producer stopped waiting as soon as the
503
+ * *last*-registered handler finished rather than when they all had. That is
504
+ * not a mistake a plugin author can see, which is why it is not left to them.
505
+ */
506
+ listenToExtensionPoint<N extends NotificationPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => void | Promise<void>): void;
507
+ addToExtensionPoint<N extends Exclude<ExtensionPointName, AccumulatingPointName | NotificationPointName>>(extensionPointName: N, callback: (extendee: ExtensionPointArgs<N>, props: ExtensionPointProps<N>) => ExtensionPointResult<N> | Promise<ExtensionPointResult<N>>): void;
508
+ addToExtensionPoint<T, S extends string = string>(extensionPointName: FoldPointName<S>, callback: (extendee: T, props: Record<string, unknown>) => T | Promise<T>): void;
509
+ /**
510
+ * The one place a callback joins a point's chain. The three public
511
+ * registration methods go through this rather than through each other:
512
+ * `contributeToExtensionPoint` and `listenToExtensionPoint` register on exactly
513
+ * the point names their own signatures reject, so routing them via
514
+ * `addToExtensionPoint` would either fail to compile or force its guard to be
515
+ * loose enough to let a plugin do the same thing by hand.
516
+ */
517
+ private pushExtensionPointCallback;
518
+ evaluateExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
519
+ evaluateExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): unknown;
520
+ /**
521
+ * Fire a *singular* component point — one where exactly one component can
522
+ * render, so a plugin that returns its own discards whatever the plugin
523
+ * before it returned. Same fold as {@link evaluateExtensionPoint}, plus a
524
+ * one-time warning naming the point when more than one callback genuinely
525
+ * takes the slot. A component built by `wrapComponent` still renders the
526
+ * one it wrapped, so it composes and is not counted.
527
+ *
528
+ * Used by {@link PluggableComponent}; producers should render through that
529
+ * rather than calling this directly.
530
+ */
531
+ evaluateComponentExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
532
+ /**
533
+ * How many callbacks are registered on `extensionPointName`. For a caller
534
+ * that has to tell "every handler declined" apart from "nobody was
535
+ * listening" — the two look identical in the folded result, and
536
+ * assemblyManager waits out the first but not the second.
537
+ */
538
+ extensionPointCallbackCount(extensionPointName: string): number;
539
+ evaluateAsyncExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
540
+ evaluateAsyncExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
541
+ evaluateAsyncExtensionPointStrict<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
542
+ evaluateAsyncExtensionPointStrict<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
124
543
  }
125
544
  export {};