@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
@@ -1,37 +1,94 @@
1
- import { getEnv, getRoot, getSnapshot, isLateType, isStateTreeNode, isType, resolveIdentifier, types, } from '@jbrowse/mobx-state-tree';
2
- import ConfigSlot from "./configurationSlot.js";
3
- import { isConfigurationSchemaType } from "./util.js";
4
- import { getContainingTrack, getSession } from "../util/index.js";
5
- import { ElementId } from "../util/types/mst.js";
6
- function isEmptyObject(thing) {
7
- return (typeof thing === 'object' &&
8
- !Array.isArray(thing) &&
9
- thing !== null &&
10
- Object.keys(thing).length === 0);
1
+ import { getEnv, isArrayType, isMapType, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
2
+ import { getContainingTrack, getSession } from '../util/mstUtils.js';
3
+ import { ElementId } from '../util/types/mst.js';
4
+ import ConfigSlot from './configurationSlot.js';
5
+ import { getConfigurationSchemaMetadata, registerConfigurationSchema, } from './schemaRegistry.js';
6
+ import { isConfigurationSchemaType, isConstantEntry, isSlotDefinitionEntry, } from './schemaTypes.js';
7
+ function hookList(hook) {
8
+ return hook === undefined ? [] : Array.isArray(hook) ? hook : [hook];
11
9
  }
12
- function isEmptyArray(thing) {
13
- return Array.isArray(thing) && thing.length === 0;
10
+ // base first, then child. Returns the single function unchanged when only one
11
+ // side declares the hook, so the common case never allocates a chain.
12
+ function chainHooks(base, child) {
13
+ return base && child
14
+ ? [...hookList(base), ...hookList(child)]
15
+ : (child ?? base);
16
+ }
17
+ /**
18
+ * Fold a subclass's schema definition over its `baseConfiguration`'s. New slots
19
+ * are added and sub-schema entries replaced wholesale, but a slot the subclass
20
+ * **redeclares merges field-by-field over the base's** — so an override states
21
+ * only what actually differs and inherits the rest. (`type` comes along
22
+ * regardless: it is what marks an entry as a slot rather than a nested
23
+ * sub-schema, per `isSlotDefinitionEntry`.)
24
+ *
25
+ * A subclass that really wants a plain slot states `promotedBase: undefined`,
26
+ * which works *because* this is a spread: a stated `undefined` overwrites the
27
+ * base's value where an omitted key would inherit it. The four cases are pinned
28
+ * by the "baseConfiguration slot override merge" tests.
29
+ */
30
+ function mergeSchemaDefinition(baseDefinition, childDefinition) {
31
+ const merged = {
32
+ ...baseDefinition,
33
+ ...childDefinition,
34
+ };
35
+ for (const [slot, childEntry] of Object.entries(childDefinition)) {
36
+ const baseEntry = baseDefinition[slot];
37
+ // both sides must be slot definitions: a sub-schema (or a constant) is an
38
+ // opaque entry with no fields to fold, so it keeps replace semantics
39
+ if (isSlotDefinitionEntry(baseEntry) && isSlotDefinitionEntry(childEntry)) {
40
+ merged[slot] = { ...baseEntry, ...childEntry };
41
+ }
42
+ }
43
+ return merged;
14
44
  }
15
45
  function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition, inputOptions = {}) {
16
46
  if (typeof modelName !== 'string') {
17
47
  throw new Error('first arg must be string name of the model that this config schema goes with');
18
48
  }
49
+ // if we have a base configuration schema that we are
50
+ // extending, grab the slot definitions from that
19
51
  let schemaDefinition = inputSchemaDefinition;
20
52
  let options = inputOptions;
21
- if (inputOptions.baseConfiguration?.jbrowseSchemaDefinition) {
22
- schemaDefinition = {
23
- ...inputOptions.baseConfiguration.jbrowseSchemaDefinition,
24
- ...schemaDefinition,
25
- };
53
+ const baseMeta = inputOptions.baseConfiguration
54
+ ? getConfigurationSchemaMetadata(inputOptions.baseConfiguration)
55
+ : undefined;
56
+ // A base with no registry entry used to be skipped in silence, producing a
57
+ // schema missing every inherited slot with nothing thrown anywhere, and
58
+ // reachable without doing anything obviously wrong: `isBareConfigurationSchemaType`
59
+ // answers true for a `types.late` wrapper, and
60
+ // `pluginManager.pluggableConfigSchemaType(…)` hands back a `types.union`.
61
+ // Neither is registered, because only the type `ConfigurationSchema` itself
62
+ // returns carries the slot table.
63
+ if (inputOptions.baseConfiguration && !baseMeta) {
64
+ throw new Error(`${modelName}'s baseConfiguration is not a configuration schema: it has no registered slot table, so every slot it was meant to inherit would be dropped silently. Pass the type ConfigurationSchema() returned, not a types.late wrapper, a union (pluginManager.pluggableConfigSchemaType), or a plain MST model.`);
65
+ }
66
+ if (baseMeta) {
67
+ schemaDefinition = mergeSchemaDefinition(baseMeta.definition, schemaDefinition);
68
+ // Everything else merges as a shallow `{...base, ...child}` spread, where
69
+ // the child's value replaces the base's. The four hooks below must not:
70
+ // `createBaseTrackConfig` alone declares two of them, so replace-semantics
71
+ // meant no track config schema could ever declare its own without silently
72
+ // dropping display-stub injection and the legacy-key migration. They
73
+ // compose instead, base first. See MergedConfigurationSchemaOptions.
74
+ const basePreProcess = baseMeta.options.preProcessSnapshot;
75
+ const childPreProcess = inputOptions.preProcessSnapshot;
26
76
  options = {
27
- ...inputOptions.baseConfiguration.jbrowseSchemaOptions,
77
+ ...baseMeta.options,
28
78
  ...inputOptions,
29
79
  baseConfiguration: undefined,
80
+ actions: chainHooks(baseMeta.options.actions, inputOptions.actions),
81
+ views: chainHooks(baseMeta.options.views, inputOptions.views),
82
+ extend: chainHooks(baseMeta.options.extend, inputOptions.extend),
83
+ preProcessSnapshot: basePreProcess && childPreProcess
84
+ ? snapshot => childPreProcess(basePreProcess(snapshot))
85
+ : (childPreProcess ?? basePreProcess),
30
86
  };
31
87
  }
32
88
  return { schemaDefinition, options };
33
89
  }
34
90
  function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
91
+ // now assemble the MST model of the configuration schema
35
92
  const modelDefinition = {};
36
93
  let identifier;
37
94
  if (options.explicitlyTyped) {
@@ -40,54 +97,68 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
40
97
  if (options.explicitIdentifier && options.implicitIdentifier) {
41
98
  throw new Error(`Cannot have both explicit and implicit identifiers in ${modelName}`);
42
99
  }
43
- if (options.explicitIdentifier) {
44
- if (typeof options.explicitIdentifier === 'string') {
45
- modelDefinition[options.explicitIdentifier] = types.identifier;
46
- identifier = options.explicitIdentifier;
47
- }
48
- else {
49
- modelDefinition.id = types.identifier;
50
- identifier = 'id';
51
- }
100
+ // explicit identifiers are plain MST identifiers (caller-supplied id);
101
+ // implicit identifiers auto-generate via ElementId. Both name the field after
102
+ // the option string, or default to `id` when the option is just `true`.
103
+ const idSpec = options.explicitIdentifier
104
+ ? { name: options.explicitIdentifier, idType: types.identifier }
105
+ : options.implicitIdentifier
106
+ ? { name: options.implicitIdentifier, idType: ElementId }
107
+ : undefined;
108
+ if (idSpec) {
109
+ identifier = typeof idSpec.name === 'string' ? idSpec.name : 'id';
110
+ modelDefinition[identifier] = idSpec.idType;
52
111
  }
53
- else if (options.implicitIdentifier) {
54
- if (typeof options.implicitIdentifier === 'string') {
55
- modelDefinition[options.implicitIdentifier] = ElementId;
56
- identifier = options.implicitIdentifier;
57
- }
58
- else {
59
- modelDefinition.id = ElementId;
60
- identifier = 'id';
61
- }
62
- }
63
- const volatileConstants = {
64
- isJBrowseConfigurationSchema: true,
65
- jbrowseSchema: {
66
- modelName,
67
- definition: schemaDefinition,
68
- options,
69
- },
70
- };
112
+ // String/number entries in the schema definition become volatile instance
113
+ // constants (read via `model.someName`). Per-slot metadata lives in the
114
+ // schema registry (a WeakMap keyed by the MST type, see schemaRegistry.ts),
115
+ // not on the instance.
116
+ const volatileConstants = {};
117
+ // Keys of single sub-schema slots (not array/map-of-sub-schema). setSubschema
118
+ // replaces such a node via `.create(data)`, which throws a confusing MST
119
+ // validation error if pointed at an array/map-typed slot, so those are
120
+ // excluded here — collected as the loop classifies each entry rather than
121
+ // re-scanning modelDefinition afterward.
122
+ const subSchemaKeys = new Set();
123
+ // The actual slots, which is a strictly smaller set than `modelDefinition`:
124
+ // that also holds the sub-schema properties and the identifier, neither of
125
+ // which setSlot may write. Same collect-as-you-classify as subSchemaKeys.
126
+ const slotKeys = new Set();
71
127
  for (const [slotName, slotDefinition] of Object.entries(schemaDefinition)) {
72
- if ((isType(slotDefinition) && isLateType(slotDefinition)) ||
73
- isConfigurationSchemaType(slotDefinition)) {
74
- modelDefinition[slotName] = slotDefinition;
128
+ if (isConfigurationSchemaType(slotDefinition)) {
129
+ // a sub-configuration. A bare sub-schema is already stripDefault-wrapped
130
+ // (so it strips when all-default); an array/map of sub-schemas gets
131
+ // wrapped so an empty/default collection is likewise omitted from the
132
+ // snapshot.
133
+ if (isArrayType(slotDefinition)) {
134
+ modelDefinition[slotName] = types.stripDefault(slotDefinition, []);
135
+ }
136
+ else if (isMapType(slotDefinition)) {
137
+ modelDefinition[slotName] = types.stripDefault(slotDefinition, {});
138
+ }
139
+ else {
140
+ modelDefinition[slotName] = slotDefinition;
141
+ subSchemaKeys.add(slotName);
142
+ }
75
143
  }
76
- else if (typeof slotDefinition === 'string' ||
77
- typeof slotDefinition === 'number') {
144
+ else if (isConstantEntry(slotDefinition)) {
78
145
  volatileConstants[slotName] = slotDefinition;
79
146
  }
80
- else if (typeof slotDefinition === 'object') {
81
- if (!slotDefinition.type) {
82
- throw new Error(`no type set for config slot ${modelName}.${slotName}`);
83
- }
147
+ else if (isSlotDefinitionEntry(slotDefinition)) {
148
+ // slotDefinition is narrowed to ConfigSlotDefinition here (no cast)
149
+ slotKeys.add(slotName);
84
150
  try {
85
- modelDefinition[slotName] = ConfigSlot(slotName, slotDefinition);
151
+ modelDefinition[slotName] = ConfigSlot(slotDefinition);
86
152
  }
87
153
  catch (e) {
88
- throw new Error(`invalid config slot definition for ${modelName}.${slotName}: ${e}`);
154
+ throw new Error(`invalid config slot definition for ${modelName}.${slotName}: ${e}`, { cause: e });
89
155
  }
90
156
  }
157
+ else if (typeof slotDefinition === 'object') {
158
+ // an object that's neither a sub-schema nor a slot is almost always a
159
+ // slot definition missing its required `type` field
160
+ throw new Error(`no type set for config slot ${modelName}.${slotName}`);
161
+ }
91
162
  else {
92
163
  throw new Error(`invalid configuration schema definition, "${slotName}" must be either a valid configuration slot definition, a constant, or a nested configuration schema`);
93
164
  }
@@ -96,7 +167,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
96
167
  .model(`${modelName}ConfigurationSchema`, modelDefinition)
97
168
  .actions(self => ({
98
169
  setSubschema(slotName, data) {
99
- if (!isConfigurationSchemaType(modelDefinition[slotName])) {
170
+ if (!subSchemaKeys.has(slotName)) {
100
171
  throw new Error(`${slotName} is not a subschema, cannot replace`);
101
172
  }
102
173
  const newSchema = isStateTreeNode(data)
@@ -105,126 +176,276 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
105
176
  self[slotName] = newSchema;
106
177
  return newSchema;
107
178
  },
179
+ // generic slot setter the config editor's slot facade routes through. A
180
+ // slot is a bare value-union property, so this is a plain assignment.
181
+ //
182
+ // **Don't weaken the membership check to a warning, and don't check
183
+ // against `modelDefinition`** — that also holds the identifier and the
184
+ // sub-schema properties, neither of which is a write this action is for.
185
+ // Slot-name safety is a write guard (ADR-052); `setSlot`'s tests in
186
+ // `configurationSchema.test.ts` pin both halves. `slotKeys` already has
187
+ // base-schema slots merged in, so an inherited slot passes.
188
+ setSlot(slotName, value) {
189
+ if (!slotKeys.has(slotName)) {
190
+ // the sub-schema branch re-classifies off the definition rather than
191
+ // carrying a second Set: it runs only on the way to a throw, and the
192
+ // predicate is the same one the loop above classified with
193
+ throw new Error(isConfigurationSchemaType(schemaDefinition[slotName])
194
+ ? `${slotName} is a sub-schema on ${modelName}, not a config slot — replace it with setSubschema`
195
+ : `${modelName} has no config slot "${slotName}". Valid slots: ${[
196
+ ...slotKeys,
197
+ ]
198
+ .sort()
199
+ .join(', ')}`);
200
+ }
201
+ self[slotName] = value;
202
+ },
108
203
  }));
109
204
  if (Object.keys(volatileConstants).length) {
110
- completeModel = completeModel.volatile(() => volatileConstants);
205
+ completeModel = completeModel.volatile(( /* self */) => volatileConstants);
111
206
  }
112
- if (options.actions) {
113
- completeModel = completeModel.actions(options.actions);
207
+ // one MST call per entry, base's before the subclass's — chaining is what
208
+ // makes the base's members visible on `self` inside the subclass's function
209
+ for (const hook of hookList(options.actions)) {
210
+ completeModel = completeModel.actions(hook);
114
211
  }
115
- if (options.views) {
116
- completeModel = completeModel.views(options.views);
212
+ for (const hook of hookList(options.views)) {
213
+ completeModel = completeModel.views(hook);
117
214
  }
118
- if (options.extend) {
119
- completeModel = completeModel.extend(options.extend);
215
+ for (const hook of hookList(options.extend)) {
216
+ completeModel = completeModel.extend(hook);
217
+ }
218
+ if (options.preProcessSnapshot) {
219
+ completeModel = completeModel.preProcessSnapshot(options.preProcessSnapshot);
120
220
  }
121
221
  const identifierDefault = identifier ? { [identifier]: 'placeholderId' } : {};
122
222
  const modelDefault = options.explicitlyTyped
123
223
  ? { type: modelName, ...identifierDefault }
124
224
  : identifierDefault;
125
- const defaultSnap = getSnapshot(completeModel.create(modelDefault));
126
- completeModel = completeModel.postProcessSnapshot(snap => {
127
- const newSnap = {};
128
- let matchesDefault = true;
129
- for (const [key, value] of Object.entries(snap)) {
130
- if (matchesDefault) {
131
- if (typeof defaultSnap[key] === 'object' && typeof value === 'object') {
132
- if (JSON.stringify(defaultSnap[key]) !== JSON.stringify(value)) {
133
- matchesDefault = false;
134
- }
135
- }
136
- else if (defaultSnap[key] !== value) {
137
- matchesDefault = false;
138
- }
139
- }
140
- if (value !== undefined &&
141
- volatileConstants[key] === undefined &&
142
- !isEmptyObject(value) &&
143
- !isEmptyArray(value)) {
144
- newSnap[key] = value;
145
- }
146
- }
147
- if (matchesDefault) {
148
- return {};
149
- }
150
- return newSnap;
151
- });
152
- if (options.preProcessSnapshot) {
153
- completeModel = completeModel.preProcessSnapshot(options.preProcessSnapshot);
154
- }
155
- return types.optional(completeModel, modelDefault);
225
+ // stripDefault (not optional) so a nested all-default sub-schema is omitted
226
+ // from its parent's snapshot: the slot props strip themselves, the sub-schema
227
+ // collapses to its default, and the parent's stripDefault drops the key.
228
+ const wrappedModel = types.stripDefault(completeModel, modelDefault);
229
+ // Register metadata against BOTH handles: the inner model (what getType(node)
230
+ // returns for a live config — the config editor's slot facade looks it up
231
+ // from there) and the stripDefault wrapper (what ConfigurationSchema returns
232
+ // and what sub-schema properties hold), so a lookup succeeds from either.
233
+ const metadata = { definition: schemaDefinition, options };
234
+ registerConfigurationSchema(completeModel, metadata);
235
+ registerConfigurationSchema(wrappedModel, metadata);
236
+ return wrappedModel;
156
237
  }
157
238
  export function ConfigurationSchema(modelName, inputSchemaDefinition, inputOptions) {
158
239
  const { schemaDefinition, options } = preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition, inputOptions);
159
- const schemaType = makeConfigurationSchemaModel(modelName, schemaDefinition, options);
160
- schemaType.isJBrowseConfigurationSchema = true;
161
- schemaType.jbrowseSchemaDefinition = schemaDefinition;
162
- schemaType.jbrowseSchemaOptions = options;
163
- return schemaType;
240
+ return makeConfigurationSchemaModel(modelName, schemaDefinition, options);
164
241
  }
242
+ // The hydration cache lives on the PluginManager instance (see
243
+ // trackConfigHydrationCache's doc comment there and ADR-031), not as a
244
+ // module-level singleton: it must never hand a track resolved on one
245
+ // PluginManager instance a node built with another instance's env, and
246
+ // scoping it to the instance rules that out structurally rather than by
247
+ // convention. Nested a second level by schemaType, since one PluginManager
248
+ // registers a distinct schemaType per track type.
249
+ function frozenTrackHydrationCache(pluginManager, schemaType) {
250
+ const byType = pluginManager.trackConfigHydrationCache;
251
+ let cache = byType.get(schemaType);
252
+ if (!cache) {
253
+ cache = new WeakMap();
254
+ byType.set(schemaType, cache);
255
+ }
256
+ return cache;
257
+ }
258
+ // The frozen -> live half of TrackConfigurationReference's `get`, shared with
259
+ // hydrateTrackConfig below so there is one hydration and one cache rather than
260
+ // two that can drift on which env or which key they use.
261
+ function hydrateInto(pluginManager, schemaType, frozen) {
262
+ const cache = frozenTrackHydrationCache(pluginManager, schemaType);
263
+ const cached = cache.get(frozen);
264
+ if (cached) {
265
+ return cached;
266
+ }
267
+ const model = schemaType.create(frozen, { pluginManager });
268
+ cache.set(frozen, model);
269
+ return model;
270
+ }
271
+ /**
272
+ * #api core/configuration
273
+ * Hydrate a plain track config into a live config node, dispatching on its
274
+ * `type` to find the schema. `session.tracks` holds `types.frozen` plain
275
+ * objects until something references a track (ADR-031), so a caller handed one
276
+ * of those has a config that reads nothing but what was literally authored: a
277
+ * slot at its schema default is absent, `preProcessSnapshot` has not run, and
278
+ * nothing that walks a live node — the promotable cascade above all — applies
279
+ * to it.
280
+ *
281
+ * For the callers that need the resolved answer rather than the authored one
282
+ * and cannot know which of the two they were handed. The About dialog's "Copy
283
+ * config" is the case this exists for: it is reached from two menus, and one of
284
+ * them passes a `session.tracks` entry.
285
+ *
286
+ * Returns **undefined** rather than throwing when the config names a track type
287
+ * no plugin registered, or when it is invalid enough that `create` rejects it —
288
+ * an un-hydrated config has never been validated, so a dialog that opens over
289
+ * it must not be the thing that discovers this. Callers fall back to treating
290
+ * it as the plain object it is.
291
+ *
292
+ * Shares `TrackConfigurationReference`'s per-PluginManager cache, so hydrating
293
+ * the same entry twice returns the same node and a track that gets opened later
294
+ * reuses it.
295
+ */
296
+ export function hydrateTrackConfig(pluginManager, config) {
297
+ const type = config.type;
298
+ if (typeof type !== 'string') {
299
+ return undefined;
300
+ }
301
+ try {
302
+ // getTrackType throws on an unregistered name rather than returning
303
+ // undefined, so it is inside the guard with `create` — the two failures are
304
+ // the same failure (nothing here can build this config) and neither should
305
+ // reach a dialog that is only trying to show it
306
+ const { configSchema } = pluginManager.getTrackType(type);
307
+ return hydrateInto(pluginManager, configSchema, config);
308
+ }
309
+ catch (e) {
310
+ console.error(e);
311
+ return undefined;
312
+ }
313
+ }
314
+ // A slot holding either an id string (resolved through `ref`) or a full inline
315
+ // config snapshot (held as a standalone schema instance). Both reference kinds
316
+ // resolve to `schemaType` instances, so MST can't auto-dispatch on the instance
317
+ // side — the explicit snapshot dispatcher (string → ref, object → schema)
318
+ // disambiguates. Shared by TrackConfigurationReference/DisplayConfigurationReference.
319
+ function idOrSnapshotUnion(ref, schemaType) {
320
+ return types.union({
321
+ dispatcher: snapshot => (typeof snapshot === 'string' ? ref : schemaType),
322
+ }, ref, schemaType);
323
+ }
324
+ /**
325
+ * Reference to a track configuration. Snapshot output is the trackId string.
326
+ *
327
+ * One load-bearing complication: **`types.union(trackRef, schemaType)` accepts a
328
+ * string id OR a full config.** A view that synthesizes a track nobody else can
329
+ * draw — a read-vs-ref synteny band, an SV inspector row, a circular view's
330
+ * added track — writes the config here rather than registering it in
331
+ * `session.tracks`, and it then lives and dies with the track that holds it.
332
+ * `ReadVsRef.test.tsx` and `SVInspector.test.tsx` are the canaries.
333
+ *
334
+ * NOTE: don't add `as SCHEMATYPE` to the return value. It narrows SnapshotIn
335
+ * to just the object branch, forcing callers to wrap string ids in
336
+ * `@ts-expect-error`. The inferred union SnapshotIn is `string | SnapshotIn<schema>`.
337
+ */
165
338
  export function TrackConfigurationReference(schemaType) {
166
339
  const trackRef = types.reference(schemaType, {
167
340
  get(id, parent) {
168
341
  const session = getSession(parent);
169
- let ret = session.getTracksById()[id];
342
+ // Per-id lookup: subscribes only to this trackId's derivation, so
343
+ // resolving one track's config doesn't re-render the others. Derived on
344
+ // read, so it's fresh during hydration and add-and-show — no dual path.
345
+ let ret = session.getTrackById(String(id));
170
346
  if (!ret) {
171
- ret = resolveIdentifier(schemaType, getRoot(parent), id);
347
+ throw new Error(`Could not resolve trackId "${id}"`);
172
348
  }
173
- if (!ret) {
174
- throw new Error(`Could not resolve identifier "${id}"`);
349
+ if (!isStateTreeNode(ret)) {
350
+ // A non-admin session hands back a private, per-track working copy so a
351
+ // shown track's in-place quick-edits (setSlot) mutate that copy and
352
+ // never the shared frozen base node (see agent-docs/ADR-032). Admin and
353
+ // embedded sessions return undefined here and fall through to the frozen
354
+ // hydration cache (ADR-031) — admin edits the frozen entry in place.
355
+ const editable = session.getEditableTrackConfig?.(String(id), ret, schemaType);
356
+ if (editable) {
357
+ ret = editable;
358
+ }
359
+ else {
360
+ const env = getEnv(parent);
361
+ ret = hydrateInto(env.pluginManager, schemaType, ret);
362
+ }
175
363
  }
176
- return isStateTreeNode(ret) ? ret : schemaType.create(ret, getEnv(parent));
364
+ return ret;
177
365
  },
178
366
  set(value) {
179
367
  return value.trackId;
180
368
  },
181
369
  });
182
- return types.snapshotProcessor(types.union({
183
- dispatcher: snapshot => typeof snapshot === 'string' ? trackRef : schemaType,
184
- }, trackRef, schemaType), {
185
- postProcessor(snapshot) {
186
- if (typeof snapshot === 'object' &&
187
- snapshot !== null &&
188
- 'trackId' in snapshot) {
189
- return snapshot.trackId;
190
- }
191
- return snapshot;
192
- },
193
- });
370
+ return idOrSnapshotUnion(trackRef, schemaType);
194
371
  }
372
+ /**
373
+ * Reference to a display configuration. Looked up inside the containing track
374
+ * config's `displays` array. Snapshot output is the displayId string.
375
+ *
376
+ * Resolution order:
377
+ * 1. by displayId
378
+ * 2. by `parent.type` — handles old sessions where the saved displayId
379
+ * no longer matches but a display of the same type exists on the track
380
+ *
381
+ * Step 2 is the safety net because `baseTrackConfig.preProcessSnapshot`
382
+ * already injects a stub display for every registered displayType on the
383
+ * track, so a same-type lookup always succeeds at runtime for properly
384
+ * loaded tracks. An older third step auto-created a *detached* config when
385
+ * neither matched — that produced an orphaned MST node whose edits silently
386
+ * didn't persist. Removed in favor of a clear throw, since
387
+ * preProcessSnapshot's injection makes the path effectively dead.
388
+ *
389
+ * Union-with-schemaType branch is for the same reason as `TrackConfigurationReference`:
390
+ * `CircularView.addTrackConf` passes inline display configs as MST instances.
391
+ */
195
392
  export function DisplayConfigurationReference(schemaType) {
196
393
  const displayRef = types.reference(schemaType, {
197
394
  get(id, parent) {
395
+ // track.configuration is a hydrated MST node (hydrated lazily via
396
+ // TrackConfigurationReference), so its displays array contains MST nodes.
198
397
  const track = getContainingTrack(parent);
199
- const displays = track.configuration.displays || [];
200
- let ret = displays.find((d) => d.displayId === id);
201
- if (!ret) {
202
- const displayType = `${id}`.split('-').slice(1).join('-');
203
- if (displayType) {
204
- ret = { displayId: `${id}`, type: displayType };
205
- }
398
+ const displays = track.configuration.displays;
399
+ const displayType = parent.type;
400
+ let ret = displays.find(d => d.displayId === id);
401
+ // Fallback: match by display type when the displayId isn't found.
402
+ // baseTrackConfig.preProcessSnapshot injects a display entry for every
403
+ // registered displayType for the track, so id-mismatch (e.g. an old
404
+ // session with a different displayId convention) finds a same-type
405
+ // entry here. The `if (displayType)` guard prevents an undefined
406
+ // parent.type from silently matching a display whose `.type` is also
407
+ // undefined.
408
+ if (!ret && displayType) {
409
+ ret = displays.find(d => d.type === displayType);
206
410
  }
207
411
  if (!ret) {
208
- throw new Error(`Display configuration "${id}" not found`);
412
+ const trackId = track.configuration.trackId;
413
+ throw new Error(`Display configuration "${id}" not found on track "${trackId}" (looked up by displayId, then by type "${displayType ?? '<no type on parent>'}")`);
209
414
  }
210
- return isStateTreeNode(ret) ? ret : schemaType.create(ret, getEnv(parent));
415
+ return ret;
211
416
  },
212
417
  set(value) {
213
418
  return value.displayId;
214
419
  },
215
420
  });
216
- return types.union({
217
- dispatcher: snapshot => typeof snapshot === 'string' ? displayRef : schemaType,
218
- }, displayRef, schemaType);
421
+ return idOrSnapshotUnion(displayRef, schemaType);
219
422
  }
423
+ /**
424
+ * Dispatch by the schema's identifier: `trackId` → track-ref (resolves through
425
+ * `session.getTrackById`), `displayId` → display-ref (resolves through the
426
+ * parent track's displays array), anything else → plain reference.
427
+ *
428
+ * Display schemas must declare `explicitIdentifier: 'displayId'` (directly or
429
+ * via `baseConfiguration: baseLinearDisplayConfigSchema`, which merges its
430
+ * options through `preprocessConfigurationSchemaArguments`).
431
+ *
432
+ * The return is annotated `IConfigurationReference<SCHEMATYPE>` (see its doc)
433
+ * so `self.configuration` carries the concrete schema. The three runtime
434
+ * branches produce MST reference/union types over `schemaType` that are
435
+ * assignable to that annotation, so `return ref` needs no cast — and must not
436
+ * get one: a prior `as SCHEMATYPE` was dropped because it narrowed `SnapshotIn`
437
+ * to just the object branch and forced callers pushing string ids to
438
+ * `@ts-expect-error` (see `TrackConfigurationReference`'s note).
439
+ */
220
440
  export function ConfigurationReference(schemaType) {
221
- const name = schemaType.name;
222
- if (name.includes('TrackConfigurationSchema') &&
223
- !name.includes('DisplayConfigurationSchema')) {
224
- return TrackConfigurationReference(schemaType);
225
- }
226
- if (name.includes('DisplayConfigurationSchema')) {
227
- return DisplayConfigurationReference(schemaType);
228
- }
229
- return types.union(types.reference(schemaType), schemaType);
441
+ const id = getConfigurationSchemaMetadata(schemaType)?.options.explicitIdentifier;
442
+ const ref = id === 'trackId'
443
+ ? TrackConfigurationReference(schemaType)
444
+ : id === 'displayId'
445
+ ? DisplayConfigurationReference(schemaType)
446
+ : // Plain (non-track/display) ref. The union accepts either an id
447
+ // string (resolved via `types.reference`) or an inline schema
448
+ // snapshot (held as a standalone schema instance).
449
+ types.union(types.reference(schemaType), schemaType);
450
+ return ref;
230
451
  }