@jbrowse/core 4.3.0 → 5.0.0-beta.10

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 (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  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 -5
  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 +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  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 +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
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  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
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  1046. package/esm/util/sessionStorage.d.ts +1 -0
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  1052. package/esm/util/shapeNames.d.ts +7 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
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  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
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  1106. package/esm/util/types/isAny.d.ts +11 -0
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  1110. package/esm/util/types/predicate.d.ts +9 -0
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  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,239 +1,246 @@
1
1
  import { types } from '@jbrowse/mobx-state-tree';
2
- import { getEnv } from "../util/index.js";
3
- import { stringToJexlExpression } from "../util/jexlStrings.js";
4
- import { FileLocation } from "../util/types/mst.js";
5
- function isValidColorString(_str) {
6
- return true;
2
+ import { isCssColor } from '../util/cssColorParse.js';
3
+ import { isJexl, stringToJexlExpression } from '../util/jexlStrings.js';
4
+ import { FileLocation, JexlExpressionString } from '../util/types/mst.js';
5
+ import { isCallbackValue } from './slotValueUtils.js';
6
+ // What a color slot admits is what the painters parse (`isCssColor`), plus the
7
+ // empty string a slot such as `outlineColor` spells "none" with; a field name
8
+ // written where a color goes used to load and paint the invalid sentinel.
9
+ function notAColor(value) {
10
+ return `${JSON.stringify(value)} is not a color. A color is a CSS color: a name like "red" or "steelblue", "#rgb" / "#rrggbb" / "#rrggbbaa", "rgb()" / "rgba()" / "hsl()" / "hsla()", or "transparent"; a color computed per feature is a "jexl:" callback, in a slot that takes one`;
7
11
  }
8
- const typeModels = {
9
- stringArray: types.array(types.string),
10
- stringArrayMap: types.map(types.array(types.string)),
11
- numberMap: types.map(types.number),
12
- boolean: types.boolean,
13
- color: types.refinement('Color', types.string, isValidColorString),
14
- integer: types.integer,
15
- number: types.number,
16
- string: types.string,
17
- text: types.string,
18
- fileLocation: FileLocation,
19
- frozen: types.frozen(),
20
- };
21
- const fallbackDefaults = {
22
- stringArray: [],
23
- stringArrayMap: {},
24
- numberMap: {},
25
- boolean: true,
26
- color: 'black',
27
- integer: 1,
28
- number: 1,
29
- string: '',
30
- text: '',
31
- fileLocation: { uri: '/path/to/resource.txt', locationType: 'UriLocation' },
32
- frozen: {},
33
- };
34
- const literalJSON = (self) => ({
35
- views: {
36
- get valueJSON() {
37
- return self.value;
38
- },
39
- },
12
+ const CssColorType = types.refinement('CssColor', types.string, value => value === '' || isCssColor(value), notAColor);
13
+ // An entry of a colour list has no "none" to spell, so '' is refused with the
14
+ // rest of what is not a colour.
15
+ const CssColorEntryType = types.refinement('CssColorEntry', types.string, isCssColor, notAColor);
16
+ const MaybeFileLocation = types.snapshotProcessor(types.maybe(FileLocation), {
17
+ preProcessor: (snap) => snap && 'uri' in snap && snap.uri === '' ? undefined : snap,
40
18
  });
41
- const objectJSON = (self) => ({
42
- views: {
43
- get valueJSON() {
44
- return JSON.stringify(self.value);
45
- },
19
+ // Single source of truth for the builtin slot type names, pairing each with its
20
+ // MST value type and its editor fallback default. Keeping model + fallback in
21
+ // one table means adding a slot type is one edit and can't half-register.
22
+ //
23
+ // `satisfies` rather than an annotation: a `Record<string, …>` annotation
24
+ // widens the keys to `string`, which is what let `type: 'enum'` — a name this
25
+ // table has never had — compile for years and silently lose the config
26
+ // editor's dropdown. The literal keys are what `ConfigSlotType` below is made
27
+ // of.
28
+ const slotTypes = {
29
+ stringArray: { model: types.array(types.string), fallbackDefault: [] },
30
+ expressionArray: {
31
+ model: types.array(JexlExpressionString),
32
+ fallbackDefault: [],
46
33
  },
47
- });
48
- const typeModelExtensions = {
49
- fileLocation: objectJSON,
50
- number: literalJSON,
51
- integer: literalJSON,
52
- boolean: literalJSON,
53
- frozen: objectJSON,
54
- stringArray: (self) => ({
55
- views: {
56
- get valueJSON() {
57
- return JSON.stringify(self.value);
58
- },
59
- },
60
- actions: {
61
- add(val) {
62
- self.value.push(val);
63
- },
64
- removeAtIndex(idx) {
65
- self.value.splice(idx, 1);
66
- },
67
- setAtIndex(idx, val) {
68
- self.value[idx] = val;
69
- },
70
- },
71
- }),
72
- stringArrayMap: (self) => ({
73
- views: {
74
- get valueJSON() {
75
- return JSON.stringify(self.value);
76
- },
77
- },
78
- actions: {
79
- add(key, val) {
80
- self.value.set(key, val);
81
- },
82
- remove(key) {
83
- self.value.delete(key);
84
- },
85
- addToKey(key, val) {
86
- const ar = self.value.get(key);
87
- if (!ar) {
88
- throw new Error(`${key} not found`);
89
- }
90
- ar.push(val);
91
- },
92
- removeAtKeyIndex(key, idx) {
93
- const ar = self.value.get(key);
94
- if (!ar) {
95
- throw new Error(`${key} not found`);
96
- }
97
- ar.splice(idx, 1);
98
- },
99
- setAtKeyIndex(key, idx, val) {
100
- const ar = self.value.get(key);
101
- if (!ar) {
102
- throw new Error(`${key} not found`);
103
- }
104
- ar[idx] = val;
105
- },
106
- },
107
- }),
108
- numberMap: (self) => ({
109
- views: {
110
- get valueJSON() {
111
- return JSON.stringify(self.value);
112
- },
113
- },
114
- actions: {
115
- add(key, val) {
116
- self.value.set(key, val);
117
- },
118
- remove(key) {
119
- self.value.delete(key);
120
- },
34
+ colorArray: { model: types.array(CssColorEntryType), fallbackDefault: [] },
35
+ stringArrayMap: {
36
+ model: types.map(types.array(types.string)),
37
+ fallbackDefault: {},
38
+ },
39
+ numberMap: { model: types.map(types.number), fallbackDefault: {} },
40
+ stringMap: { model: types.map(types.string), fallbackDefault: {} },
41
+ boolean: { model: types.boolean, fallbackDefault: true },
42
+ color: { model: CssColorType, fallbackDefault: 'black' },
43
+ integer: { model: types.integer, fallbackDefault: 1 },
44
+ number: { model: types.number, fallbackDefault: 1 },
45
+ // The `maybe*` types spend `undefined` on "not explicitly set", which is the
46
+ // one value no config can spell and so the only reliable way to say it — a
47
+ // computed/auto fallback, e.g. a drag-resized track height.
48
+ maybeNumber: { model: types.maybe(types.number) },
49
+ maybeBoolean: { model: types.maybe(types.boolean) },
50
+ // for a slot whose unset state means "decide from the data" — a feature's own
51
+ // BED itemRgb, say
52
+ maybeColor: { model: types.maybe(CssColorType) },
53
+ // object-valued, e.g. alignments `sortedBy`
54
+ maybeFrozen: { model: types.maybe(types.frozen()) },
55
+ // for text whose unset state is a third thing beside some text and none: an
56
+ // axis title is derived while unset, and drawn bare once it is ''
57
+ maybeString: { model: types.maybe(types.string) },
58
+ string: { model: types.string, fallbackDefault: '' },
59
+ text: { model: types.string, fallbackDefault: '' },
60
+ // a field the display reads per feature: a name, a dotted path, or a
61
+ // `jexl:` expression, which the display evaluates and the reader never does
62
+ featureField: { model: types.string, fallbackDefault: '' },
63
+ fileLocation: {
64
+ model: FileLocation,
65
+ fallbackDefault: {
66
+ uri: '/path/to/resource.txt',
67
+ locationType: 'UriLocation',
121
68
  },
122
- }),
69
+ },
70
+ // for a sidecar the adapter works without: unset means no file is
71
+ // configured, and so does the `{ uri: '' }` a cleared URL field in the
72
+ // config editor writes
73
+ maybeFileLocation: { model: MaybeFileLocation },
74
+ frozen: { model: types.frozen(), fallbackDefault: {} },
123
75
  };
124
- const JexlStringType = types.refinement('JexlString', types.string, str => str.startsWith('jexl:'));
125
- function json(value) {
126
- return value?.toJSON ? value.toJSON() : `"${value}"`;
76
+ // The types with no builtin table entry, because the author supplies the
77
+ // `types.enumeration` as `model` and `ConfigSlot` wraps it: in `types.maybe`
78
+ // for `maybeStringEnum`, in `types.array` for `stringEnumArray`. Named once,
79
+ // and spliced into both the type union and the runtime set below so those two
80
+ // cannot drift apart.
81
+ const ENUM_SLOT_TYPES = [
82
+ 'stringEnum',
83
+ 'maybeStringEnum',
84
+ 'stringEnumArray',
85
+ ];
86
+ /**
87
+ * The same closed set, at runtime, because the type alone does not close it for
88
+ * the callers that matter most: `ConfigSlot` is plugin-facing, and a JS plugin
89
+ * or one built against an older core reaches it with no checking at all. Those
90
+ * are exactly the callers that hit the silent-degradation trap above, and
91
+ * `type: 'enum'` — a name this table has never had — is the one that did.
92
+ *
93
+ * Typed `Set<string>` rather than `Set<ConfigSlotType>` so the membership test
94
+ * stays a question TypeScript has not already answered for in-tree callers. It
95
+ * is a real runtime check, not a restatement of the signature.
96
+ */
97
+ const CONFIG_SLOT_TYPE_NAMES = new Set([
98
+ ...Object.keys(slotTypes),
99
+ ...ENUM_SLOT_TYPES,
100
+ ]);
101
+ // Lookup view over the table. The two enum types are legal `ConfigSlotType`s
102
+ // with no entry, so indexing by the union has to tolerate a miss — this states
103
+ // that in the type rather than casting it away at each call.
104
+ const builtinSlotTypes = slotTypes;
105
+ // The slot types whose default is `undefined` — the genuine "unset" state,
106
+ // distinguishable from every value a config can spell. Mostly derived from the
107
+ // table above (they're exactly the entries with no `fallbackDefault`, since
108
+ // "unset" is their fixed form) so the two can't drift. `maybeStringEnum` is
109
+ // named explicitly because, like plain `stringEnum`, it has no builtin model:
110
+ // the author supplies the enumeration and `ConfigSlot` wraps it in
111
+ // `types.maybe`.
112
+ const MAYBE_TYPES = new Set([
113
+ ...Object.entries(slotTypes)
114
+ .filter(([, spec]) => spec.fallbackDefault === undefined)
115
+ .map(([name]) => name),
116
+ 'maybeStringEnum',
117
+ ]);
118
+ const JexlStringType = types.refinement('JexlString', types.string, isJexl);
119
+ const CALLBACK_SLOTS = 'a slot that takes a callback declares the names it reads, which its config docs list as callback args';
120
+ function notACallbackSlot(value) {
121
+ return `${JSON.stringify(value)} is a jexl: callback, and this slot takes a value: ${CALLBACK_SLOTS}`;
127
122
  }
128
- export default function ConfigSlot(slotName, { description = '', model, type, defaultValue, contextVariable = [], }) {
129
- if (!type) {
130
- throw new Error('type name required');
131
- }
132
- if (!model) {
133
- model = typeModels[type];
123
+ /** Why the slot `name`, of type `type`, refuses `value` on a write. */
124
+ export function slotWriteRefusal(name, type, value) {
125
+ const bare = type === 'expressionArray' && Array.isArray(value)
126
+ ? value.find(entry => !isJexl(entry))
127
+ : undefined;
128
+ return isJexl(value)
129
+ ? `${name} takes no jexl: callback, and ${JSON.stringify(value)} is one: ${CALLBACK_SLOTS}`
130
+ : bare !== undefined
131
+ ? `${name} takes jexl: expressions, and ${JSON.stringify(bare)} is not an expression: write it with its prefix, as "jexl:${String(bare)}"`
132
+ : `${name} is a ${type} slot and cannot take ${JSON.stringify(value)}`;
133
+ }
134
+ function refusingCallbacks(model) {
135
+ return types.refinement(model, value => !isJexl(value), notACallbackSlot);
136
+ }
137
+ /**
138
+ * A configuration slot is a plain MST property holding the slot's value type,
139
+ * or, where the slot declares a `contextVariable`, that or a `jexl:...`
140
+ * callback string. Every other slot refuses a `jexl:` string, so a callback
141
+ * the reader would evaluate is one the schema says it takes. A `featureField`
142
+ * holds a `jexl:` expression as its value, which the display evaluates per
143
+ * feature. The value lives directly on the parent configuration model — there
144
+ * is no per-slot sub-model. `types.stripDefault` omits the property from the
145
+ * parent snapshot when it equals the default, so saved sessions stay minimal.
146
+ * Per-slot metadata (type/description/defaultValue/contextVariable) lives in
147
+ * the schema registry (a WeakMap keyed by the MST type, see
148
+ * schemaRegistry.ts); jexl callbacks are evaluated on read by
149
+ * `readConfObject`.
150
+ *
151
+ * Interning the returned type on `(type, model, defaultValue)` was prototyped
152
+ * and declined: a session builds 1197 slot types for 222 distinct ones, and
153
+ * removing the repeats moves neither the time nor the heap
154
+ * (`config-schema-construction`, published in `reference/EAGER_BUNDLE.md`).
155
+ */
156
+ export default function ConfigSlot(definition) {
157
+ const { model, type, defaultValue } = definition;
158
+ if (!CONFIG_SLOT_TYPE_NAMES.has(type)) {
159
+ throw new Error(`config slot needs a known type name, got ${JSON.stringify(type)}`);
134
160
  }
135
- if (!model) {
161
+ const valueModel = model ?? builtinSlotTypes[type]?.model;
162
+ if (!valueModel) {
136
163
  throw new Error(`no builtin config slot type "${type}", and no 'model' param provided`);
137
164
  }
138
- if (defaultValue === undefined) {
165
+ // the `maybe*` types intentionally default to `undefined` (the "unset"
166
+ // state); every other slot type must declare a concrete default so a missing
167
+ // one is caught as an authoring mistake.
168
+ if (defaultValue === undefined && !MAYBE_TYPES.has(type)) {
139
169
  throw new Error("no 'defaultValue' provided");
140
170
  }
141
- const configSlotModelName = `${slotName.charAt(0).toUpperCase()}${slotName.slice(1)}ConfigSlot`;
142
- let slot = types
143
- .model(configSlotModelName, {
144
- name: types.literal(slotName),
145
- description: types.literal(description),
146
- type: types.literal(type),
147
- value: types.optional(types.union(JexlStringType, model), defaultValue),
148
- })
149
- .volatile(() => ({
150
- contextVariable,
151
- }))
152
- .views(self => ({
153
- get isCallback() {
154
- return String(self.value).startsWith('jexl:');
155
- },
156
- }))
157
- .views(self => ({
158
- get expr() {
159
- return self.isCallback
160
- ? stringToJexlExpression(String(self.value), getEnv(self).pluginManager.jexl)
161
- : {
162
- eval: () => self.value,
163
- };
164
- },
165
- get valueJSON() {
166
- return self.isCallback ? undefined : json(self.value);
167
- },
168
- }))
169
- .views(self => ({
170
- getValue(args = {}) {
171
- const v = self.value;
172
- return typeof v === 'string' && v.startsWith('jexl:')
173
- ? self.expr.eval(args)
174
- : v;
175
- },
176
- }))
177
- .preProcessSnapshot(val => typeof val === 'object' && val.name === slotName
178
- ? val
179
- : {
180
- name: slotName,
181
- description,
182
- type,
183
- value: val,
184
- })
185
- .postProcessSnapshot(snap => {
186
- if (typeof snap.value === 'object') {
187
- return JSON.stringify(snap.value) !== JSON.stringify(defaultValue)
188
- ? snap.value
189
- : undefined;
171
+ // The inverse of the `defaultValue === undefined` check above, and the half
172
+ // that had no guard. A `maybe*` slot whose default is concrete can never *be*
173
+ // unset — no config can spell `undefined` — so the unset state such a slot
174
+ // exists to express (auto-fit, decide-from-the-data, inherit) is unreachable
175
+ // and the branch reading it never runs. There is no symptom: the slot reads as
176
+ // a perfectly good value everywhere.
177
+ //
178
+ // The way this happens is **inheritance**, which is why the type can't catch
179
+ // it: a `maybe*` override of a plain base slot inherits the base's concrete
180
+ // default through the definition spread, and the override's own literal looks
181
+ // right. `LinearMafDisplay.height` over `BaseLinearDisplay`'s `number`/100 is
182
+ // the case in the repo, and only that display's own tests noticed.
183
+ if (defaultValue !== undefined && MAYBE_TYPES.has(type)) {
184
+ throw new Error(`a "${type}" slot cannot have a concrete defaultValue (${JSON.stringify(defaultValue)}): unset is the state a maybe* slot exists for, and no config can spell undefined, so it would be unreachable. If this slot overrides a base slot, the base's defaultValue merged in — state 'defaultValue: undefined' to overwrite it. Otherwise use the non-maybe form of the type.`);
185
+ }
186
+ const callback = !!definition.contextVariable?.length;
187
+ if (type === 'featureField' && callback) {
188
+ throw new Error('a "featureField" slot names a field the display reads per feature, and its jexl: expression is evaluated there, never called with a contextVariable. If this slot overrides a base callback slot, state \'contextVariable: undefined\'.');
189
+ }
190
+ if (!callback && isJexl(defaultValue)) {
191
+ throw new Error(`the defaultValue ${JSON.stringify(defaultValue)} is a jexl: callback, so the slot declares the contextVariable names it reads`);
192
+ }
193
+ const value = enumShaped(type, valueModel);
194
+ return types.stripDefault(callback
195
+ ? types.union(JexlStringType, value)
196
+ : type === 'featureField'
197
+ ? value
198
+ : refusingCallbacks(value), defaultValue);
199
+ }
200
+ // The author writes an enum slot's plain vocabulary, and the slot's shape
201
+ // around it is added here.
202
+ function enumShaped(type, model) {
203
+ return type === 'maybeStringEnum'
204
+ ? types.maybe(model)
205
+ : type === 'stringEnumArray'
206
+ ? types.array(model)
207
+ : model;
208
+ }
209
+ /**
210
+ * New value when converting a fixed-value slot to a jexl callback. Already-
211
+ * callback values are returned unchanged.
212
+ *
213
+ * A single JSON.stringify covers every type: `jexl:${42}` and
214
+ * `jexl:${JSON.stringify(42)}` are identical for numbers/booleans, and the rest
215
+ * need the quoting/serialization anyway.
216
+ */
217
+ export function toCallbackValue(value) {
218
+ return isCallbackValue(value) ? value : `jexl:${JSON.stringify(value)}`;
219
+ }
220
+ /**
221
+ * New value when converting a jexl callback back to a fixed value: try
222
+ * evaluating with no args, else fall back to the slot default (and to the slot
223
+ * type's `fallbackDefault` if the default is itself a callback).
224
+ */
225
+ export function toFixedValue(value, type, defaultValue, jexl) {
226
+ if (!isCallbackValue(value)) {
227
+ return value;
228
+ }
229
+ try {
230
+ const result = stringToJexlExpression(value, jexl).eval();
231
+ if (result !== undefined) {
232
+ return result;
190
233
  }
191
- return snap.value !== defaultValue ? snap.value : undefined;
192
- })
193
- .actions(self => ({
194
- set(newVal) {
195
- self.value = newVal;
196
- },
197
- reset() {
198
- self.value = defaultValue;
199
- },
200
- convertToCallback() {
201
- if (self.isCallback) {
202
- return;
203
- }
204
- self.value = `jexl:${self.valueJSON || "''"}`;
205
- },
206
- convertToValue() {
207
- if (!self.isCallback) {
208
- return;
209
- }
210
- try {
211
- const funcResult = self.expr.eval();
212
- if (funcResult !== undefined) {
213
- self.value = funcResult;
214
- return;
215
- }
216
- }
217
- catch (e) {
218
- }
219
- self.value = defaultValue;
220
- if (!(type in fallbackDefaults)) {
221
- throw new Error(`no fallbackDefault defined for type ${type}`);
222
- }
223
- self.value = fallbackDefaults[type];
224
- },
225
- }));
226
- if (typeModelExtensions[type]) {
227
- slot = slot.extend(typeModelExtensions[type]);
228
234
  }
229
- const completeModel = types.optional(slot, {
230
- name: slotName,
231
- type,
232
- description,
233
- value: defaultValue,
234
- });
235
- Object.defineProperty(completeModel, 'isJBrowseConfigurationSlot', {
236
- value: true,
237
- });
238
- return completeModel;
235
+ catch {
236
+ /* fall through to default */
237
+ }
238
+ if (isCallbackValue(defaultValue)) {
239
+ const spec = builtinSlotTypes[type];
240
+ if (spec?.fallbackDefault === undefined) {
241
+ throw new Error(`no fallbackDefault defined for type ${type}`);
242
+ }
243
+ return spec.fallbackDefault;
244
+ }
245
+ return defaultValue;
239
246
  }
@@ -0,0 +1,14 @@
1
+ /**
2
+ * A shorthand snapshot with its location slots filled in: `derived` supplies
3
+ * what the shorthand implies, and any key the config spells out for itself
4
+ * wins.
5
+ *
6
+ * Spread the other way round — derived over the snapshot — a config naming both
7
+ * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
8
+ * faiLocation: { uri: 'custom.fai' } }`, silently lost the index it named to
9
+ * the one the shorthand invents. Every adapter's normalizer had its own copy of
10
+ * the spread, so the precedence had to be got right 30-odd times.
11
+ */
12
+ export declare function fillLocations(snap: Record<string, unknown>, derived: Record<string, unknown>): {
13
+ [x: string]: unknown;
14
+ };
@@ -0,0 +1,14 @@
1
+ /**
2
+ * A shorthand snapshot with its location slots filled in: `derived` supplies
3
+ * what the shorthand implies, and any key the config spells out for itself
4
+ * wins.
5
+ *
6
+ * Spread the other way round — derived over the snapshot — a config naming both
7
+ * a `uri` and a location that is not the sibling of it, `{ uri: 'x.fa',
8
+ * faiLocation: { uri: 'custom.fai' } }`, silently lost the index it named to
9
+ * the one the shorthand invents. Every adapter's normalizer had its own copy of
10
+ * the spread, so the precedence had to be got right 30-odd times.
11
+ */
12
+ export function fillLocations(snap, derived) {
13
+ return { ...derived, ...snap };
14
+ }
@@ -0,0 +1,41 @@
1
+ /**
2
+ * #config FormatAbout
3
+ * #category root
4
+ * jexl callbacks that add, rewrite or hide fields in a track's About dialog.
5
+ * The same schema hangs off every track and off the session as
6
+ * `configuration.formatAbout`, which applies to every track at once. Where both
7
+ * are set the track's object is spread over the session's, so a track can
8
+ * override individual keys the global callback added.
9
+ *
10
+ * #example
11
+ * On a track. The callback's variable is `config`, not `feature`, since the
12
+ * dialog shows the track's own configuration rather than a feature:
13
+ * ```js
14
+ * {
15
+ * type: 'FeatureTrack',
16
+ * trackId: 'genes',
17
+ * name: 'Genes',
18
+ * assemblyNames: ['hg38'],
19
+ * adapter: {
20
+ * type: 'Gff3TabixAdapter',
21
+ * uri: 'https://example.com/genes.gff.gz',
22
+ * },
23
+ * formatAbout: {
24
+ * hideUris: true,
25
+ * config: "jexl:{Source:'GENCODE v44', adapter:undefined}",
26
+ * },
27
+ * }
28
+ * ```
29
+ */
30
+ export declare function FormatAboutConfigSchemaFactory(): import("./configurationSchema.ts").ConfigurationSchemaType<{
31
+ readonly config: {
32
+ type: "frozen";
33
+ } & {
34
+ defaultValue: unknown;
35
+ };
36
+ readonly hideUris: {
37
+ type: "boolean";
38
+ } & {
39
+ defaultValue: boolean;
40
+ };
41
+ }, import("./configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined, undefined, import("./requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
@@ -0,0 +1,58 @@
1
+ import { ConfigurationSchema } from './configurationSchema.js';
2
+ /**
3
+ * #config FormatAbout
4
+ * #category root
5
+ * jexl callbacks that add, rewrite or hide fields in a track's About dialog.
6
+ * The same schema hangs off every track and off the session as
7
+ * `configuration.formatAbout`, which applies to every track at once. Where both
8
+ * are set the track's object is spread over the session's, so a track can
9
+ * override individual keys the global callback added.
10
+ *
11
+ * #example
12
+ * On a track. The callback's variable is `config`, not `feature`, since the
13
+ * dialog shows the track's own configuration rather than a feature:
14
+ * ```js
15
+ * {
16
+ * type: 'FeatureTrack',
17
+ * trackId: 'genes',
18
+ * name: 'Genes',
19
+ * assemblyNames: ['hg38'],
20
+ * adapter: {
21
+ * type: 'Gff3TabixAdapter',
22
+ * uri: 'https://example.com/genes.gff.gz',
23
+ * },
24
+ * formatAbout: {
25
+ * hideUris: true,
26
+ * config: "jexl:{Source:'GENCODE v44', adapter:undefined}",
27
+ * },
28
+ * }
29
+ * ```
30
+ */
31
+ export function FormatAboutConfigSchemaFactory() {
32
+ return ConfigurationSchema('FormatAbout', {
33
+ /**
34
+ * #slot formatAbout.config
35
+ * callback returning an object of fields to merge over the config shown
36
+ */
37
+ config: {
38
+ type: 'frozen',
39
+ description: 'formats configuration object in about dialog',
40
+ defaultValue: {},
41
+ contextVariable: ['config'],
42
+ },
43
+ /**
44
+ * #slot formatAbout.hideUris
45
+ * leave file locations out of the About dialog, for a deployment that would
46
+ * rather not show users where the data sits. Hides URIs and local paths
47
+ * alike, drops the "Copy config" button, and suppresses the File info panel
48
+ * — a BAM's `@SQ UR:` and `@PG CL:` lines are locations too. "Show ref
49
+ * names" stays, since it exposes none. The two tiers are OR'd, so a
50
+ * session-wide `true` cannot be turned back on by a track. It hides the
51
+ * locations from the dialog only, not from `config.json`
52
+ */
53
+ hideUris: {
54
+ type: 'boolean',
55
+ defaultValue: false,
56
+ },
57
+ });
58
+ }
@@ -0,0 +1,54 @@
1
+ /**
2
+ * Levels of subfeature the `subfeatures` callback runs on when no tier sets
3
+ * `depth`. Applied by the reader rather than as the slot's `defaultValue`, so
4
+ * the slot can still read as unset and the session's value reach a track.
5
+ */
6
+ export declare const DEFAULT_FORMAT_DETAILS_DEPTH = 2;
7
+ /**
8
+ * #config FormatDetails
9
+ * #category root
10
+ * jexl callbacks that add, rewrite or hide fields in the feature-details panel.
11
+ * The same schema hangs off every track and off the session as
12
+ * `configuration.formatDetails`, which applies to every track at once. Where
13
+ * both are set, the callbacks merge with the track's object over the session's,
14
+ * so a track can override individual keys the global callback added, and the
15
+ * numeric slots take the track's value when the track sets one.
16
+ *
17
+ * #example
18
+ * On a track. The callback returns an object merged over the feature: a new key
19
+ * adds a row, an existing key rewrites it, and `undefined` hides it. A bare URL
20
+ * is turned into a link for you, so no `<a>` markup is needed:
21
+ * ```js
22
+ * {
23
+ * type: 'FeatureTrack',
24
+ * trackId: 'genes',
25
+ * name: 'Genes',
26
+ * assemblyNames: ['hg38'],
27
+ * adapter: {
28
+ * type: 'Gff3TabixAdapter',
29
+ * uri: 'https://example.com/genes.gff.gz',
30
+ * },
31
+ * formatDetails: {
32
+ * feature: "jexl:{ncbi:'https://www.ncbi.nlm.nih.gov/gene/?term='+feature.name, phase:undefined}",
33
+ * },
34
+ * }
35
+ * ```
36
+ */
37
+ export declare function FormatDetailsConfigSchemaFactory(): import("./configurationSchema.ts").ConfigurationSchemaType<{
38
+ readonly feature: {
39
+ type: "frozen";
40
+ } & {
41
+ defaultValue: unknown;
42
+ };
43
+ readonly subfeatures: {
44
+ type: "frozen";
45
+ } & {
46
+ defaultValue: unknown;
47
+ };
48
+ readonly depth: {
49
+ type: "maybeNumber";
50
+ };
51
+ readonly maxDepth: {
52
+ type: "maybeNumber";
53
+ };
54
+ }, import("./configurationSchema.ts").ConfigurationSchemaOptions<undefined, undefined, undefined, import("./requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;