@jbrowse/core 4.3.0 → 5.0.0-beta.1

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 (1124) hide show
  1. package/README.md +783 -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 +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  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 +84 -65
  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/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
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  1025. package/esm/util/viewStatus.js +20 -0
  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /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 +37,111 @@ 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
+ /**
117
+ * Lazy-hydration cache for `TrackConfigurationReference`/
118
+ * `DisplayConfigurationReference` (configuration/configurationSchema.ts).
119
+ * `jbrowse.tracks` is `types.frozen` for large-tracklist performance, so a
120
+ * track config is a plain JS object until first referenced; hydrating it
121
+ * into an MST node is deferred to that read. MST's custom-reference
122
+ * `getValue` has no memoization of its own — it reruns on every property
123
+ * access — so without this cache, every read of `track.configuration` would
124
+ * fabricate a fresh, non-identical MST node. Keyed by schemaType (each track
125
+ * type's config schema is rebuilt fresh per PluginManager instance, see
126
+ * addTrackType) then by the frozen object itself, so a cache hit can only
127
+ * ever come from this same PluginManager instance and this same track type.
128
+ * See ADR-031.
129
+ *
130
+ * This node is never mutated: admin edits replace the frozen entry (new
131
+ * identity drops the WeakMap entry), and a non-admin's edits go to a private
132
+ * session working copy, not here (ADR-032). Both levels are `WeakMap`s so
133
+ * entries collect normally — no manual invalidation needed.
134
+ */
135
+ trackConfigHydrationCache = new WeakMap();
64
136
  constructor(initialPlugins = []) {
137
+ // add the core plugin
65
138
  this.addPlugin({
66
139
  plugin: new CorePlugin(),
67
140
  metadata: {
68
141
  isCore: true,
69
142
  },
70
143
  });
144
+ // add all the initial plugins
71
145
  for (const plugin of initialPlugins) {
72
146
  this.addPlugin(plugin);
73
147
  }
@@ -82,25 +156,19 @@ export default class PluginManager {
82
156
  return configurationSchemas;
83
157
  }
84
158
  pluginConfigurationUnnamespacedSchemas() {
85
- let configurationSchemas = {};
159
+ const configurationSchemas = {};
86
160
  for (const plugin of this.plugins) {
87
161
  if (plugin.configurationSchemaUnnamespaced) {
88
- configurationSchemas = {
89
- ...configurationSchemas,
90
- ...plugin.configurationSchemaUnnamespaced,
91
- };
162
+ Object.assign(configurationSchemas, plugin.configurationSchemaUnnamespaced);
92
163
  }
93
164
  }
94
165
  return configurationSchemas;
95
166
  }
96
167
  pluginConfigurationRootSchemas() {
97
- let configurationSchemas = {};
168
+ const configurationSchemas = {};
98
169
  for (const plugin of this.plugins) {
99
170
  if (plugin.rootConfigurationSchema) {
100
- configurationSchemas = {
101
- ...configurationSchemas,
102
- ...plugin.rootConfigurationSchema(this),
103
- };
171
+ Object.assign(configurationSchemas, plugin.rootConfigurationSchema(this));
104
172
  }
105
173
  }
106
174
  return configurationSchemas;
@@ -109,11 +177,29 @@ export default class PluginManager {
109
177
  if (this.configured) {
110
178
  throw new Error('JBrowse already configured, cannot add plugins');
111
179
  }
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');
180
+ const [plugin, metadata] = 'plugin' in load
181
+ ? [load.plugin, load.metadata ?? {}]
182
+ : [load, {}];
183
+ // Refuse a second copy of the same plugin, matched by name rather than by
184
+ // object identity: the two copies of a plugin a product bundles AND a
185
+ // config names are different classes from different bundles, so an
186
+ // identity check never sees them.
187
+ //
188
+ // The pluggable-element registry has its own first-wins guard, but a
189
+ // plugin's install()/configure() side effects have none — appendToMenu is a
190
+ // plain push, so a second copy silently doubles that plugin's menu items.
191
+ // Enforcing it here means a product does not have to remember to drop the
192
+ // config entry for everything it vendors.
193
+ //
194
+ // Warn and skip rather than throw. A config naming a plugin some product
195
+ // bundles is a legitimate config — jbrowse.org's hub configs do exactly
196
+ // that, so Web (which bundles less than Desktop) still gets the plugin —
197
+ // and failing the whole session over it would be worse than the duplicate
198
+ // this prevents. First registration wins, which is the core copy, since
199
+ // core plugins are added before a config's.
200
+ if (this.plugins.some(p => p.name === plugin.name)) {
201
+ console.warn(`plugin ${plugin.name} is already installed, ignoring the second copy`);
202
+ return this;
117
203
  }
118
204
  this.pluginMetadata[plugin.name] = metadata;
119
205
  if ('definition' in load) {
@@ -129,10 +215,23 @@ export default class PluginManager {
129
215
  hasPlugin(name) {
130
216
  return this.getPlugin(name) !== undefined;
131
217
  }
218
+ removePlugin(pluginName) {
219
+ const plugin = this.getPlugin(pluginName);
220
+ if (!plugin) {
221
+ throw new Error(`Plugin '${pluginName}' not found`);
222
+ }
223
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
224
+ plugin.uninstall?.(this);
225
+ this.plugins = this.plugins.filter(p => p.name !== pluginName);
226
+ delete this.pluginMetadata[pluginName];
227
+ return this;
228
+ }
132
229
  createPluggableElements() {
133
- if (this.elementCreationSchedule) {
230
+ // run the creation callbacks for each element type in order.
231
+ // see elementCreationSchedule above for the creation order
232
+ if (!this.pluggableElementsCreated) {
134
233
  this.elementCreationSchedule.run();
135
- this.elementCreationSchedule = undefined;
234
+ this.pluggableElementsCreated = true;
136
235
  }
137
236
  return this;
138
237
  }
@@ -160,8 +259,6 @@ export default class PluginManager {
160
259
  return this.connectionTypes;
161
260
  case 'widget':
162
261
  return this.widgetTypes;
163
- case 'renderer':
164
- return this.rendererTypes;
165
262
  case 'display':
166
263
  return this.displayTypes;
167
264
  case 'track':
@@ -174,8 +271,6 @@ export default class PluginManager {
174
271
  return this.internetAccountTypes;
175
272
  case 'add track workflow':
176
273
  return this.addTrackWidgets;
177
- case 'glyph':
178
- return this.glyphTypes;
179
274
  default:
180
275
  throw new Error(`invalid element type '${groupName}'`);
181
276
  }
@@ -184,8 +279,11 @@ export default class PluginManager {
184
279
  if (typeof creationCallback !== 'function') {
185
280
  throw new Error('must provide a callback function that returns the new type object');
186
281
  }
282
+ if (this.pluggableElementsCreated) {
283
+ throw new Error(`Cannot add element type after createPluggableElements() has been called`);
284
+ }
187
285
  const typeRecord = this.getElementTypeRecord(groupName);
188
- this.elementCreationSchedule?.add(groupName, () => {
286
+ this.elementCreationSchedule.add(groupName, () => {
189
287
  const newElement = creationCallback(this);
190
288
  if (!newElement.name) {
191
289
  throw new Error(`cannot add a ${groupName} with no name`);
@@ -194,7 +292,9 @@ export default class PluginManager {
194
292
  console.warn(`${groupName} ${newElement.name} already registered, cannot register it again`);
195
293
  }
196
294
  else {
197
- typeRecord.add(newElement.name, this.evaluateExtensionPoint('Core-extendPluggableElement', newElement));
295
+ typeRecord.add(newElement.name, this.evaluateExtensionPoint(
296
+ /** #extensionPoint Core-extendPluggableElement | sync | Mutate any pluggable element after it is created */
297
+ 'Core-extendPluggableElement', newElement, { group: groupName }));
198
298
  }
199
299
  });
200
300
  return this;
@@ -226,17 +326,18 @@ export default class PluginManager {
226
326
  getAdapterElements() {
227
327
  return this.getElementTypesInGroup('adapter');
228
328
  }
329
+ /** get a MST type for the union of all specified pluggable MST types */
229
330
  pluggableMstType(groupName, fieldName, fallback = types.maybe(types.null)) {
230
331
  const pluggableTypes = this.getElementTypeRecord(groupName)
231
332
  .all()
232
333
  .map(t => t[fieldName])
233
334
  .filter(t => isType(t) && isModelType(t));
234
- if (pluggableTypes.length === 0 && typeof jest === 'undefined') {
235
- console.warn(`No pluggable types found matching ('${groupName}','${fieldName}')`);
335
+ if (pluggableTypes.length === 0) {
236
336
  return fallback;
237
337
  }
238
338
  return types.union(...pluggableTypes);
239
339
  }
340
+ /** get a MST type for the union of all specified pluggable config schemas */
240
341
  pluggableConfigSchemaType(typeGroup, fieldName = 'configSchema') {
241
342
  const pluggableTypes = this.getElementTypeRecord(typeGroup)
242
343
  .all()
@@ -245,42 +346,70 @@ export default class PluginManager {
245
346
  if (pluggableTypes.length === 0) {
246
347
  pluggableTypes.push(ConfigurationSchema('Null', {}));
247
348
  }
248
- return types.union(...pluggableTypes);
349
+ // deliberately unannotated: this really is a union, not a model type, and
350
+ // the `as IAnyModelType` it used to carry was checked against the whole
351
+ // repo and needed by nothing. Claiming model-ness here is also what makes a
352
+ // schema taking its base from this look concrete while its own slot reads
353
+ // have already degraded to `any` — see configuration/CLAUDE.md.
354
+ const union = types.union(...pluggableTypes);
355
+ // A track union dispatches on `type`, so the loose `{ trackId, uri }` form
356
+ // has to become a full config before the union sees it. Here rather than
357
+ // at each array that holds tracks, so a session track, a connection track
358
+ // and a direct `create` all take it.
359
+ return typeGroup === 'track'
360
+ ? types.snapshotProcessor(union, {
361
+ preProcessor: (snap) => expandLooseTrackConfig(snap, this),
362
+ })
363
+ : union;
249
364
  }
250
365
  jbrequireCache = new Map();
251
- lib = ReExports;
366
+ // populated by PluginLoader once a runtime plugin is actually being loaded,
367
+ // which is the only thing that can call jbrequire — see ReExports/registry.ts
368
+ get lib() {
369
+ return getReExportRegistry();
370
+ }
252
371
  load = (lib) => {
253
372
  if (!this.jbrequireCache.has(lib)) {
254
373
  this.jbrequireCache.set(lib, lib(this));
255
374
  }
256
375
  return this.jbrequireCache.get(lib);
257
376
  };
377
+ /**
378
+ * Get the re-exported version of the given package name.
379
+ * Throws an error if the package is not re-exported by the plugin manager.
380
+ *
381
+ * @returns the library's default export
382
+ */
258
383
  jbrequire = (lib) => {
259
384
  if (typeof lib === 'string') {
260
385
  const pack = this.lib[lib];
261
386
  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.`);
387
+ 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
388
  }
264
389
  return pack;
265
390
  }
266
391
  else if (typeof lib === 'function') {
267
392
  return this.load(lib);
268
393
  }
394
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
269
395
  else if (lib.default) {
270
396
  console.warn('initiated jbrequire on a {default:Function}');
271
397
  return this.jbrequire(lib.default);
272
398
  }
273
399
  throw new TypeError('lib passed to jbrequire must be either a string or a function');
274
400
  };
275
- getRendererType(typeName) {
276
- return this.rendererTypes.get(typeName);
277
- }
278
- getRendererTypes() {
279
- return this.rendererTypes.all();
280
- }
281
401
  getAdapterType(typeName) {
282
402
  return this.adapterTypes.get(typeName);
283
403
  }
404
+ /**
405
+ * Whether an adapter type is registered, for a caller walking a config where
406
+ * `type` names a track, a display and an adapter alike — `getAdapterType`
407
+ * throws on a miss, which is right when the name came from a config that
408
+ * claims to be an adapter and wrong when you are asking whether it is one.
409
+ */
410
+ hasAdapterType(typeName) {
411
+ return this.adapterTypes.has(typeName);
412
+ }
284
413
  getTextSearchAdapterType(typeName) {
285
414
  return this.textSearchAdapterTypes.get(typeName);
286
415
  }
@@ -308,9 +437,6 @@ export default class PluginManager {
308
437
  getInternetAccountType(name) {
309
438
  return this.internetAccountTypes.get(name);
310
439
  }
311
- addRendererType(cb) {
312
- return this.addElementType('renderer', cb);
313
- }
314
440
  addAdapterType(cb) {
315
441
  return this.addElementType('adapter', cb);
316
442
  }
@@ -318,10 +444,13 @@ export default class PluginManager {
318
444
  return this.addElementType('text search adapter', cb);
319
445
  }
320
446
  addTrackType(cb) {
447
+ // Goes through the already-created displays and registers the ones that
448
+ // specify this track type
321
449
  const callback = () => {
322
450
  const track = cb(this);
323
451
  const displays = this.getElementTypesInGroup('display');
324
452
  for (const display of displays) {
453
+ // track may have already added the displayType in its cb
325
454
  if (display.trackType === track.name &&
326
455
  !track.displayTypes.includes(display)) {
327
456
  track.addDisplayType(display);
@@ -339,6 +468,8 @@ export default class PluginManager {
339
468
  const newView = cb(this);
340
469
  const displays = this.getElementTypesInGroup('display');
341
470
  for (const display of displays) {
471
+ // view may have already added the displayType in its callback
472
+ // see ViewType for description of extendedName
342
473
  if ((display.viewType === newView.name ||
343
474
  display.viewType === newView.extendedName) &&
344
475
  !newView.displayTypes.includes(display)) {
@@ -364,16 +495,82 @@ export default class PluginManager {
364
495
  addAddTrackWorkflowType(cb) {
365
496
  return this.addElementType('add track workflow', cb);
366
497
  }
367
- addGlyphType(cb) {
368
- return this.addElementType('glyph', cb);
369
- }
370
- getGlyphType(typeName) {
371
- return this.glyphTypes.get(typeName);
498
+ /**
499
+ * Contribute entries to an accumulating point.
500
+ *
501
+ * The callback is handed only the props and returns what it wants to add —
502
+ * one entry, several, or `undefined` to add nothing. It never receives the
503
+ * array, which is the whole point: the concatenation happens here, once, so
504
+ * no plugin can write the `[MyEntry]` that silently drops every other
505
+ * plugin's entries. That mistake looked correct to whoever made it, because
506
+ * with one plugin registered there is nothing to drop.
507
+ */
508
+ contributeToExtensionPoint(extensionPointName, callback) {
509
+ this.pushExtensionPointCallback(extensionPointName, (entries, props) => {
510
+ const contributed = callback(props);
511
+ const accumulated = entries;
512
+ return contributed === undefined
513
+ ? accumulated
514
+ : [
515
+ ...accumulated,
516
+ ...(Array.isArray(contributed) ? contributed : [contributed]),
517
+ ];
518
+ });
372
519
  }
373
- getGlyphTypes() {
374
- return this.glyphTypes.all();
520
+ /**
521
+ * Listen to a notification point — one that carries its payload in `props`
522
+ * and whose return value nothing reads. The callback returns nothing;
523
+ * `addToExtensionPoint` rejects these names, so this is the only way in.
524
+ *
525
+ * The reason it is the only way in is the async join below, not the shorter
526
+ * callback. A handler that works asynchronously states so by returning a
527
+ * promise, and the producer waits on the folded value; written by hand
528
+ * through `addToExtensionPoint`, the second async handler's promise silently
529
+ * replaced the first's, so the producer stopped waiting as soon as the
530
+ * *last*-registered handler finished rather than when they all had. That is
531
+ * not a mistake a plugin author can see, which is why it is not left to them.
532
+ */
533
+ listenToExtensionPoint(extensionPointName, callback) {
534
+ this.pushExtensionPointCallback(extensionPointName, (extendee, props) => {
535
+ const ret = callback(props);
536
+ // An async handler is awaited — by evaluateAsyncExtensionPoint, or by a
537
+ // producer that checks the folded value for a thenable to learn when
538
+ // handlers have finished. A sync one passes through whatever an earlier
539
+ // handler left, so its promise is not dropped on the way past.
540
+ //
541
+ // Two async ones are joined rather than the later replacing the earlier;
542
+ // under the sync runner nothing awaits between callbacks. waitForAssembly
543
+ // is the producer that depends on it.
544
+ if (!(ret instanceof Promise)) {
545
+ return extendee;
546
+ }
547
+ return extendee instanceof Promise
548
+ ? Promise.all([extendee, ret]).then(() => undefined)
549
+ : ret.then(() => undefined);
550
+ });
375
551
  }
376
552
  addToExtensionPoint(extensionPointName, callback) {
553
+ this.pushExtensionPointCallback(extensionPointName, callback);
554
+ }
555
+ /**
556
+ * The one place a callback joins a point's chain. The three public
557
+ * registration methods go through this rather than through each other:
558
+ * `contributeToExtensionPoint` and `listenToExtensionPoint` register on exactly
559
+ * the point names their own signatures reject, so routing them via
560
+ * `addToExtensionPoint` would either fail to compile or force its guard to be
561
+ * loose enough to let a plugin do the same thing by hand.
562
+ */
563
+ pushExtensionPointCallback(extensionPointName, callback) {
564
+ // `Core-extendPluggableElement` fires once per element, inside
565
+ // createPluggableElements(). Registering after that run joins a fold that
566
+ // has already happened, so the extension never applies — the same mistake
567
+ // `addElementType` throws on, and the reason it throws: from `configure()`
568
+ // instead of `install()`, an extendViewType call compiles, runs, and
569
+ // silently extends nothing.
570
+ if (extensionPointName === 'Core-extendPluggableElement' &&
571
+ this.pluggableElementsCreated) {
572
+ 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().");
573
+ }
377
574
  let callbacks = this.extensionPoints.get(extensionPointName);
378
575
  if (!callbacks) {
379
576
  callbacks = [];
@@ -387,28 +584,72 @@ export default class PluginManager {
387
584
  if (callbacks) {
388
585
  for (const callback of callbacks) {
389
586
  try {
390
- accumulator = callback(accumulator, props);
587
+ accumulator = nextAccumulator(extensionPointName, accumulator, callback(accumulator, props));
391
588
  }
392
589
  catch (error) {
393
- console.error(error);
590
+ logCallbackError(extensionPointName, error);
394
591
  }
395
592
  }
396
593
  }
397
594
  return accumulator;
398
595
  }
596
+ evaluateComponentExtensionPoint(extensionPointName, extendee, props) {
597
+ const callbacks = this.extensionPoints.get(extensionPointName);
598
+ let accumulator = extendee;
599
+ let claims = 0;
600
+ if (callbacks) {
601
+ for (const callback of callbacks) {
602
+ try {
603
+ const result = nextAccumulator(extensionPointName, accumulator, callback(accumulator, props));
604
+ if (result !== accumulator &&
605
+ result?.[wrappedComponent] !== accumulator) {
606
+ claims++;
607
+ }
608
+ accumulator = result;
609
+ }
610
+ catch (error) {
611
+ logCallbackError(extensionPointName, error);
612
+ }
613
+ }
614
+ }
615
+ if (claims > 1 && !this.warnedClobber.has(extensionPointName)) {
616
+ this.warnedClobber.add(extensionPointName);
617
+ 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`);
618
+ }
619
+ return accumulator;
620
+ }
621
+ /**
622
+ * How many callbacks are registered on `extensionPointName`. For a caller
623
+ * that has to tell "every handler declined" apart from "nobody was
624
+ * listening" — the two look identical in the folded result, and
625
+ * assemblyManager waits out the first but not the second.
626
+ */
627
+ extensionPointCallbackCount(extensionPointName) {
628
+ return this.extensionPoints.get(extensionPointName)?.length ?? 0;
629
+ }
399
630
  async evaluateAsyncExtensionPoint(extensionPointName, extendee, props) {
400
631
  const callbacks = this.extensionPoints.get(extensionPointName);
401
632
  let accumulator = extendee;
402
633
  if (callbacks) {
403
634
  for (const callback of callbacks) {
404
635
  try {
405
- accumulator = await callback(accumulator, props);
636
+ accumulator = nextAccumulator(extensionPointName, accumulator, await callback(accumulator, props));
406
637
  }
407
638
  catch (error) {
408
- console.error(error);
639
+ logCallbackError(extensionPointName, error);
409
640
  }
410
641
  }
411
642
  }
412
643
  return accumulator;
413
644
  }
645
+ async evaluateAsyncExtensionPointStrict(extensionPointName, extendee, props) {
646
+ const callbacks = this.extensionPoints.get(extensionPointName);
647
+ let accumulator = extendee;
648
+ if (callbacks) {
649
+ for (const callback of callbacks) {
650
+ accumulator = nextAccumulator(extensionPointName, accumulator, await callback(accumulator, props));
651
+ }
652
+ }
653
+ return accumulator;
654
+ }
414
655
  }
@@ -1,9 +1,10 @@
1
1
  import { lazy } from 'react';
2
- import { lazyMap } from "./lazify.js";
2
+ import { lazyMap } from './lazify.js';
3
3
  export const BaseFeatureDetail = lazyMap({
4
- Attributes: lazy(() => import("../BaseFeatureWidget/BaseFeatureDetail/Attributes.js")),
5
- FeatureDetails: lazy(() => import("../BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js")),
6
- BaseCard: lazy(() => import("../BaseFeatureWidget/BaseFeatureDetail/BaseCard.js")),
7
- BaseAttributes: lazy(() => import("../BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js")),
8
- BaseCoreDetails: lazy(() => import("../BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js")),
4
+ Attributes: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/Attributes.js')),
5
+ FeatureDetails: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js')),
6
+ FeatureWash: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js')),
7
+ BaseCard: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/BaseCard.js')),
8
+ BaseAttributes: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js')),
9
+ BaseCoreDetails: lazy(() => import('../BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js')),
9
10
  }, '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/');
@@ -1,2 +1,2 @@
1
- import { type LazyExoticComponent } from 'react';
2
- export declare const DataGridEntries: Record<string, LazyExoticComponent<any>>;
1
+ import type { ComponentType } from 'react';
2
+ export declare const DataGridEntries: Record<string, ComponentType<any>>;