@jbrowse/core 4.3.0 → 5.0.0-beta.2

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 (1140) hide show
  1. package/README.md +822 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  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 -2
  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 +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  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 +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +62 -93
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
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  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1,40 +1,291 @@
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 AdapterType from './pluggableElementTypes/AdapterType.ts';
5
+ import type AddTrackWorkflowType from './pluggableElementTypes/AddTrackWorkflowType.ts';
6
+ import type ConnectionType from './pluggableElementTypes/ConnectionType.ts';
7
+ import type DisplayType from './pluggableElementTypes/DisplayType.ts';
8
+ import type InternetAccountType from './pluggableElementTypes/InternetAccountType.ts';
17
9
  import type PluggableElementBase from './pluggableElementTypes/PluggableElementBase.ts';
10
+ import type RpcMethodType from './pluggableElementTypes/RpcMethodType.ts';
11
+ import type TextSearchAdapterType from './pluggableElementTypes/TextSearchAdapterType.ts';
12
+ import type TrackType from './pluggableElementTypes/TrackType.ts';
13
+ import type ViewType from './pluggableElementTypes/ViewType.ts';
14
+ import type WidgetType from './pluggableElementTypes/WidgetType.ts';
18
15
  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';
16
+ import './pluggableElementTypes/models/migrateTrackConfig.ts';
17
+ import type { PluginDefinition } from './pluginDefinitions.ts';
18
+ import './rpc/WebWorkerRpcDriver.ts';
19
+ import './ui/buildExtraTrackMenuItems.ts';
20
+ import './ui/multiTrackMenuItems.ts';
21
+ import './util/addTrackComponent.ts';
22
+ import type { AbstractRootModel, AbstractSessionModel, SimpleFeatureSerialized } from './util/index.ts';
23
+ import type { IAnyModelType, IStateTreeNode, IAnyType, SnapshotIn } from '@jbrowse/mobx-state-tree';
24
+ import type { ComponentType, ReactNode } from 'react';
25
+ /**
26
+ * Every pluggable element group, in the order `elementCreationSchedule` builds
27
+ * them. The array is the declaration and the union is derived from it, so a
28
+ * consumer that has to visit every group — `pruneUnbuildableNodes` walking a
29
+ * session snapshot for containers of a pluggable union — enumerates them at
30
+ * runtime instead of keeping a second hand-written list that goes stale.
31
+ */
32
+ export declare const pluggableElementTypeGroups: readonly ['adapter', 'text search adapter', 'display', 'track', 'connection', 'view', 'widget', 'rpc method', 'internet account', 'add track workflow'];
33
+ export type PluggableElementTypeGroup = (typeof pluggableElementTypeGroups)[number];
34
+ /** internal class that holds the info for a certain element type */
22
35
  declare class TypeRecord<ElementClass extends PluggableElementBase> {
23
- typeName: string;
24
- baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
25
- prototype: ElementClass;
26
- });
27
36
  registeredTypes: Record<string, ElementClass>;
28
- constructor(typeName: string, baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
29
- prototype: ElementClass;
30
- }));
37
+ typeName: string;
38
+ constructor(typeName: string);
31
39
  add(name: string, t: ElementClass): void;
32
40
  has(name: string): boolean;
33
- get(name: string): ElementClass | undefined;
41
+ get(name: string): ElementClass;
42
+ registeredNames(): string;
34
43
  all(): ElementClass[];
35
44
  }
36
45
  type AnyFunction = (...args: any) => any;
37
- export type PluginMetadata = Record<string, unknown>;
46
+ type ExtensionPointCallback = (extendee: unknown, props?: Record<string, unknown>) => unknown;
47
+ /**
48
+ * Marks a component built by wrapping the one the extension point accumulated
49
+ * so far, so {@link PluginManager.evaluateComponentExtensionPoint} can tell
50
+ * composition (two plugins each wrapping, both still visible) from a genuine
51
+ * clobber (a second plugin discarding the first). Set by `wrapComponent`.
52
+ */
53
+ export declare const wrappedComponent: unique symbol;
54
+ /**
55
+ * A point that resolves to one component — a slot with a default, which a
56
+ * plugin wraps or replaces. Declared as
57
+ * `'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>`, produced by
58
+ * {@link PluggableComponent}, registered on with `wrapComponent`.
59
+ */
60
+ export interface ComponentSlot<P> {
61
+ args: ComponentType<P>;
62
+ result: ComponentType<P>;
63
+ props: P;
64
+ /**
65
+ * Type-only: never present at runtime, and what makes the shape *declared*
66
+ * rather than guessed. Reading it off the value cannot work — a
67
+ * `TrackTypeGuesser` takes an argument and returns a string, which is also
68
+ * what a function component does, so a structural test admits it as a slot.
69
+ */
70
+ kind: 'componentSlot';
71
+ }
72
+ /**
73
+ * A point that accumulates an array of components — the panel points. Produced
74
+ * by {@link PluggableComponents}, registered on with
75
+ * {@link PluginManager.contributeToExtensionPoint}; each panel scopes itself
76
+ * and draws its own chrome.
77
+ */
78
+ export interface ComponentList<P> {
79
+ args: ComponentType<P>[];
80
+ result: ComponentType<P>[];
81
+ props: P;
82
+ /** type-only, see {@link ComponentSlot.kind} */
83
+ kind: 'componentList';
84
+ }
85
+ /**
86
+ * A point that accumulates already-rendered elements — the overlay points.
87
+ * Produced by {@link PluggableElements}, registered on with
88
+ * `addExtensionElement`, which fixes the React key at registration time.
89
+ */
90
+ export interface ElementList<P> {
91
+ args: ReactNode[];
92
+ result: ReactNode[];
93
+ props: P;
94
+ /** type-only, see {@link ComponentSlot.kind} */
95
+ kind: 'elementList';
96
+ }
97
+ /** The names of the points declared as `K`. */
98
+ export type PointsOfKind<K extends string> = {
99
+ [N in ExtensionPointName]: ExtensionPointRegistry[N] extends {
100
+ kind: K;
101
+ } ? N : never;
102
+ }[ExtensionPointName];
103
+ type FeatureWidgetModel = IStateTreeNode & {
104
+ trackId?: string;
105
+ trackType?: string;
106
+ };
107
+ type WidgetModel = FeatureWidgetModel & {
108
+ type: string;
109
+ };
110
+ export interface FeaturePanelProps {
111
+ /** has `trackId` and `trackType` */
112
+ model: FeatureWidgetModel;
113
+ /** snapshot of the feature being shown */
114
+ feature: SimpleFeatureSerialized;
115
+ /**
116
+ * how far down the subfeature tree this card is: 0 is the feature the user
117
+ * clicked, 1 its subfeatures, and so on. The point fires for every card, so a
118
+ * panel that belongs only on the clicked feature selects on `depth === 0`
119
+ */
120
+ depth: number;
121
+ }
122
+ export interface ReplaceWidgetProps {
123
+ session: AbstractSessionModel;
124
+ /** has `type`; feature detail widgets also have `trackId` and `trackType` */
125
+ model: WidgetModel;
126
+ toolbarHeight?: number;
127
+ }
128
+ /**
129
+ * Typed registries of the view and display types a plugin can extend, in the
130
+ * same shape as {@link ExtensionPointRegistry} and augmented the same way:
131
+ *
132
+ * declare module '@jbrowse/core/PluginManager' {
133
+ * interface ViewTypeRegistry {
134
+ * LinearGenomeView: LinearGenomeViewStateModel
135
+ * }
136
+ * }
137
+ *
138
+ * That is what makes `extendViewType(pm, 'LinearGenomeView', …)` hand back a
139
+ * typed state model, and a misspelled or renamed name a compile error rather
140
+ * than an extension that quietly never applies. `getViewType` reads it too, so
141
+ * a caller composing another view's model into its own gets the real type
142
+ * instead of `IAnyModelType`.
143
+ *
144
+ * AN AUGMENTATION IS HAND-WRITTEN, so each registration annotates the model it
145
+ * passes to `ViewType` against its own entry here (`const stateModel:
146
+ * ViewTypeRegistry['CircularView'] = …`). That one line is what makes the
147
+ * registry earn what `getViewType` promises: without it a drifted entry is
148
+ * worse than the `IAnyModelType` it replaced, since a caller would get a
149
+ * confidently wrong type rather than an unchecked one. It cannot live on
150
+ * `ViewType`'s constructor — TypeScript forbids type parameters there, and a
151
+ * class parameter widens `name` to `string`, so the conditional never fires. Declaring them here rather than
152
+ * beside the helpers is load-bearing: an interface can only be augmented
153
+ * through the module that declares it, and a barrel re-exporting the type would
154
+ * give every augmentation its own unrelated copy.
155
+ */
156
+ export interface ViewTypeRegistry {
157
+ }
158
+ export interface DisplayTypeRegistry {
159
+ }
160
+ export type ViewTypeName = keyof ViewTypeRegistry;
161
+ export type DisplayTypeName = keyof DisplayTypeRegistry;
162
+ /**
163
+ * What `addView(name, snapshot)` takes for a view type name. A registered name
164
+ * gets the view's authored shape — the snapshot type `withLaunchInput` widened
165
+ * to accept the launch keys beside the declared properties — so a misspelled
166
+ * key is a compile error at the literal site. `type` is optional because
167
+ * `addView` writes it. An unregistered name stays `Record<string, unknown>`,
168
+ * which is what an out-of-tree view's `addView` has always been.
169
+ *
170
+ * Read off `ViewTypeRegistry` rather than registered a second time, so the
171
+ * snapshot type cannot drift from the model: a view that augments the registry
172
+ * has typed `addView`, `replaceView` and `addOrReplaceView` for free.
173
+ */
174
+ export type ViewSnapshotInput<N extends string> = N extends ViewTypeName ? Omit<SnapshotIn<ViewTypeRegistry[N]>, 'type'> & {
175
+ type?: N;
176
+ } : Record<string, unknown>;
177
+ export interface ExtensionPointRegistry {
178
+ 'Core-extendSession': {
179
+ args: IAnyModelType;
180
+ result: IAnyModelType;
181
+ };
182
+ 'Core-handleUnrecognizedAssembly': {
183
+ args: undefined;
184
+ result: undefined | Promise<void>;
185
+ props: {
186
+ assemblyName: string;
187
+ /**
188
+ * the session the lookup came from. `unknown` because the assembly
189
+ * manager holds it as the narrow shape it needs rather than the whole
190
+ * session model, and nothing in tree reads it — narrow it yourself if you
191
+ * do
192
+ */
193
+ session?: unknown;
194
+ };
195
+ };
196
+ 'Core-extendPluggableElement': {
197
+ args: PluggableElementType;
198
+ result: PluggableElementType;
199
+ props: {
200
+ group: PluggableElementTypeGroup;
201
+ };
202
+ };
203
+ 'Core-extraFeaturePanel': ComponentList<FeaturePanelProps>;
204
+ /** #extensionPoint Core-replaceWidget | sync | Replace or wrap the component that renders a widget */
205
+ 'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>;
206
+ }
207
+ export type ExtensionPointName = keyof ExtensionPointRegistry;
208
+ export type ExtensionPointArgs<N extends ExtensionPointName> = ExtensionPointRegistry[N]['args'];
209
+ export type ExtensionPointResult<N extends ExtensionPointName> = ExtensionPointRegistry[N]['result'];
210
+ export type ExtensionPointProps<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? ExtensionPointRegistry[N]['props'] : Record<string, unknown>;
211
+ /**
212
+ * Points that carry their whole payload in `props` and whose return value
213
+ * nothing reads — a notification rather than a fold. Registered with
214
+ * {@link PluginManager.listenToExtensionPoint}.
215
+ */
216
+ export type NotificationPointName = {
217
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends undefined ? N : never;
218
+ }[ExtensionPointName];
219
+ /**
220
+ * Points whose `args` are an array accumulate: the value threaded through the
221
+ * fold is every plugin's entries so far. They are registered with
222
+ * {@link PluginManager.contributeToExtensionPoint}, never
223
+ * {@link PluginManager.addToExtensionPoint} — see the entry type below for why.
224
+ */
225
+ export type AccumulatingPointName = {
226
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends readonly unknown[] ? N : never;
227
+ }[ExtensionPointName];
228
+ /** One element of an accumulating point's array — what a plugin contributes. */
229
+ export type ExtensionPointEntry<N extends AccumulatingPointName> = ExtensionPointArgs<N> extends readonly (infer E)[] ? E : never;
230
+ /**
231
+ * The trailing `props` parameter of the evaluate methods, required exactly when
232
+ * the point declares one. Omitting it there used to typecheck and then hand
233
+ * `undefined` to every callback, so each one threw on destructuring the props
234
+ * it was promised.
235
+ */
236
+ export type ExtensionPointPropsArgs<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? [props: ExtensionPointProps<N>] : [props?: Record<string, unknown>];
237
+ /**
238
+ * A point name that is *not* in the registry, which is what the loose evaluate
239
+ * overloads accept. Keeping a registered name out of them is what makes the
240
+ * typed overload binding: they otherwise match whenever it doesn't, so a call
241
+ * that omitted a required `props` or passed the wrong `extendee` fell through
242
+ * and compiled. Plugin-defined points, and any name that isn't a literal, are
243
+ * unaffected.
244
+ *
245
+ * A registered name resolves to a message-shaped type rather than `never`
246
+ * because this overload is the last one tried, so its error is the one TS
247
+ * reports: `not assignable to never` says nothing about what to fix.
248
+ */
249
+ export type UnregisteredPointName<S extends string> = S extends ExtensionPointName ? {
250
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the extendee type, and pass props if it declares them';
251
+ } : S;
252
+ /**
253
+ * The same guard for `addToExtensionPoint`'s loose overload. Each excluded kind
254
+ * needs its own message, because the useful thing to say is which method the
255
+ * point does belong to.
256
+ *
257
+ * Excluding those names from the *typed* overload is not enough on its own. The
258
+ * loose overload matches whenever the typed one doesn't, so
259
+ * `addToExtensionPoint('Core-extraFeaturePanel', panels => [MyPanel])` — the one
260
+ * call `contributeToExtensionPoint` exists to make impossible — fell through and
261
+ * compiled, with `T` inferred from whatever the callback returned, dropping every
262
+ * other plugin's panels exactly as if the exclusion weren't there.
263
+ *
264
+ * `S` is inferred from the name, so this binds on the ordinary call. It does not
265
+ * bind when a caller writes the type argument out — `addToExtensionPoint<T>(…)`
266
+ * pins `T` and leaves `S` on its default — which is the price of keeping that
267
+ * arity working for plugins compiled against the older signature.
268
+ */
269
+ export type FoldPointName<S extends string> = S extends AccumulatingPointName ? {
270
+ ERROR: 'this extension point accumulates a list; register with contributeToExtensionPoint, whose callback returns only its own entries';
271
+ } : S extends NotificationPointName ? {
272
+ ERROR: 'this extension point is a notification; register with listenToExtensionPoint, which joins async handlers rather than letting the last one registered replace the rest';
273
+ } : S extends ExtensionPointName ? {
274
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the callback against its args/result types';
275
+ } : S;
276
+ /**
277
+ * metadata related to the instance of this plugin. `isCore` is set when the
278
+ * plugin was loaded as part of the "core" set of plugins for this application,
279
+ * and `url` records the resolved location it was loaded from. The index
280
+ * signature keeps it free-form so other things about why the plugin is loaded
281
+ * (where it came from, what depends on it, etc.) can be stashed too.
282
+ */
283
+ export interface PluginMetadata {
284
+ isCore?: boolean;
285
+ isGlobal?: boolean;
286
+ url?: string;
287
+ [key: string]: unknown;
288
+ }
38
289
  export interface PluginLoadRecord {
39
290
  metadata?: PluginMetadata;
40
291
  plugin: Plugin;
@@ -43,13 +294,13 @@ export interface RuntimePluginLoadRecord extends PluginLoadRecord {
43
294
  definition: PluginDefinition;
44
295
  }
45
296
  export default class PluginManager {
297
+ #private;
46
298
  plugins: Plugin[];
47
299
  jexl: import("@jbrowse/jexl").Jexl;
48
300
  pluginMetadata: Record<string, PluginMetadata>;
49
301
  runtimePluginDefinitions: PluginDefinition[];
50
- elementCreationSchedule: PhasedScheduler<PluggableElementTypeGroup> | undefined;
51
- glyphTypes: TypeRecord<GlyphType>;
52
- rendererTypes: TypeRecord<RendererType>;
302
+ elementCreationSchedule: PhasedScheduler<"adapter" | "add track workflow" | "connection" | "display" | "internet account" | "rpc method" | "text search adapter" | "track" | "view" | "widget">;
303
+ pluggableElementsCreated: boolean;
53
304
  adapterTypes: TypeRecord<AdapterType>;
54
305
  textSearchAdapterTypes: TypeRecord<TextSearchAdapterType>;
55
306
  trackTypes: TypeRecord<TrackType>;
@@ -57,25 +308,49 @@ export default class PluginManager {
57
308
  connectionTypes: TypeRecord<ConnectionType>;
58
309
  viewTypes: TypeRecord<ViewType>;
59
310
  widgetTypes: TypeRecord<WidgetType>;
60
- rpcMethods: TypeRecord<RpcMethodType>;
311
+ rpcMethods: TypeRecord<RpcMethodType<string>>;
61
312
  addTrackWidgets: TypeRecord<AddTrackWorkflowType>;
62
313
  internetAccountTypes: TypeRecord<InternetAccountType>;
63
314
  configured: boolean;
64
315
  rootModel?: AbstractRootModel;
65
- extensionPoints: Map<string, Function[]>;
66
- constructor(initialPlugins?: (Plugin | PluginLoadRecord)[]);
316
+ extensionPoints: Map<string, ExtensionPointCallback[]>;
317
+ warnedClobber: Set<string>;
318
+ /**
319
+ * The lazily-hydrated MST config node for one frozen track config, built by
320
+ * `build` on first ask and returned by identity after that.
321
+ * `configuration/configurationSchema.ts` is the only caller.
322
+ *
323
+ * `jbrowse.tracks` is `types.frozen` for large-tracklist performance, so a
324
+ * track config is a plain JS object until first referenced; hydrating it into
325
+ * an MST node is deferred to that read. MST's custom-reference `getValue` has
326
+ * no memoization of its own — it reruns on every property access — so without
327
+ * this, every read of `track.configuration` would fabricate a fresh,
328
+ * non-identical node. Keyed by schemaType (each track type's config schema is
329
+ * rebuilt fresh per PluginManager instance, see addTrackType) then by the
330
+ * frozen object, so a hit can only ever come from this same instance and this
331
+ * same track type. See ADR-031.
332
+ *
333
+ * The node is never mutated: admin edits replace the frozen entry (new
334
+ * identity drops the WeakMap entry), and a non-admin's edits go to a private
335
+ * session working copy, not here (ADR-032). Both levels are `WeakMap`s so
336
+ * entries collect normally — no manual invalidation needed, which is why this
337
+ * is a memo and not a cache with a lifecycle to expose.
338
+ */
339
+ hydratedTrackConfig(schemaType: IAnyType, frozen: object, build: () => unknown): unknown;
340
+ constructor(initialPlugins?: (Plugin | PluginLoadRecord | RuntimePluginLoadRecord)[]);
67
341
  pluginConfigurationNamespacedSchemas(): Record<string, unknown>;
68
342
  pluginConfigurationUnnamespacedSchemas(): Record<string, unknown>;
69
343
  pluginConfigurationRootSchemas(): Record<string, unknown>;
70
344
  addPlugin(load: Plugin | PluginLoadRecord | RuntimePluginLoadRecord): this;
71
345
  getPlugin(name: string): Plugin | undefined;
72
346
  hasPlugin(name: string): boolean;
347
+ removePlugin(pluginName: string): this;
73
348
  createPluggableElements(): this;
74
349
  setRootModel(rootModel: AbstractRootModel): this;
75
350
  configure(): this;
76
351
  getElementTypeRecord(groupName: PluggableElementTypeGroup): TypeRecord<PluggableElementBase>;
77
352
  addElementType(groupName: PluggableElementTypeGroup, creationCallback: (pluginManager: PluginManager) => PluggableElementType): this;
78
- getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase | undefined;
353
+ getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase;
79
354
  getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
80
355
  getViewElements(): ViewType[];
81
356
  getTrackElements(): TrackType[];
@@ -84,27 +359,63 @@ export default class PluginManager {
84
359
  getRpcElements(): RpcMethodType[];
85
360
  getDisplayElements(): DisplayType[];
86
361
  getAdapterElements(): AdapterType[];
362
+ /**
363
+ * get a MST type for the union of all specified pluggable MST types.
364
+ * Membership is late-bound, so a lazily registered state model joins when
365
+ * its loader resolves; a snapshot naming one cannot be cast until then.
366
+ */
87
367
  pluggableMstType(groupName: PluggableElementTypeGroup, fieldName: string, fallback?: IAnyType): IAnyType;
88
- pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): IAnyModelType;
368
+ /** get a MST type for the union of all specified pluggable config schemas */
369
+ pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): IAnyType;
89
370
  jbrequireCache: Map<any, any>;
90
- lib: any;
371
+ get lib(): Record<string, unknown>;
91
372
  load: <FTYPE extends AnyFunction>(lib: FTYPE) => ReturnType<FTYPE>;
92
- jbrequire: (lib: keyof typeof ReExports | AnyFunction | {
373
+ /**
374
+ * Get the re-exported version of the given package name.
375
+ * Throws an error if the package is not re-exported by the plugin manager.
376
+ *
377
+ * @returns the library's default export
378
+ */
379
+ jbrequire: (lib: string | AnyFunction | {
93
380
  default: AnyFunction;
94
381
  }) => 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;
382
+ getAdapterType(typeName: string): AdapterType;
383
+ /**
384
+ * Whether an adapter type is registered, for a caller walking a config where
385
+ * `type` names a track, a display and an adapter alike — `getAdapterType`
386
+ * throws on a miss, which is right when the name came from a config that
387
+ * claims to be an adapter and wrong when you are asking whether it is one.
388
+ */
389
+ hasAdapterType(typeName: string): boolean;
390
+ getTextSearchAdapterType(typeName: string): TextSearchAdapterType;
391
+ getTrackType(typeName: string): TrackType;
392
+ getDisplayType(typeName: string): DisplayType;
393
+ getViewType<N extends ViewTypeName>(typeName: N): Omit<ViewType, 'stateModel'> & {
394
+ stateModel: ViewTypeRegistry[N];
395
+ };
396
+ getViewType(typeName: string): ViewType;
397
+ private sessionTypeNames;
398
+ /**
399
+ * Every async code path that hands a snapshot to a synchronous session
400
+ * instantiation (`setSession`, `cast`) must await this first.
401
+ */
402
+ preloadSessionTypes(sessionSnapshot: unknown): Promise<void>;
403
+ unloadedSessionTypes(sessionSnapshot: unknown): string[];
404
+ /**
405
+ * Without this, a snapshot naming an unloaded lazy type fails inside MST as
406
+ * a union mismatch that reads like a corrupt snapshot.
407
+ */
408
+ assertSessionTypesLoaded(sessionSnapshot: unknown): void;
409
+ /**
410
+ * Aliases resolve here because a legacy session names the alias, and the
411
+ * model that remaps it cannot be consulted before it is loaded.
412
+ */
413
+ resolveDisplayTypeRecord(name: string): DisplayType | undefined;
414
+ getAddTrackWorkflow(typeName: string): AddTrackWorkflowType;
415
+ getWidgetType(typeName: string): WidgetType;
416
+ getConnectionType(typeName: string): ConnectionType;
417
+ getRpcMethodType(methodName: string): RpcMethodType<string>;
418
+ getInternetAccountType(name: string): InternetAccountType;
108
419
  addAdapterType(cb: (pm: PluginManager) => AdapterType): this;
109
420
  addTextSearchAdapterType(cb: (pm: PluginManager) => TextSearchAdapterType): this;
110
421
  addTrackType(cb: (pm: PluginManager) => TrackType): this;
@@ -115,11 +426,66 @@ export default class PluginManager {
115
426
  addRpcMethod(cb: (pm: PluginManager) => RpcMethodType): this;
116
427
  addInternetAccountType(cb: (pm: PluginManager) => InternetAccountType): this;
117
428
  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>;
429
+ /**
430
+ * Contribute entries to an accumulating point.
431
+ *
432
+ * The callback is handed only the props and returns what it wants to add —
433
+ * one entry, several, or `undefined` to add nothing. It never receives the
434
+ * array, which is the whole point: the concatenation happens here, once, so
435
+ * no plugin can write the `[MyEntry]` that silently drops every other
436
+ * plugin's entries. That mistake looked correct to whoever made it, because
437
+ * with one plugin registered there is nothing to drop.
438
+ */
439
+ contributeToExtensionPoint<N extends AccumulatingPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => ExtensionPointEntry<N> | ExtensionPointEntry<N>[] | undefined): void;
440
+ /**
441
+ * Listen to a notification point — one that carries its payload in `props`
442
+ * and whose return value nothing reads. The callback returns nothing;
443
+ * `addToExtensionPoint` rejects these names, so this is the only way in.
444
+ *
445
+ * The reason it is the only way in is the async join below, not the shorter
446
+ * callback. A handler that works asynchronously states so by returning a
447
+ * promise, and the producer waits on the folded value; written by hand
448
+ * through `addToExtensionPoint`, the second async handler's promise silently
449
+ * replaced the first's, so the producer stopped waiting as soon as the
450
+ * *last*-registered handler finished rather than when they all had. That is
451
+ * not a mistake a plugin author can see, which is why it is not left to them.
452
+ */
453
+ listenToExtensionPoint<N extends NotificationPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => void | Promise<void>): void;
454
+ addToExtensionPoint<N extends Exclude<ExtensionPointName, AccumulatingPointName | NotificationPointName>>(extensionPointName: N, callback: (extendee: ExtensionPointArgs<N>, props: ExtensionPointProps<N>) => ExtensionPointResult<N> | Promise<ExtensionPointResult<N>>): void;
455
+ addToExtensionPoint<T, S extends string = string>(extensionPointName: FoldPointName<S>, callback: (extendee: T, props: Record<string, unknown>) => T | Promise<T>): void;
456
+ /**
457
+ * The one place a callback joins a point's chain. The three public
458
+ * registration methods go through this rather than through each other:
459
+ * `contributeToExtensionPoint` and `listenToExtensionPoint` register on exactly
460
+ * the point names their own signatures reject, so routing them via
461
+ * `addToExtensionPoint` would either fail to compile or force its guard to be
462
+ * loose enough to let a plugin do the same thing by hand.
463
+ */
464
+ private pushExtensionPointCallback;
465
+ evaluateExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
466
+ evaluateExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): unknown;
467
+ /**
468
+ * Fire a *singular* component point — one where exactly one component can
469
+ * render, so a plugin that returns its own discards whatever the plugin
470
+ * before it returned. Same fold as {@link evaluateExtensionPoint}, plus a
471
+ * one-time warning naming the point when more than one callback genuinely
472
+ * takes the slot. A component built by `wrapComponent` still renders the
473
+ * one it wrapped, so it composes and is not counted.
474
+ *
475
+ * Used by {@link PluggableComponent}; producers should render through that
476
+ * rather than calling this directly.
477
+ */
478
+ evaluateComponentExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
479
+ /**
480
+ * How many callbacks are registered on `extensionPointName`. For a caller
481
+ * that has to tell "every handler declined" apart from "nobody was
482
+ * listening" — the two look identical in the folded result, and
483
+ * assemblyManager waits out the first but not the second.
484
+ */
485
+ extensionPointCallbackCount(extensionPointName: string): number;
486
+ evaluateAsyncExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
487
+ evaluateAsyncExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
488
+ evaluateAsyncExtensionPointStrict<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
489
+ evaluateAsyncExtensionPointStrict<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
124
490
  }
125
491
  export {};