@jbrowse/core 4.2.1 → 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 +196 -55
  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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  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
@@ -1,40 +1,265 @@
1
1
  import PhasedScheduler from './PhasedScheduler.ts';
2
- import ReExports from './ReExports/index.ts';
3
- import AdapterType from './pluggableElementTypes/AdapterType.ts';
4
- import AddTrackWorkflowType from './pluggableElementTypes/AddTrackWorkflowType.ts';
5
- import ConnectionType from './pluggableElementTypes/ConnectionType.ts';
6
- import DisplayType from './pluggableElementTypes/DisplayType.ts';
7
- import GlyphType from './pluggableElementTypes/GlyphType.ts';
8
- import InternetAccountType from './pluggableElementTypes/InternetAccountType.ts';
9
- import RpcMethodType from './pluggableElementTypes/RpcMethodType.ts';
10
- import TextSearchAdapterType from './pluggableElementTypes/TextSearchAdapterType.ts';
11
- import TrackType from './pluggableElementTypes/TrackType.ts';
12
- import ViewType from './pluggableElementTypes/ViewType.ts';
13
- import WidgetType from './pluggableElementTypes/WidgetType.ts';
14
- import RendererType from './pluggableElementTypes/renderers/RendererType.tsx';
2
+ import './util/tracks.ts';
15
3
  import type Plugin from './Plugin.ts';
16
- import type { PluginDefinition } from './PluginLoader.ts';
4
+ import type AdapterType from './pluggableElementTypes/AdapterType.ts';
5
+ import type AddTrackWorkflowType from './pluggableElementTypes/AddTrackWorkflowType.ts';
6
+ import type ConnectionType from './pluggableElementTypes/ConnectionType.ts';
7
+ import type DisplayType from './pluggableElementTypes/DisplayType.ts';
8
+ import type InternetAccountType from './pluggableElementTypes/InternetAccountType.ts';
17
9
  import type PluggableElementBase from './pluggableElementTypes/PluggableElementBase.ts';
10
+ import type RpcMethodType from './pluggableElementTypes/RpcMethodType.ts';
11
+ import type TextSearchAdapterType from './pluggableElementTypes/TextSearchAdapterType.ts';
12
+ import type TrackType from './pluggableElementTypes/TrackType.ts';
13
+ import type ViewType from './pluggableElementTypes/ViewType.ts';
14
+ import type WidgetType from './pluggableElementTypes/WidgetType.ts';
18
15
  import type { PluggableElementType } from './pluggableElementTypes/index.ts';
19
- import type { AbstractRootModel } from './util/index.ts';
20
- import type { IAnyModelType, IAnyType } from '@jbrowse/mobx-state-tree';
21
- type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' | 'connection' | 'view' | 'widget' | 'rpc method' | 'internet account' | 'text search adapter' | 'add track workflow' | 'glyph';
16
+ import './pluggableElementTypes/models/migrateTrackConfig.ts';
17
+ import type { PluginDefinition } from './pluginDefinitions.ts';
18
+ import './rpc/WebWorkerRpcDriver.ts';
19
+ import './ui/buildExtraTrackMenuItems.ts';
20
+ import './ui/multiTrackMenuItems.ts';
21
+ import './util/addTrackComponent.ts';
22
+ import type { AbstractRootModel, AbstractSessionModel, SimpleFeatureSerialized } from './util/index.ts';
23
+ import type { IAnyModelType, IStateTreeNode, IAnyType } from '@jbrowse/mobx-state-tree';
24
+ import type { ComponentType, ReactNode } from 'react';
25
+ /**
26
+ * Every pluggable element group, in the order `elementCreationSchedule` builds
27
+ * them. The array is the declaration and the union is derived from it, so a
28
+ * consumer that has to visit every group — `pruneUnbuildableNodes` walking a
29
+ * session snapshot for containers of a pluggable union — enumerates them at
30
+ * runtime instead of keeping a second hand-written list that goes stale.
31
+ */
32
+ export declare const pluggableElementTypeGroups: readonly ['adapter', 'text search adapter', 'display', 'track', 'connection', 'view', 'widget', 'rpc method', 'internet account', 'add track workflow'];
33
+ export type PluggableElementTypeGroup = (typeof pluggableElementTypeGroups)[number];
34
+ /** internal class that holds the info for a certain element type */
22
35
  declare class TypeRecord<ElementClass extends PluggableElementBase> {
23
- typeName: string;
24
- baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
25
- prototype: ElementClass;
26
- });
27
36
  registeredTypes: Record<string, ElementClass>;
28
- constructor(typeName: string, baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
29
- prototype: ElementClass;
30
- }));
37
+ typeName: string;
38
+ constructor(typeName: string);
31
39
  add(name: string, t: ElementClass): void;
32
40
  has(name: string): boolean;
33
- get(name: string): ElementClass | undefined;
41
+ get(name: string): ElementClass;
42
+ registeredNames(): string;
34
43
  all(): ElementClass[];
35
44
  }
36
45
  type AnyFunction = (...args: any) => any;
37
- export type PluginMetadata = Record<string, unknown>;
46
+ type ExtensionPointCallback = (extendee: unknown, props?: Record<string, unknown>) => unknown;
47
+ /**
48
+ * Marks a component built by wrapping the one the extension point accumulated
49
+ * so far, so {@link PluginManager.evaluateComponentExtensionPoint} can tell
50
+ * composition (two plugins each wrapping, both still visible) from a genuine
51
+ * clobber (a second plugin discarding the first). Set by `wrapComponent`.
52
+ */
53
+ export declare const wrappedComponent: unique symbol;
54
+ /**
55
+ * A point that resolves to one component — a slot with a default, which a
56
+ * plugin wraps or replaces. Declared as
57
+ * `'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>`, produced by
58
+ * {@link PluggableComponent}, registered on with `wrapComponent`.
59
+ */
60
+ export interface ComponentSlot<P> {
61
+ args: ComponentType<P>;
62
+ result: ComponentType<P>;
63
+ props: P;
64
+ /**
65
+ * Type-only: never present at runtime, and what makes the shape *declared*
66
+ * rather than guessed. Reading it off the value cannot work — a
67
+ * `TrackTypeGuesser` takes an argument and returns a string, which is also
68
+ * what a function component does, so a structural test admits it as a slot.
69
+ */
70
+ kind: 'componentSlot';
71
+ }
72
+ /**
73
+ * A point that accumulates an array of components — the panel points. Produced
74
+ * by {@link PluggableComponents}, registered on with
75
+ * {@link PluginManager.contributeToExtensionPoint}; each panel scopes itself
76
+ * and draws its own chrome.
77
+ */
78
+ export interface ComponentList<P> {
79
+ args: ComponentType<P>[];
80
+ result: ComponentType<P>[];
81
+ props: P;
82
+ /** type-only, see {@link ComponentSlot.kind} */
83
+ kind: 'componentList';
84
+ }
85
+ /**
86
+ * A point that accumulates already-rendered elements — the overlay points.
87
+ * Produced by {@link PluggableElements}, registered on with
88
+ * `addExtensionElement`, which fixes the React key at registration time.
89
+ */
90
+ export interface ElementList<P> {
91
+ args: ReactNode[];
92
+ result: ReactNode[];
93
+ props: P;
94
+ /** type-only, see {@link ComponentSlot.kind} */
95
+ kind: 'elementList';
96
+ }
97
+ /** The names of the points declared as `K`. */
98
+ export type PointsOfKind<K extends string> = {
99
+ [N in ExtensionPointName]: ExtensionPointRegistry[N] extends {
100
+ kind: K;
101
+ } ? N : never;
102
+ }[ExtensionPointName];
103
+ type FeatureWidgetModel = IStateTreeNode & {
104
+ trackId?: string;
105
+ trackType?: string;
106
+ };
107
+ type WidgetModel = FeatureWidgetModel & {
108
+ type: string;
109
+ };
110
+ export interface FeaturePanelProps {
111
+ /** has `trackId` and `trackType` */
112
+ model: FeatureWidgetModel;
113
+ /** snapshot of the feature being shown */
114
+ feature: SimpleFeatureSerialized;
115
+ /**
116
+ * how far down the subfeature tree this card is: 0 is the feature the user
117
+ * clicked, 1 its subfeatures, and so on. The point fires for every card, so a
118
+ * panel that belongs only on the clicked feature selects on `depth === 0`
119
+ */
120
+ depth: number;
121
+ }
122
+ export interface ReplaceWidgetProps {
123
+ session: AbstractSessionModel;
124
+ /** has `type`; feature detail widgets also have `trackId` and `trackType` */
125
+ model: WidgetModel;
126
+ toolbarHeight?: number;
127
+ }
128
+ /**
129
+ * Typed registries of the view and display types a plugin can extend, in the
130
+ * same shape as {@link ExtensionPointRegistry} and augmented the same way:
131
+ *
132
+ * declare module '@jbrowse/core/PluginManager' {
133
+ * interface ViewTypeRegistry {
134
+ * LinearGenomeView: LinearGenomeViewStateModel
135
+ * }
136
+ * }
137
+ *
138
+ * That is what makes `extendViewType(pm, 'LinearGenomeView', …)` hand back a
139
+ * typed state model, and a misspelled or renamed name a compile error rather
140
+ * than an extension that quietly never applies. Declaring them here rather than
141
+ * beside the helpers is load-bearing: an interface can only be augmented
142
+ * through the module that declares it, and a barrel re-exporting the type would
143
+ * give every augmentation its own unrelated copy.
144
+ */
145
+ export interface ViewTypeRegistry {
146
+ }
147
+ export interface DisplayTypeRegistry {
148
+ }
149
+ export type ViewTypeName = keyof ViewTypeRegistry;
150
+ export type DisplayTypeName = keyof DisplayTypeRegistry;
151
+ export interface ExtensionPointRegistry {
152
+ 'Core-extendSession': {
153
+ args: IAnyModelType;
154
+ result: IAnyModelType;
155
+ };
156
+ 'Core-handleUnrecognizedAssembly': {
157
+ args: undefined;
158
+ result: undefined | Promise<void>;
159
+ props: {
160
+ assemblyName: string;
161
+ /**
162
+ * the session the lookup came from. `unknown` because the assembly
163
+ * manager holds it as the narrow shape it needs rather than the whole
164
+ * session model, and nothing in tree reads it — narrow it yourself if you
165
+ * do
166
+ */
167
+ session?: unknown;
168
+ };
169
+ };
170
+ 'Core-extendPluggableElement': {
171
+ args: PluggableElementType;
172
+ result: PluggableElementType;
173
+ props: {
174
+ group: PluggableElementTypeGroup;
175
+ };
176
+ };
177
+ 'Core-extraFeaturePanel': ComponentList<FeaturePanelProps>;
178
+ /** #extensionPoint Core-replaceWidget | sync | Replace or wrap the component that renders a widget */
179
+ 'Core-replaceWidget': ComponentSlot<ReplaceWidgetProps>;
180
+ }
181
+ export type ExtensionPointName = keyof ExtensionPointRegistry;
182
+ export type ExtensionPointArgs<N extends ExtensionPointName> = ExtensionPointRegistry[N]['args'];
183
+ export type ExtensionPointResult<N extends ExtensionPointName> = ExtensionPointRegistry[N]['result'];
184
+ export type ExtensionPointProps<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? ExtensionPointRegistry[N]['props'] : Record<string, unknown>;
185
+ /**
186
+ * Points that carry their whole payload in `props` and whose return value
187
+ * nothing reads — a notification rather than a fold. Registered with
188
+ * {@link PluginManager.listenToExtensionPoint}.
189
+ */
190
+ export type NotificationPointName = {
191
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends undefined ? N : never;
192
+ }[ExtensionPointName];
193
+ /**
194
+ * Points whose `args` are an array accumulate: the value threaded through the
195
+ * fold is every plugin's entries so far. They are registered with
196
+ * {@link PluginManager.contributeToExtensionPoint}, never
197
+ * {@link PluginManager.addToExtensionPoint} — see the entry type below for why.
198
+ */
199
+ export type AccumulatingPointName = {
200
+ [N in ExtensionPointName]: ExtensionPointArgs<N> extends readonly unknown[] ? N : never;
201
+ }[ExtensionPointName];
202
+ /** One element of an accumulating point's array — what a plugin contributes. */
203
+ export type ExtensionPointEntry<N extends AccumulatingPointName> = ExtensionPointArgs<N> extends readonly (infer E)[] ? E : never;
204
+ /**
205
+ * The trailing `props` parameter of the evaluate methods, required exactly when
206
+ * the point declares one. Omitting it there used to typecheck and then hand
207
+ * `undefined` to every callback, so each one threw on destructuring the props
208
+ * it was promised.
209
+ */
210
+ export type ExtensionPointPropsArgs<N extends ExtensionPointName> = 'props' extends keyof ExtensionPointRegistry[N] ? [props: ExtensionPointProps<N>] : [props?: Record<string, unknown>];
211
+ /**
212
+ * A point name that is *not* in the registry, which is what the loose evaluate
213
+ * overloads accept. Keeping a registered name out of them is what makes the
214
+ * typed overload binding: they otherwise match whenever it doesn't, so a call
215
+ * that omitted a required `props` or passed the wrong `extendee` fell through
216
+ * and compiled. Plugin-defined points, and any name that isn't a literal, are
217
+ * unaffected.
218
+ *
219
+ * A registered name resolves to a message-shaped type rather than `never`
220
+ * because this overload is the last one tried, so its error is the one TS
221
+ * reports: `not assignable to never` says nothing about what to fix.
222
+ */
223
+ export type UnregisteredPointName<S extends string> = S extends ExtensionPointName ? {
224
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the extendee type, and pass props if it declares them';
225
+ } : S;
226
+ /**
227
+ * The same guard for `addToExtensionPoint`'s loose overload. Each excluded kind
228
+ * needs its own message, because the useful thing to say is which method the
229
+ * point does belong to.
230
+ *
231
+ * Excluding those names from the *typed* overload is not enough on its own. The
232
+ * loose overload matches whenever the typed one doesn't, so
233
+ * `addToExtensionPoint('Core-extraFeaturePanel', panels => [MyPanel])` — the one
234
+ * call `contributeToExtensionPoint` exists to make impossible — fell through and
235
+ * compiled, with `T` inferred from whatever the callback returned, dropping every
236
+ * other plugin's panels exactly as if the exclusion weren't there.
237
+ *
238
+ * `S` is inferred from the name, so this binds on the ordinary call. It does not
239
+ * bind when a caller writes the type argument out — `addToExtensionPoint<T>(…)`
240
+ * pins `T` and leaves `S` on its default — which is the price of keeping that
241
+ * arity working for plugins compiled against the older signature.
242
+ */
243
+ export type FoldPointName<S extends string> = S extends AccumulatingPointName ? {
244
+ ERROR: 'this extension point accumulates a list; register with contributeToExtensionPoint, whose callback returns only its own entries';
245
+ } : S extends NotificationPointName ? {
246
+ ERROR: 'this extension point is a notification; register with listenToExtensionPoint, which joins async handlers rather than letting the last one registered replace the rest';
247
+ } : S extends ExtensionPointName ? {
248
+ ERROR: 'this extension point is in ExtensionPointRegistry; check the callback against its args/result types';
249
+ } : S;
250
+ /**
251
+ * metadata related to the instance of this plugin. `isCore` is set when the
252
+ * plugin was loaded as part of the "core" set of plugins for this application,
253
+ * and `url` records the resolved location it was loaded from. The index
254
+ * signature keeps it free-form so other things about why the plugin is loaded
255
+ * (where it came from, what depends on it, etc.) can be stashed too.
256
+ */
257
+ export interface PluginMetadata {
258
+ isCore?: boolean;
259
+ isGlobal?: boolean;
260
+ url?: string;
261
+ [key: string]: unknown;
262
+ }
38
263
  export interface PluginLoadRecord {
39
264
  metadata?: PluginMetadata;
40
265
  plugin: Plugin;
@@ -47,9 +272,8 @@ export default class PluginManager {
47
272
  jexl: import("@jbrowse/jexl").Jexl;
48
273
  pluginMetadata: Record<string, PluginMetadata>;
49
274
  runtimePluginDefinitions: PluginDefinition[];
50
- elementCreationSchedule: PhasedScheduler<PluggableElementTypeGroup> | undefined;
51
- glyphTypes: TypeRecord<GlyphType>;
52
- rendererTypes: TypeRecord<RendererType>;
275
+ elementCreationSchedule: PhasedScheduler<"adapter" | "add track workflow" | "connection" | "display" | "internet account" | "rpc method" | "text search adapter" | "track" | "view" | "widget">;
276
+ pluggableElementsCreated: boolean;
53
277
  adapterTypes: TypeRecord<AdapterType>;
54
278
  textSearchAdapterTypes: TypeRecord<TextSearchAdapterType>;
55
279
  trackTypes: TypeRecord<TrackType>;
@@ -57,25 +281,47 @@ export default class PluginManager {
57
281
  connectionTypes: TypeRecord<ConnectionType>;
58
282
  viewTypes: TypeRecord<ViewType>;
59
283
  widgetTypes: TypeRecord<WidgetType>;
60
- rpcMethods: TypeRecord<RpcMethodType>;
284
+ rpcMethods: TypeRecord<RpcMethodType<string>>;
61
285
  addTrackWidgets: TypeRecord<AddTrackWorkflowType>;
62
286
  internetAccountTypes: TypeRecord<InternetAccountType>;
63
287
  configured: boolean;
64
288
  rootModel?: AbstractRootModel;
65
- extensionPoints: Map<string, Function[]>;
66
- constructor(initialPlugins?: (Plugin | PluginLoadRecord)[]);
289
+ extensionPoints: Map<string, ExtensionPointCallback[]>;
290
+ warnedClobber: Set<string>;
291
+ /**
292
+ * Lazy-hydration cache for `TrackConfigurationReference`/
293
+ * `DisplayConfigurationReference` (configuration/configurationSchema.ts).
294
+ * `jbrowse.tracks` is `types.frozen` for large-tracklist performance, so a
295
+ * track config is a plain JS object until first referenced; hydrating it
296
+ * into an MST node is deferred to that read. MST's custom-reference
297
+ * `getValue` has no memoization of its own — it reruns on every property
298
+ * access — so without this cache, every read of `track.configuration` would
299
+ * fabricate a fresh, non-identical MST node. Keyed by schemaType (each track
300
+ * type's config schema is rebuilt fresh per PluginManager instance, see
301
+ * addTrackType) then by the frozen object itself, so a cache hit can only
302
+ * ever come from this same PluginManager instance and this same track type.
303
+ * See ADR-031.
304
+ *
305
+ * This node is never mutated: admin edits replace the frozen entry (new
306
+ * identity drops the WeakMap entry), and a non-admin's edits go to a private
307
+ * session working copy, not here (ADR-032). Both levels are `WeakMap`s so
308
+ * entries collect normally — no manual invalidation needed.
309
+ */
310
+ trackConfigHydrationCache: WeakMap<object, WeakMap<object, unknown>>;
311
+ constructor(initialPlugins?: (Plugin | PluginLoadRecord | RuntimePluginLoadRecord)[]);
67
312
  pluginConfigurationNamespacedSchemas(): Record<string, unknown>;
68
313
  pluginConfigurationUnnamespacedSchemas(): Record<string, unknown>;
69
314
  pluginConfigurationRootSchemas(): Record<string, unknown>;
70
315
  addPlugin(load: Plugin | PluginLoadRecord | RuntimePluginLoadRecord): this;
71
316
  getPlugin(name: string): Plugin | undefined;
72
317
  hasPlugin(name: string): boolean;
318
+ removePlugin(pluginName: string): this;
73
319
  createPluggableElements(): this;
74
320
  setRootModel(rootModel: AbstractRootModel): this;
75
321
  configure(): this;
76
322
  getElementTypeRecord(groupName: PluggableElementTypeGroup): TypeRecord<PluggableElementBase>;
77
323
  addElementType(groupName: PluggableElementTypeGroup, creationCallback: (pluginManager: PluginManager) => PluggableElementType): this;
78
- getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase | undefined;
324
+ getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase;
79
325
  getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
80
326
  getViewElements(): ViewType[];
81
327
  getTrackElements(): TrackType[];
@@ -84,27 +330,39 @@ export default class PluginManager {
84
330
  getRpcElements(): RpcMethodType[];
85
331
  getDisplayElements(): DisplayType[];
86
332
  getAdapterElements(): AdapterType[];
333
+ /** get a MST type for the union of all specified pluggable MST types */
87
334
  pluggableMstType(groupName: PluggableElementTypeGroup, fieldName: string, fallback?: IAnyType): IAnyType;
88
- pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): IAnyModelType;
335
+ /** get a MST type for the union of all specified pluggable config schemas */
336
+ pluggableConfigSchemaType(typeGroup: PluggableElementTypeGroup, fieldName?: string): IAnyType;
89
337
  jbrequireCache: Map<any, any>;
90
- lib: any;
338
+ get lib(): Record<string, unknown>;
91
339
  load: <FTYPE extends AnyFunction>(lib: FTYPE) => ReturnType<FTYPE>;
92
- jbrequire: (lib: keyof typeof ReExports | AnyFunction | {
340
+ /**
341
+ * Get the re-exported version of the given package name.
342
+ * Throws an error if the package is not re-exported by the plugin manager.
343
+ *
344
+ * @returns the library's default export
345
+ */
346
+ jbrequire: (lib: string | AnyFunction | {
93
347
  default: AnyFunction;
94
348
  }) => any;
95
- getRendererType(typeName: string): RendererType | undefined;
96
- getRendererTypes(): RendererType[];
97
- getAdapterType(typeName: string): AdapterType | undefined;
98
- getTextSearchAdapterType(typeName: string): TextSearchAdapterType | undefined;
99
- getTrackType(typeName: string): TrackType | undefined;
100
- getDisplayType(typeName: string): DisplayType | undefined;
101
- getViewType(typeName: string): ViewType | undefined;
102
- getAddTrackWorkflow(typeName: string): AddTrackWorkflowType | undefined;
103
- getWidgetType(typeName: string): WidgetType | undefined;
104
- getConnectionType(typeName: string): ConnectionType | undefined;
105
- getRpcMethodType(methodName: string): RpcMethodType | undefined;
106
- getInternetAccountType(name: string): InternetAccountType | undefined;
107
- addRendererType(cb: (pm: PluginManager) => RendererType): this;
349
+ getAdapterType(typeName: string): AdapterType;
350
+ /**
351
+ * Whether an adapter type is registered, for a caller walking a config where
352
+ * `type` names a track, a display and an adapter alike — `getAdapterType`
353
+ * throws on a miss, which is right when the name came from a config that
354
+ * claims to be an adapter and wrong when you are asking whether it is one.
355
+ */
356
+ hasAdapterType(typeName: string): boolean;
357
+ getTextSearchAdapterType(typeName: string): TextSearchAdapterType;
358
+ getTrackType(typeName: string): TrackType;
359
+ getDisplayType(typeName: string): DisplayType;
360
+ getViewType(typeName: string): ViewType;
361
+ getAddTrackWorkflow(typeName: string): AddTrackWorkflowType;
362
+ getWidgetType(typeName: string): WidgetType;
363
+ getConnectionType(typeName: string): ConnectionType;
364
+ getRpcMethodType(methodName: string): RpcMethodType<string>;
365
+ getInternetAccountType(name: string): InternetAccountType;
108
366
  addAdapterType(cb: (pm: PluginManager) => AdapterType): this;
109
367
  addTextSearchAdapterType(cb: (pm: PluginManager) => TextSearchAdapterType): this;
110
368
  addTrackType(cb: (pm: PluginManager) => TrackType): this;
@@ -115,11 +373,66 @@ export default class PluginManager {
115
373
  addRpcMethod(cb: (pm: PluginManager) => RpcMethodType): this;
116
374
  addInternetAccountType(cb: (pm: PluginManager) => InternetAccountType): this;
117
375
  addAddTrackWorkflowType(cb: (pm: PluginManager) => AddTrackWorkflowType): this;
118
- addGlyphType(cb: (pm: PluginManager) => GlyphType): this;
119
- getGlyphType(typeName: string): GlyphType | undefined;
120
- getGlyphTypes(): GlyphType[];
121
- addToExtensionPoint<T>(extensionPointName: string, callback: (extendee: T, props: Record<string, unknown>) => T): void;
122
- evaluateExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): unknown;
123
- evaluateAsyncExtensionPoint(extensionPointName: string, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
376
+ /**
377
+ * Contribute entries to an accumulating point.
378
+ *
379
+ * The callback is handed only the props and returns what it wants to add —
380
+ * one entry, several, or `undefined` to add nothing. It never receives the
381
+ * array, which is the whole point: the concatenation happens here, once, so
382
+ * no plugin can write the `[MyEntry]` that silently drops every other
383
+ * plugin's entries. That mistake looked correct to whoever made it, because
384
+ * with one plugin registered there is nothing to drop.
385
+ */
386
+ contributeToExtensionPoint<N extends AccumulatingPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => ExtensionPointEntry<N> | ExtensionPointEntry<N>[] | undefined): void;
387
+ /**
388
+ * Listen to a notification point — one that carries its payload in `props`
389
+ * and whose return value nothing reads. The callback returns nothing;
390
+ * `addToExtensionPoint` rejects these names, so this is the only way in.
391
+ *
392
+ * The reason it is the only way in is the async join below, not the shorter
393
+ * callback. A handler that works asynchronously states so by returning a
394
+ * promise, and the producer waits on the folded value; written by hand
395
+ * through `addToExtensionPoint`, the second async handler's promise silently
396
+ * replaced the first's, so the producer stopped waiting as soon as the
397
+ * *last*-registered handler finished rather than when they all had. That is
398
+ * not a mistake a plugin author can see, which is why it is not left to them.
399
+ */
400
+ listenToExtensionPoint<N extends NotificationPointName>(extensionPointName: N, callback: (props: ExtensionPointProps<N>) => void | Promise<void>): void;
401
+ addToExtensionPoint<N extends Exclude<ExtensionPointName, AccumulatingPointName | NotificationPointName>>(extensionPointName: N, callback: (extendee: ExtensionPointArgs<N>, props: ExtensionPointProps<N>) => ExtensionPointResult<N> | Promise<ExtensionPointResult<N>>): void;
402
+ addToExtensionPoint<T, S extends string = string>(extensionPointName: FoldPointName<S>, callback: (extendee: T, props: Record<string, unknown>) => T | Promise<T>): void;
403
+ /**
404
+ * The one place a callback joins a point's chain. The three public
405
+ * registration methods go through this rather than through each other:
406
+ * `contributeToExtensionPoint` and `listenToExtensionPoint` register on exactly
407
+ * the point names their own signatures reject, so routing them via
408
+ * `addToExtensionPoint` would either fail to compile or force its guard to be
409
+ * loose enough to let a plugin do the same thing by hand.
410
+ */
411
+ private pushExtensionPointCallback;
412
+ evaluateExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
413
+ evaluateExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): unknown;
414
+ /**
415
+ * Fire a *singular* component point — one where exactly one component can
416
+ * render, so a plugin that returns its own discards whatever the plugin
417
+ * before it returned. Same fold as {@link evaluateExtensionPoint}, plus a
418
+ * one-time warning naming the point when more than one callback genuinely
419
+ * takes the slot. A component built by `wrapComponent` still renders the
420
+ * one it wrapped, so it composes and is not counted.
421
+ *
422
+ * Used by {@link PluggableComponent}; producers should render through that
423
+ * rather than calling this directly.
424
+ */
425
+ evaluateComponentExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): ExtensionPointResult<N>;
426
+ /**
427
+ * How many callbacks are registered on `extensionPointName`. For a caller
428
+ * that has to tell "every handler declined" apart from "nobody was
429
+ * listening" — the two look identical in the folded result, and
430
+ * assemblyManager waits out the first but not the second.
431
+ */
432
+ extensionPointCallbackCount(extensionPointName: string): number;
433
+ evaluateAsyncExtensionPoint<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
434
+ evaluateAsyncExtensionPoint<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
435
+ evaluateAsyncExtensionPointStrict<N extends ExtensionPointName>(extensionPointName: N, extendee: ExtensionPointArgs<N>, ...props: ExtensionPointPropsArgs<N>): Promise<ExtensionPointResult<N>>;
436
+ evaluateAsyncExtensionPointStrict<S extends string>(extensionPointName: UnregisteredPointName<S>, extendee: unknown, props?: Record<string, unknown>): Promise<unknown>;
124
437
  }
125
438
  export {};