@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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  1022. package/esm/util/useMeasure.d.ts +11 -1
  1023. package/esm/util/useMeasure.js +20 -6
  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
@@ -1,28 +1,35 @@
1
1
  import { isModelType, isType, types } from '@jbrowse/mobx-state-tree';
2
- import CorePlugin from "./CorePlugin.js";
3
- import PhasedScheduler from "./PhasedScheduler.js";
4
- import ReExports from "./ReExports/index.js";
5
- import { ConfigurationSchema, isBareConfigurationSchemaType, } from "./configuration/index.js";
6
- import AdapterType from "./pluggableElementTypes/AdapterType.js";
7
- import AddTrackWorkflowType from "./pluggableElementTypes/AddTrackWorkflowType.js";
8
- import ConnectionType from "./pluggableElementTypes/ConnectionType.js";
9
- import DisplayType from "./pluggableElementTypes/DisplayType.js";
10
- import GlyphType from "./pluggableElementTypes/GlyphType.js";
11
- import InternetAccountType from "./pluggableElementTypes/InternetAccountType.js";
12
- import RpcMethodType from "./pluggableElementTypes/RpcMethodType.js";
13
- import TextSearchAdapterType from "./pluggableElementTypes/TextSearchAdapterType.js";
14
- import TrackType from "./pluggableElementTypes/TrackType.js";
15
- import ViewType from "./pluggableElementTypes/ViewType.js";
16
- import WidgetType from "./pluggableElementTypes/WidgetType.js";
17
- import RendererType from "./pluggableElementTypes/renderers/RendererType.js";
18
- import createJexlInstance from "./util/jexl.js";
2
+ import CorePlugin from './CorePlugin.js';
3
+ import PhasedScheduler from './PhasedScheduler.js';
4
+ import { getReExportRegistry } from './ReExports/registry.js';
5
+ import { ConfigurationSchema, isBareConfigurationSchemaType, } from './configuration/index.js';
6
+ import createJexlInstance from './util/jexl.js';
7
+ import { expandLooseTrackConfig } from './util/tracks.js';
8
+ /**
9
+ * Every pluggable element group, in the order `elementCreationSchedule` builds
10
+ * them. The array is the declaration and the union is derived from it, so a
11
+ * consumer that has to visit every group — `pruneUnbuildableNodes` walking a
12
+ * session snapshot for containers of a pluggable union — enumerates them at
13
+ * runtime instead of keeping a second hand-written list that goes stale.
14
+ */
15
+ export const pluggableElementTypeGroups = [
16
+ 'adapter',
17
+ 'text search adapter',
18
+ 'display',
19
+ 'track',
20
+ 'connection',
21
+ 'view',
22
+ 'widget',
23
+ 'rpc method',
24
+ 'internet account',
25
+ 'add track workflow',
26
+ ];
27
+ /** internal class that holds the info for a certain element type */
19
28
  class TypeRecord {
20
- typeName;
21
- baseClass;
22
29
  registeredTypes = {};
23
- constructor(typeName, baseClass) {
30
+ typeName;
31
+ constructor(typeName) {
24
32
  this.typeName = typeName;
25
- this.baseClass = baseClass;
26
33
  }
27
34
  add(name, t) {
28
35
  this.registeredTypes[name] = t;
@@ -30,44 +37,126 @@ class TypeRecord {
30
37
  has(name) {
31
38
  return name in this.registeredTypes;
32
39
  }
40
+ // The message a build with the wrong plugin set gets, and usually the ONLY
41
+ // one. The lookups that reach here are mostly registration-time and
42
+ // cross-plugin — `pm.getDisplayType('LinearAlignmentsDisplay')` from a track's
43
+ // install — so in an embedded product, whose consumer supplies the plugin
44
+ // array, this throw is what lands in `pluginManagerError` and replaces the
45
+ // whole app. Naming the missing type alone still leaves "which plugin" to
46
+ // guess, which is what the registered list answers: a build short one plugin
47
+ // is visibly short that plugin's group of names.
33
48
  get(name) {
34
- if (!this.has(name)) {
35
- throw new Error(`${this.typeName} '${name}' not found, perhaps its plugin is not loaded or its plugin has not added it.`);
49
+ const type = this.registeredTypes[name];
50
+ if (!type) {
51
+ throw new Error(`${this.typeName} '${name}' is not registered: a plugin providing it either failed to load or is not in this build's plugin list. Registered ${this.typeName}s: ${this.registeredNames()}`);
52
+ }
53
+ return type;
54
+ }
55
+ registeredNames() {
56
+ const names = Object.keys(this.registeredTypes).sort();
57
+ if (names.length === 0) {
58
+ // distinguishable from "the plugin is missing", and a different bug: a
59
+ // getter called before createPluggableElements() sees every record empty
60
+ return 'none at all, so this ran before createPluggableElements()';
36
61
  }
37
- return this.registeredTypes[name];
62
+ const shown = names.slice(0, 25);
63
+ const rest = names.length - shown.length;
64
+ return rest > 0 ? `${shown.join(', ')}, and ${rest} more` : shown.join(', ');
38
65
  }
39
66
  all() {
40
67
  return Object.values(this.registeredTypes);
41
68
  }
42
69
  }
70
+ /**
71
+ * Marks a component built by wrapping the one the extension point accumulated
72
+ * so far, so {@link PluginManager.evaluateComponentExtensionPoint} can tell
73
+ * composition (two plugins each wrapping, both still visible) from a genuine
74
+ * clobber (a second plugin discarding the first). Set by `wrapComponent`.
75
+ */
76
+ export const wrappedComponent = Symbol.for('jbrowse.wrappedComponent');
77
+ // a callback that forgets to return hands `undefined` to every later callback
78
+ // and to the producer, which is a silent no-op the author has no way to see —
79
+ // the accumulator survives instead, since "return what you were passed" is the
80
+ // documented way to opt out
81
+ function nextAccumulator(name, accumulator, result) {
82
+ let next = result;
83
+ if (result === undefined && accumulator !== undefined) {
84
+ console.warn(`a ${name} extension point callback returned undefined instead of the value it was passed, so its result was ignored`);
85
+ next = accumulator;
86
+ }
87
+ return next;
88
+ }
89
+ // a bare stack from minified plugin code names nothing, so say which point
90
+ function logCallbackError(name, error) {
91
+ console.error(`error in a ${name} extension point callback`, error);
92
+ }
43
93
  export default class PluginManager {
44
94
  plugins = [];
45
95
  jexl = createJexlInstance();
46
96
  pluginMetadata = {};
47
97
  runtimePluginDefinitions = [];
48
- elementCreationSchedule = new PhasedScheduler('glyph', 'renderer', 'adapter', 'text search adapter', 'display', 'track', 'connection', 'view', 'widget', 'rpc method', 'internet account', 'add track workflow');
49
- glyphTypes = new TypeRecord('GlyphType', GlyphType);
50
- rendererTypes = new TypeRecord('RendererType', RendererType);
51
- adapterTypes = new TypeRecord('AdapterType', AdapterType);
52
- textSearchAdapterTypes = new TypeRecord('TextSearchAdapterType', TextSearchAdapterType);
53
- trackTypes = new TypeRecord('TrackType', TrackType);
54
- displayTypes = new TypeRecord('DisplayType', DisplayType);
55
- connectionTypes = new TypeRecord('ConnectionType', ConnectionType);
56
- viewTypes = new TypeRecord('ViewType', ViewType);
57
- widgetTypes = new TypeRecord('WidgetType', WidgetType);
58
- rpcMethods = new TypeRecord('RpcMethodType', RpcMethodType);
59
- addTrackWidgets = new TypeRecord('AddTrackWorkflow', AddTrackWorkflowType);
60
- internetAccountTypes = new TypeRecord('InternetAccountType', InternetAccountType);
98
+ elementCreationSchedule = new PhasedScheduler(...pluggableElementTypeGroups);
99
+ pluggableElementsCreated = false;
100
+ adapterTypes = new TypeRecord('AdapterType');
101
+ textSearchAdapterTypes = new TypeRecord('TextSearchAdapterType');
102
+ trackTypes = new TypeRecord('TrackType');
103
+ displayTypes = new TypeRecord('DisplayType');
104
+ connectionTypes = new TypeRecord('ConnectionType');
105
+ viewTypes = new TypeRecord('ViewType');
106
+ widgetTypes = new TypeRecord('WidgetType');
107
+ rpcMethods = new TypeRecord('RpcMethodType');
108
+ addTrackWidgets = new TypeRecord('AddTrackWorkflow');
109
+ internetAccountTypes = new TypeRecord('InternetAccountType');
61
110
  configured = false;
62
111
  rootModel;
63
112
  extensionPoints = new Map();
113
+ // singular component points are re-evaluated on every render, so the
114
+ // clobber warning is emitted once per point per app
115
+ warnedClobber = new Set();
116
+ #trackConfigHydrationCache = new WeakMap();
117
+ /**
118
+ * The lazily-hydrated MST config node for one frozen track config, built by
119
+ * `build` on first ask and returned by identity after that.
120
+ * `configuration/configurationSchema.ts` is the only caller.
121
+ *
122
+ * `jbrowse.tracks` is `types.frozen` for large-tracklist performance, so a
123
+ * track config is a plain JS object until first referenced; hydrating it into
124
+ * an MST node is deferred to that read. MST's custom-reference `getValue` has
125
+ * no memoization of its own — it reruns on every property access — so without
126
+ * this, every read of `track.configuration` would fabricate a fresh,
127
+ * non-identical node. Keyed by schemaType (each track type's config schema is
128
+ * rebuilt fresh per PluginManager instance, see addTrackType) then by the
129
+ * frozen object, so a hit can only ever come from this same instance and this
130
+ * same track type. See ADR-031.
131
+ *
132
+ * The node is never mutated: admin edits replace the frozen entry (new
133
+ * identity drops the WeakMap entry), and a non-admin's edits go to a private
134
+ * session working copy, not here (ADR-032). Both levels are `WeakMap`s so
135
+ * entries collect normally — no manual invalidation needed, which is why this
136
+ * is a memo and not a cache with a lifecycle to expose.
137
+ */
138
+ hydratedTrackConfig(schemaType, frozen, build) {
139
+ let byFrozen = this.#trackConfigHydrationCache.get(schemaType);
140
+ if (!byFrozen) {
141
+ byFrozen = new WeakMap();
142
+ this.#trackConfigHydrationCache.set(schemaType, byFrozen);
143
+ }
144
+ let node = byFrozen.get(frozen);
145
+ if (!node) {
146
+ node = build();
147
+ byFrozen.set(frozen, node);
148
+ }
149
+ return node;
150
+ }
64
151
  constructor(initialPlugins = []) {
152
+ // add the core plugin
65
153
  this.addPlugin({
66
154
  plugin: new CorePlugin(),
67
155
  metadata: {
68
156
  isCore: true,
69
157
  },
70
158
  });
159
+ // add all the initial plugins
71
160
  for (const plugin of initialPlugins) {
72
161
  this.addPlugin(plugin);
73
162
  }
@@ -82,25 +171,19 @@ export default class PluginManager {
82
171
  return configurationSchemas;
83
172
  }
84
173
  pluginConfigurationUnnamespacedSchemas() {
85
- let configurationSchemas = {};
174
+ const configurationSchemas = {};
86
175
  for (const plugin of this.plugins) {
87
176
  if (plugin.configurationSchemaUnnamespaced) {
88
- configurationSchemas = {
89
- ...configurationSchemas,
90
- ...plugin.configurationSchemaUnnamespaced,
91
- };
177
+ Object.assign(configurationSchemas, plugin.configurationSchemaUnnamespaced);
92
178
  }
93
179
  }
94
180
  return configurationSchemas;
95
181
  }
96
182
  pluginConfigurationRootSchemas() {
97
- let configurationSchemas = {};
183
+ const configurationSchemas = {};
98
184
  for (const plugin of this.plugins) {
99
185
  if (plugin.rootConfigurationSchema) {
100
- configurationSchemas = {
101
- ...configurationSchemas,
102
- ...plugin.rootConfigurationSchema(this),
103
- };
186
+ Object.assign(configurationSchemas, plugin.rootConfigurationSchema(this));
104
187
  }
105
188
  }
106
189
  return configurationSchemas;
@@ -109,11 +192,29 @@ export default class PluginManager {
109
192
  if (this.configured) {
110
193
  throw new Error('JBrowse already configured, cannot add plugins');
111
194
  }
112
- const [plugin, metadata = {}] = 'install' in load && 'configure' in load
113
- ? [load, {}]
114
- : [load.plugin, load.metadata];
115
- if (this.plugins.includes(plugin)) {
116
- throw new Error('plugin already installed');
195
+ const [plugin, metadata] = 'plugin' in load
196
+ ? [load.plugin, load.metadata ?? {}]
197
+ : [load, {}];
198
+ // Refuse a second copy of the same plugin, matched by name rather than by
199
+ // object identity: the two copies of a plugin a product bundles AND a
200
+ // config names are different classes from different bundles, so an
201
+ // identity check never sees them.
202
+ //
203
+ // The pluggable-element registry has its own first-wins guard, but a
204
+ // plugin's install()/configure() side effects have none — appendToMenu is a
205
+ // plain push, so a second copy silently doubles that plugin's menu items.
206
+ // Enforcing it here means a product does not have to remember to drop the
207
+ // config entry for everything it vendors.
208
+ //
209
+ // Warn and skip rather than throw. A config naming a plugin some product
210
+ // bundles is a legitimate config — jbrowse.org's hub configs do exactly
211
+ // that, so Web (which bundles less than Desktop) still gets the plugin —
212
+ // and failing the whole session over it would be worse than the duplicate
213
+ // this prevents. First registration wins, which is the core copy, since
214
+ // core plugins are added before a config's.
215
+ if (this.plugins.some(p => p.name === plugin.name)) {
216
+ console.warn(`plugin ${plugin.name} is already installed, ignoring the second copy`);
217
+ return this;
117
218
  }
118
219
  this.pluginMetadata[plugin.name] = metadata;
119
220
  if ('definition' in load) {
@@ -129,10 +230,23 @@ export default class PluginManager {
129
230
  hasPlugin(name) {
130
231
  return this.getPlugin(name) !== undefined;
131
232
  }
233
+ removePlugin(pluginName) {
234
+ const plugin = this.getPlugin(pluginName);
235
+ if (!plugin) {
236
+ throw new Error(`Plugin '${pluginName}' not found`);
237
+ }
238
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
239
+ plugin.uninstall?.(this);
240
+ this.plugins = this.plugins.filter(p => p.name !== pluginName);
241
+ delete this.pluginMetadata[pluginName];
242
+ return this;
243
+ }
132
244
  createPluggableElements() {
133
- if (this.elementCreationSchedule) {
245
+ // run the creation callbacks for each element type in order.
246
+ // see elementCreationSchedule above for the creation order
247
+ if (!this.pluggableElementsCreated) {
134
248
  this.elementCreationSchedule.run();
135
- this.elementCreationSchedule = undefined;
249
+ this.pluggableElementsCreated = true;
136
250
  }
137
251
  return this;
138
252
  }
@@ -160,8 +274,6 @@ export default class PluginManager {
160
274
  return this.connectionTypes;
161
275
  case 'widget':
162
276
  return this.widgetTypes;
163
- case 'renderer':
164
- return this.rendererTypes;
165
277
  case 'display':
166
278
  return this.displayTypes;
167
279
  case 'track':
@@ -174,8 +286,6 @@ export default class PluginManager {
174
286
  return this.internetAccountTypes;
175
287
  case 'add track workflow':
176
288
  return this.addTrackWidgets;
177
- case 'glyph':
178
- return this.glyphTypes;
179
289
  default:
180
290
  throw new Error(`invalid element type '${groupName}'`);
181
291
  }
@@ -184,8 +294,11 @@ export default class PluginManager {
184
294
  if (typeof creationCallback !== 'function') {
185
295
  throw new Error('must provide a callback function that returns the new type object');
186
296
  }
297
+ if (this.pluggableElementsCreated) {
298
+ throw new Error(`Cannot add element type after createPluggableElements() has been called`);
299
+ }
187
300
  const typeRecord = this.getElementTypeRecord(groupName);
188
- this.elementCreationSchedule?.add(groupName, () => {
301
+ this.elementCreationSchedule.add(groupName, () => {
189
302
  const newElement = creationCallback(this);
190
303
  if (!newElement.name) {
191
304
  throw new Error(`cannot add a ${groupName} with no name`);
@@ -194,7 +307,9 @@ export default class PluginManager {
194
307
  console.warn(`${groupName} ${newElement.name} already registered, cannot register it again`);
195
308
  }
196
309
  else {
197
- typeRecord.add(newElement.name, this.evaluateExtensionPoint('Core-extendPluggableElement', newElement));
310
+ typeRecord.add(newElement.name, this.evaluateExtensionPoint(
311
+ /** #extensionPoint Core-extendPluggableElement | sync | Mutate any pluggable element after it is created */
312
+ 'Core-extendPluggableElement', newElement, { group: groupName }));
198
313
  }
199
314
  });
200
315
  return this;
@@ -226,17 +341,38 @@ export default class PluginManager {
226
341
  getAdapterElements() {
227
342
  return this.getElementTypesInGroup('adapter');
228
343
  }
344
+ /**
345
+ * get a MST type for the union of all specified pluggable MST types.
346
+ * Membership is late-bound, so a lazily registered state model joins when
347
+ * its loader resolves; a snapshot naming one cannot be cast until then.
348
+ */
229
349
  pluggableMstType(groupName, fieldName, fallback = types.maybe(types.null)) {
230
- const pluggableTypes = this.getElementTypeRecord(groupName)
350
+ const record = this.getElementTypeRecord(groupName);
351
+ const anyMember = record.all().some(t => {
352
+ const element = t;
353
+ const field = element[fieldName];
354
+ return ((isType(field) && isModelType(field)) ||
355
+ typeof element[`${fieldName}Loader`] === 'function');
356
+ });
357
+ if (!anyMember) {
358
+ return fallback;
359
+ }
360
+ const modelsOf = () => record
231
361
  .all()
232
362
  .map(t => t[fieldName])
233
363
  .filter(t => isType(t) && isModelType(t));
234
- if (pluggableTypes.length === 0 && typeof jest === 'undefined') {
235
- console.warn(`No pluggable types found matching ('${groupName}','${fieldName}')`);
236
- return fallback;
237
- }
238
- return types.union(...pluggableTypes);
364
+ let members = modelsOf();
365
+ return types.union({
366
+ name: `pluggable(${groupName} ${fieldName})`,
367
+ members: () => {
368
+ if (members.length !== modelsOf().length) {
369
+ members = modelsOf();
370
+ }
371
+ return members;
372
+ },
373
+ });
239
374
  }
375
+ /** get a MST type for the union of all specified pluggable config schemas */
240
376
  pluggableConfigSchemaType(typeGroup, fieldName = 'configSchema') {
241
377
  const pluggableTypes = this.getElementTypeRecord(typeGroup)
242
378
  .all()
@@ -245,42 +381,70 @@ export default class PluginManager {
245
381
  if (pluggableTypes.length === 0) {
246
382
  pluggableTypes.push(ConfigurationSchema('Null', {}));
247
383
  }
248
- return types.union(...pluggableTypes);
384
+ // deliberately unannotated: this really is a union, not a model type, and
385
+ // the `as IAnyModelType` it used to carry was checked against the whole
386
+ // repo and needed by nothing. Claiming model-ness here is also what makes a
387
+ // schema taking its base from this look concrete while its own slot reads
388
+ // have already degraded to `any` — see configuration/CLAUDE.md.
389
+ const union = types.union(...pluggableTypes);
390
+ // A track union dispatches on `type`, so the loose `{ trackId, uri }` form
391
+ // has to become a full config before the union sees it. Here rather than
392
+ // at each array that holds tracks, so a session track, a connection track
393
+ // and a direct `create` all take it.
394
+ return typeGroup === 'track'
395
+ ? types.snapshotProcessor(union, {
396
+ preProcessor: (snap) => expandLooseTrackConfig(snap, this),
397
+ })
398
+ : union;
249
399
  }
250
400
  jbrequireCache = new Map();
251
- lib = ReExports;
401
+ // populated by PluginLoader once a runtime plugin is actually being loaded,
402
+ // which is the only thing that can call jbrequire — see ReExports/registry.ts
403
+ get lib() {
404
+ return getReExportRegistry();
405
+ }
252
406
  load = (lib) => {
253
407
  if (!this.jbrequireCache.has(lib)) {
254
408
  this.jbrequireCache.set(lib, lib(this));
255
409
  }
256
410
  return this.jbrequireCache.get(lib);
257
411
  };
412
+ /**
413
+ * Get the re-exported version of the given package name.
414
+ * Throws an error if the package is not re-exported by the plugin manager.
415
+ *
416
+ * @returns the library's default export
417
+ */
258
418
  jbrequire = (lib) => {
259
419
  if (typeof lib === 'string') {
260
420
  const pack = this.lib[lib];
261
421
  if (!pack) {
262
- throw new TypeError(`No jbrequire re-export defined for package '${lib}'. If this package must be shared between plugins, add it to ReExports.js. If it does not need to be shared, just import it normally.`);
422
+ throw new TypeError(`No jbrequire re-export defined for package '${lib}'. If this package must be shared between plugins, add it to ReExports/list.ts. If it does not need to be shared, just import it normally.`);
263
423
  }
264
424
  return pack;
265
425
  }
266
426
  else if (typeof lib === 'function') {
267
427
  return this.load(lib);
268
428
  }
429
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
269
430
  else if (lib.default) {
270
431
  console.warn('initiated jbrequire on a {default:Function}');
271
432
  return this.jbrequire(lib.default);
272
433
  }
273
434
  throw new TypeError('lib passed to jbrequire must be either a string or a function');
274
435
  };
275
- getRendererType(typeName) {
276
- return this.rendererTypes.get(typeName);
277
- }
278
- getRendererTypes() {
279
- return this.rendererTypes.all();
280
- }
281
436
  getAdapterType(typeName) {
282
437
  return this.adapterTypes.get(typeName);
283
438
  }
439
+ /**
440
+ * Whether an adapter type is registered, for a caller walking a config where
441
+ * `type` names a track, a display and an adapter alike — `getAdapterType`
442
+ * throws on a miss, which is right when the name came from a config that
443
+ * claims to be an adapter and wrong when you are asking whether it is one.
444
+ */
445
+ hasAdapterType(typeName) {
446
+ return this.adapterTypes.has(typeName);
447
+ }
284
448
  getTextSearchAdapterType(typeName) {
285
449
  return this.textSearchAdapterTypes.get(typeName);
286
450
  }
@@ -293,6 +457,102 @@ export default class PluginManager {
293
457
  getViewType(typeName) {
294
458
  return this.viewTypes.get(typeName);
295
459
  }
460
+ sessionTypeNames(sessionSnapshot) {
461
+ const viewNames = new Set();
462
+ const displayNames = new Set();
463
+ const collectTracks = (tracks) => {
464
+ if (Array.isArray(tracks)) {
465
+ for (const track of tracks) {
466
+ const { displays } = track && typeof track === 'object'
467
+ ? track
468
+ : {};
469
+ if (Array.isArray(displays)) {
470
+ for (const display of displays) {
471
+ const type = display && typeof display === 'object'
472
+ ? display.type
473
+ : undefined;
474
+ if (typeof type === 'string') {
475
+ displayNames.add(type);
476
+ }
477
+ }
478
+ }
479
+ }
480
+ }
481
+ };
482
+ const collectViews = (views) => {
483
+ if (Array.isArray(views)) {
484
+ for (const view of views) {
485
+ if (view && typeof view === 'object') {
486
+ const { type, views: children, tracks, levels, } = view;
487
+ if (typeof type === 'string') {
488
+ viewNames.add(type);
489
+ }
490
+ collectViews(children);
491
+ collectTracks(tracks);
492
+ if (Array.isArray(levels)) {
493
+ for (const level of levels) {
494
+ collectTracks(level && typeof level === 'object'
495
+ ? level.tracks
496
+ : undefined);
497
+ }
498
+ }
499
+ }
500
+ }
501
+ }
502
+ };
503
+ if (sessionSnapshot && typeof sessionSnapshot === 'object') {
504
+ const { view, views } = sessionSnapshot;
505
+ collectViews(views);
506
+ collectViews(view ? [view] : undefined);
507
+ }
508
+ return { viewNames, displayNames };
509
+ }
510
+ /**
511
+ * Every async code path that hands a snapshot to a synchronous session
512
+ * instantiation (`setSession`, `cast`) must await this first.
513
+ */
514
+ async preloadSessionTypes(sessionSnapshot) {
515
+ const { viewNames, displayNames } = this.sessionTypeNames(sessionSnapshot);
516
+ await Promise.all([
517
+ ...[...viewNames]
518
+ .filter(name => this.viewTypes.has(name))
519
+ .map(name => this.getViewType(name).loadStateModel()),
520
+ ...[...displayNames]
521
+ .map(name => this.resolveDisplayTypeRecord(name))
522
+ .flatMap(display => (display ? [display.loadStateModel()] : [])),
523
+ ]);
524
+ }
525
+ unloadedSessionTypes(sessionSnapshot) {
526
+ const { viewNames, displayNames } = this.sessionTypeNames(sessionSnapshot);
527
+ return [
528
+ ...[...viewNames].filter(name => this.viewTypes.has(name) &&
529
+ !this.getViewType(name).isStateModelLoaded),
530
+ ...[...displayNames].filter(name => {
531
+ const display = this.resolveDisplayTypeRecord(name);
532
+ return display !== undefined && !display.isStateModelLoaded;
533
+ }),
534
+ ];
535
+ }
536
+ /**
537
+ * Without this, a snapshot naming an unloaded lazy type fails inside MST as
538
+ * a union mismatch that reads like a corrupt snapshot.
539
+ */
540
+ assertSessionTypesLoaded(sessionSnapshot) {
541
+ const unloaded = this.unloadedSessionTypes(sessionSnapshot);
542
+ if (unloaded.length > 0) {
543
+ throw new Error(`session names lazily loaded types that are not loaded yet: ${unloaded.join(', ')}. Await pluginManager.preloadSessionTypes(snapshot) before setting the session`);
544
+ }
545
+ }
546
+ /**
547
+ * Aliases resolve here because a legacy session names the alias, and the
548
+ * model that remaps it cannot be consulted before it is loaded.
549
+ */
550
+ resolveDisplayTypeRecord(name) {
551
+ if (this.displayTypes.has(name)) {
552
+ return this.getDisplayType(name);
553
+ }
554
+ return this.getDisplayElements().find(d => d.aliases?.includes(name));
555
+ }
296
556
  getAddTrackWorkflow(typeName) {
297
557
  return this.addTrackWidgets.get(typeName);
298
558
  }
@@ -308,9 +568,6 @@ export default class PluginManager {
308
568
  getInternetAccountType(name) {
309
569
  return this.internetAccountTypes.get(name);
310
570
  }
311
- addRendererType(cb) {
312
- return this.addElementType('renderer', cb);
313
- }
314
571
  addAdapterType(cb) {
315
572
  return this.addElementType('adapter', cb);
316
573
  }
@@ -318,10 +575,13 @@ export default class PluginManager {
318
575
  return this.addElementType('text search adapter', cb);
319
576
  }
320
577
  addTrackType(cb) {
578
+ // Goes through the already-created displays and registers the ones that
579
+ // specify this track type
321
580
  const callback = () => {
322
581
  const track = cb(this);
323
582
  const displays = this.getElementTypesInGroup('display');
324
583
  for (const display of displays) {
584
+ // track may have already added the displayType in its cb
325
585
  if (display.trackType === track.name &&
326
586
  !track.displayTypes.includes(display)) {
327
587
  track.addDisplayType(display);
@@ -339,6 +599,8 @@ export default class PluginManager {
339
599
  const newView = cb(this);
340
600
  const displays = this.getElementTypesInGroup('display');
341
601
  for (const display of displays) {
602
+ // view may have already added the displayType in its callback
603
+ // see ViewType for description of extendedName
342
604
  if ((display.viewType === newView.name ||
343
605
  display.viewType === newView.extendedName) &&
344
606
  !newView.displayTypes.includes(display)) {
@@ -364,16 +626,82 @@ export default class PluginManager {
364
626
  addAddTrackWorkflowType(cb) {
365
627
  return this.addElementType('add track workflow', cb);
366
628
  }
367
- addGlyphType(cb) {
368
- return this.addElementType('glyph', cb);
369
- }
370
- getGlyphType(typeName) {
371
- return this.glyphTypes.get(typeName);
629
+ /**
630
+ * Contribute entries to an accumulating point.
631
+ *
632
+ * The callback is handed only the props and returns what it wants to add —
633
+ * one entry, several, or `undefined` to add nothing. It never receives the
634
+ * array, which is the whole point: the concatenation happens here, once, so
635
+ * no plugin can write the `[MyEntry]` that silently drops every other
636
+ * plugin's entries. That mistake looked correct to whoever made it, because
637
+ * with one plugin registered there is nothing to drop.
638
+ */
639
+ contributeToExtensionPoint(extensionPointName, callback) {
640
+ this.pushExtensionPointCallback(extensionPointName, (entries, props) => {
641
+ const contributed = callback(props);
642
+ const accumulated = entries;
643
+ return contributed === undefined
644
+ ? accumulated
645
+ : [
646
+ ...accumulated,
647
+ ...(Array.isArray(contributed) ? contributed : [contributed]),
648
+ ];
649
+ });
372
650
  }
373
- getGlyphTypes() {
374
- return this.glyphTypes.all();
651
+ /**
652
+ * Listen to a notification point — one that carries its payload in `props`
653
+ * and whose return value nothing reads. The callback returns nothing;
654
+ * `addToExtensionPoint` rejects these names, so this is the only way in.
655
+ *
656
+ * The reason it is the only way in is the async join below, not the shorter
657
+ * callback. A handler that works asynchronously states so by returning a
658
+ * promise, and the producer waits on the folded value; written by hand
659
+ * through `addToExtensionPoint`, the second async handler's promise silently
660
+ * replaced the first's, so the producer stopped waiting as soon as the
661
+ * *last*-registered handler finished rather than when they all had. That is
662
+ * not a mistake a plugin author can see, which is why it is not left to them.
663
+ */
664
+ listenToExtensionPoint(extensionPointName, callback) {
665
+ this.pushExtensionPointCallback(extensionPointName, (extendee, props) => {
666
+ const ret = callback(props);
667
+ // An async handler is awaited — by evaluateAsyncExtensionPoint, or by a
668
+ // producer that checks the folded value for a thenable to learn when
669
+ // handlers have finished. A sync one passes through whatever an earlier
670
+ // handler left, so its promise is not dropped on the way past.
671
+ //
672
+ // Two async ones are joined rather than the later replacing the earlier;
673
+ // under the sync runner nothing awaits between callbacks. waitForAssembly
674
+ // is the producer that depends on it.
675
+ if (!(ret instanceof Promise)) {
676
+ return extendee;
677
+ }
678
+ return extendee instanceof Promise
679
+ ? Promise.all([extendee, ret]).then(() => undefined)
680
+ : ret.then(() => undefined);
681
+ });
375
682
  }
376
683
  addToExtensionPoint(extensionPointName, callback) {
684
+ this.pushExtensionPointCallback(extensionPointName, callback);
685
+ }
686
+ /**
687
+ * The one place a callback joins a point's chain. The three public
688
+ * registration methods go through this rather than through each other:
689
+ * `contributeToExtensionPoint` and `listenToExtensionPoint` register on exactly
690
+ * the point names their own signatures reject, so routing them via
691
+ * `addToExtensionPoint` would either fail to compile or force its guard to be
692
+ * loose enough to let a plugin do the same thing by hand.
693
+ */
694
+ pushExtensionPointCallback(extensionPointName, callback) {
695
+ // `Core-extendPluggableElement` fires once per element, inside
696
+ // createPluggableElements(). Registering after that run joins a fold that
697
+ // has already happened, so the extension never applies — the same mistake
698
+ // `addElementType` throws on, and the reason it throws: from `configure()`
699
+ // instead of `install()`, an extendViewType call compiles, runs, and
700
+ // silently extends nothing.
701
+ if (extensionPointName === 'Core-extendPluggableElement' &&
702
+ this.pluggableElementsCreated) {
703
+ throw new Error("Cannot register on Core-extendPluggableElement after createPluggableElements() has been called: the point has already fired for every element, so this callback would never run. Register it from a plugin's install(), not configure().");
704
+ }
377
705
  let callbacks = this.extensionPoints.get(extensionPointName);
378
706
  if (!callbacks) {
379
707
  callbacks = [];
@@ -387,28 +715,72 @@ export default class PluginManager {
387
715
  if (callbacks) {
388
716
  for (const callback of callbacks) {
389
717
  try {
390
- accumulator = callback(accumulator, props);
718
+ accumulator = nextAccumulator(extensionPointName, accumulator, callback(accumulator, props));
719
+ }
720
+ catch (error) {
721
+ logCallbackError(extensionPointName, error);
722
+ }
723
+ }
724
+ }
725
+ return accumulator;
726
+ }
727
+ evaluateComponentExtensionPoint(extensionPointName, extendee, props) {
728
+ const callbacks = this.extensionPoints.get(extensionPointName);
729
+ let accumulator = extendee;
730
+ let claims = 0;
731
+ if (callbacks) {
732
+ for (const callback of callbacks) {
733
+ try {
734
+ const result = nextAccumulator(extensionPointName, accumulator, callback(accumulator, props));
735
+ if (result !== accumulator &&
736
+ result?.[wrappedComponent] !== accumulator) {
737
+ claims++;
738
+ }
739
+ accumulator = result;
391
740
  }
392
741
  catch (error) {
393
- console.error(error);
742
+ logCallbackError(extensionPointName, error);
394
743
  }
395
744
  }
396
745
  }
746
+ if (claims > 1 && !this.warnedClobber.has(extensionPointName)) {
747
+ this.warnedClobber.add(extensionPointName);
748
+ console.warn(`more than one plugin replaced the ${extensionPointName} slot; only the last one registered is visible. Use a wrapper if the intent was to add to the default rather than replace it`);
749
+ }
397
750
  return accumulator;
398
751
  }
752
+ /**
753
+ * How many callbacks are registered on `extensionPointName`. For a caller
754
+ * that has to tell "every handler declined" apart from "nobody was
755
+ * listening" — the two look identical in the folded result, and
756
+ * assemblyManager waits out the first but not the second.
757
+ */
758
+ extensionPointCallbackCount(extensionPointName) {
759
+ return this.extensionPoints.get(extensionPointName)?.length ?? 0;
760
+ }
399
761
  async evaluateAsyncExtensionPoint(extensionPointName, extendee, props) {
400
762
  const callbacks = this.extensionPoints.get(extensionPointName);
401
763
  let accumulator = extendee;
402
764
  if (callbacks) {
403
765
  for (const callback of callbacks) {
404
766
  try {
405
- accumulator = await callback(accumulator, props);
767
+ accumulator = nextAccumulator(extensionPointName, accumulator, await callback(accumulator, props));
406
768
  }
407
769
  catch (error) {
408
- console.error(error);
770
+ logCallbackError(extensionPointName, error);
409
771
  }
410
772
  }
411
773
  }
412
774
  return accumulator;
413
775
  }
776
+ async evaluateAsyncExtensionPointStrict(extensionPointName, extendee, props) {
777
+ const callbacks = this.extensionPoints.get(extensionPointName);
778
+ let accumulator = extendee;
779
+ if (callbacks) {
780
+ for (const callback of callbacks) {
781
+ accumulator = nextAccumulator(extensionPointName, accumulator, await callback(accumulator, props));
782
+ }
783
+ }
784
+ return accumulator;
785
+ }
414
786
  }