@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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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,7 +1,18 @@
1
- export default function ArrayValue({ name, value, description, formatter, prefix, }: {
1
+ import type { FeatureFormatter, FieldActions } from '../types.tsx';
2
+ /**
3
+ * An array of objects renders each element as its own `Attributes` block and
4
+ * draws no label row at this level; anything else is one labelled row like any
5
+ * other field, and so takes its place in the card's shared label column.
6
+ * Exported because `Attributes` measures that column before rendering and has
7
+ * to make the same call.
8
+ */
9
+ export declare function isObjectArray(value: unknown[]): value is Record<string, unknown>[];
10
+ export default function ArrayValue({ name, value, description, formatter, fieldActions, prefix, width, }: {
2
11
  description?: React.ReactNode;
3
12
  name: string;
4
13
  value: unknown[];
5
- formatter?: (value: unknown, key: string) => React.ReactNode;
14
+ formatter?: FeatureFormatter;
15
+ fieldActions?: FieldActions;
6
16
  prefix?: string[];
7
- }): import("react/jsx-runtime").JSX.Element;
17
+ width?: number;
18
+ }): import("react").JSX.Element;
@@ -1,11 +1,16 @@
1
- import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import { useState } from 'react';
3
- import Attributes from "./Attributes.js";
4
- import BasicValue from "./BasicValue.js";
5
- import FieldName from "./FieldName.js";
6
- import { isObject } from "../../util/index.js";
7
- import { makeStyles } from "../../util/tss-react/index.js";
3
+ import { isObject } from '../../util/index.js';
4
+ import { makeStyles } from '../../util/tss-react/index.js';
5
+ import Attributes from './Attributes.js';
6
+ import BasicValue from './BasicValue.js';
7
+ import FieldActionsButton, { useRevealFieldActions, } from './FieldActionsButton.js';
8
+ import FieldName from './FieldName.js';
8
9
  const MAX_ARRAY_LENGTH = 100;
10
+ // Numeric arrays (e.g. base-modification probabilities, per-base scores) are
11
+ // rarely read element-by-element and can be thousands long, so only a handful
12
+ // are shown until expanded
13
+ const MAX_NUMERIC_ARRAY_LENGTH = 5;
9
14
  const useStyles = makeStyles()(theme => ({
10
15
  field: {
11
16
  display: 'flex',
@@ -20,22 +25,30 @@ const useStyles = makeStyles()(theme => ({
20
25
  overflow: 'auto',
21
26
  },
22
27
  }));
23
- export default function ArrayValue({ name, value, description, formatter, prefix = [], }) {
24
- const { classes } = useStyles();
28
+ /**
29
+ * An array of objects renders each element as its own `Attributes` block and
30
+ * draws no label row at this level; anything else is one labelled row like any
31
+ * other field, and so takes its place in the card's shared label column.
32
+ * Exported because `Attributes` measures that column before rendering and has
33
+ * to make the same call.
34
+ */
35
+ export function isObjectArray(value) {
36
+ return value.every(isObject);
37
+ }
38
+ export default function ArrayValue({ name, value, description, formatter, fieldActions, prefix = [], width, }) {
39
+ const { classes, cx } = useStyles();
40
+ const reveal = useRevealFieldActions();
25
41
  const [showAll, setShowAll] = useState(false);
26
- const needsTruncation = value.length > MAX_ARRAY_LENGTH;
27
- const displayedValues = needsTruncation && !showAll ? value.slice(0, MAX_ARRAY_LENGTH) : value;
28
- if (value.length === 1) {
29
- return isObject(value[0]) ? (_jsx(Attributes, { formatter: formatter, attributes: value[0], prefix: [...prefix, name] })) : (_jsxs("div", { className: classes.field, children: [_jsx(FieldName, { prefix: prefix, description: description, name: name }), _jsx(BasicValue, { value: formatter ? formatter(value[0], name) : value[0] })] }));
30
- }
31
- else if (value.every(val => isObject(val))) {
32
- return (_jsx(_Fragment, { children: value.map((val, i) => (_jsx(Attributes, { formatter: formatter, attributes: val, prefix: [...prefix, `${name}-${i}`] }, `${JSON.stringify(val)}-${i}`))) }));
33
- }
34
- else {
35
- return (_jsxs("div", { className: classes.field, children: [_jsx(FieldName, { prefix: prefix, description: description, name: name }), displayedValues.map((val, i) => (_jsx("div", { className: classes.fieldSubvalue, children: _jsx(BasicValue, { value: formatter ? formatter(val, name) : val }) }, `${JSON.stringify(val)}-${i}`))), needsTruncation ? (_jsx("button", { type: "button", onClick: () => {
36
- setShowAll(val => !val);
37
- }, children: showAll
38
- ? 'Show less'
39
- : `Showing ${MAX_ARRAY_LENGTH} of ${value.length}. Show all...` })) : null] }));
40
- }
42
+ const limit = value.every(v => typeof v === 'number')
43
+ ? MAX_NUMERIC_ARRAY_LENGTH
44
+ : MAX_ARRAY_LENGTH;
45
+ const needsTruncation = value.length > limit;
46
+ const displayedValues = needsTruncation && !showAll ? value.slice(0, limit) : value;
47
+ return isObjectArray(value) ? (value.length === 1 ? (_jsx(Attributes, { formatter: formatter, attributes: value[0], prefix: [...prefix, name] })) : (_jsx(_Fragment, { children: value.map((val, i) => (_jsx(Attributes
48
+ // eslint-disable-next-line @eslint-react/no-array-index-key -- static positional list of attribute objects, no unique field available
49
+ , { formatter: formatter, attributes: val, prefix: [...prefix, `${name}-${i}`] }, i))) }))) : (_jsxs("div", { className: cx(classes.field, reveal), children: [_jsx(FieldName, { prefix: prefix, description: description, name: name, width: width }), value.length === 1 ? (_jsxs(_Fragment, { children: [_jsx(BasicValue, { value: formatter ? formatter(value[0], name, 0) : value[0] }), _jsx(FieldActionsButton, { path: [...prefix, name], value: value[0], fieldActions: fieldActions })] })) : (_jsxs(_Fragment, { children: [displayedValues.map((val, i) => (_jsx("div", { className: classes.fieldSubvalue, children: _jsx(BasicValue, { value: formatter ? formatter(val, name, i) : val }) }, `${String(val)}-${i}`))), needsTruncation ? (_jsx("button", { type: "button", onClick: () => {
50
+ setShowAll(v => !v);
51
+ }, children: showAll
52
+ ? 'Show less'
53
+ : `Showing ${limit} of ${value.length}. Show all...` })) : null] }))] }));
41
54
  }
@@ -1,13 +1,16 @@
1
- import type { Descriptors } from '../types.tsx';
1
+ import type { Descriptors, FeatureFormatter, FieldActions } from '../types.tsx';
2
2
  export default function Attributes(props: {
3
- attributes: {
4
- [key: string]: unknown;
5
- __jbrowsefmt?: Record<string, unknown>;
6
- };
3
+ attributes: Record<string, unknown>;
7
4
  omit?: string[];
8
5
  omitSingleLevel?: string[];
9
- formatter?: (val: unknown, key: string) => React.ReactNode;
6
+ formatter?: FeatureFormatter;
7
+ fieldActions?: FieldActions;
10
8
  descriptions?: Descriptors;
11
9
  prefix?: string[];
12
10
  hideUris?: boolean;
13
- }): import("react/jsx-runtime").JSX.Element;
11
+ /**
12
+ * The label column's width, measured once for the whole card and threaded
13
+ * down the recursion. Set by `Attributes` itself; a caller leaves it alone.
14
+ */
15
+ labelWidth?: number;
16
+ }): import("react").JSX.Element;
@@ -1,43 +1,146 @@
1
- import { jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
2
- import ArrayValue from "./ArrayValue.js";
3
- import DataGridDetails from "./DataGridDetails.js";
4
- import SimpleField from "./SimpleField.js";
5
- import UriAttribute from "./UriField.js";
6
- import { accessNested, generateMaxWidth } from "./util.js";
7
- import { isObject, isUriLocation } from "../../util/index.js";
1
+ import { Fragment as _Fragment, jsx as _jsx } from "react/jsx-runtime";
2
+ import { Suspense, lazy } from 'react';
3
+ import { isLocalPathLocation, isObject, isUriLocation, measureText, } from '../../util/index.js';
4
+ import ArrayValue, { isObjectArray } from './ArrayValue.js';
5
+ import SimpleField from './SimpleField.js';
6
+ import UriField from './UriField.js';
7
+ import { accessNested } from './util.js';
8
+ // Lazy: reaches @mui/x-data-grid, and this module sits on the eager startup
9
+ // path via product-core's ui barrel (AboutDialog -> AboutDialogContents).
10
+ // Only a homogeneous object array actually renders a grid.
11
+ const DataGridDetails = lazy(() => import('./DataGridDetails.js'));
8
12
  const MAX_FIELD_NAME_WIDTH = 170;
13
+ // must match FieldName's own font size and horizontal padding, or the measured
14
+ // column is not the width the label needs
15
+ const FIELD_NAME_FONT_SIZE = 12;
16
+ const FIELD_NAME_PADDING = 10;
17
+ // Max extra unique columns vs. first row before falling back to per-row field
18
+ // sections instead of the data grid (avoids a mostly-empty, hard-to-read grid)
19
+ const DATAGRID_SCHEMA_TOLERANCE = 5;
20
+ function isHomogeneousObjectArray(arr) {
21
+ if (arr.length <= 1 || !arr.every(isObject)) {
22
+ return false;
23
+ }
24
+ const firstKeyCount = Object.keys(arr[0]).length;
25
+ const unionKeyCount = new Set(arr.flatMap(Object.keys)).size;
26
+ return unionKeyCount < firstKeyCount + DATAGRID_SCHEMA_TOLERANCE;
27
+ }
28
+ // these are always omitted as too detailed
9
29
  const globalOmit = [
10
- '__jbrowsefmt',
11
30
  'length',
12
31
  'position',
13
32
  'subfeatures',
14
33
  'uniqueId',
15
34
  'exonFrames',
35
+ '_exonFrames',
16
36
  'parentId',
17
37
  'thickStart',
18
38
  'thickEnd',
19
- '_lineHash',
39
+ // BED12/bigGenePred parsing internals (block/CDS-shape bookkeeping, not
40
+ // meaningful feature attributes)
41
+ 'chromStarts',
42
+ 'blockStarts',
43
+ 'blockSizes',
44
+ 'blockCount',
45
+ 'reserved',
46
+ 'cdsStartStat',
47
+ 'cdsEndStat',
20
48
  ];
49
+ function isLocation(value) {
50
+ return isUriLocation(value) || isLocalPathLocation(value);
51
+ }
52
+ // hideUris prunes the data rather than each render branch checking: an array
53
+ // of objects reaches the data grid and ArrayValue, which print locations too
54
+ function withoutLocations(attributes) {
55
+ return Object.fromEntries(Object.entries(attributes)
56
+ .filter(([, value]) => !isLocation(value))
57
+ .map(([key, value]) => [key, valueWithoutLocations(value)]));
58
+ }
59
+ function valueWithoutLocations(value) {
60
+ return Array.isArray(value)
61
+ ? value.filter(v => !isLocation(v)).map(valueWithoutLocations)
62
+ : isObject(value)
63
+ ? withoutLocations(value)
64
+ : value;
65
+ }
66
+ /**
67
+ * The widest label `Attributes` will actually render under `attributes`, in
68
+ * text units — the padding is added once by `widestLabel`, not per level.
69
+ *
70
+ * Follows the same branches the render below does: a flat array is one labelled
71
+ * row, an array of objects renders each element as its own block with no label
72
+ * at this level, a data grid heads its own grid rather than sharing a row, a
73
+ * `UriLocation` is one field, any other object recurses. `Attributes.test.tsx`
74
+ * fails if the two stop agreeing.
75
+ */
76
+ function measureLabels(attributes, opts) {
77
+ const { omits, deepOmits, prefix } = opts;
78
+ let widest = 0;
79
+ const measure = (key) => measureText([...prefix, key].join('.'), FIELD_NAME_FONT_SIZE);
80
+ for (const [key, value] of Object.entries(attributes)) {
81
+ if (value == null || omits.has(key)) {
82
+ continue;
83
+ }
84
+ if (Array.isArray(value)) {
85
+ // a data grid's FieldName is a heading above the grid, not a cell beside
86
+ // a value, so it takes no part in the column either
87
+ if (!isHomogeneousObjectArray(value) && !isObjectArray(value)) {
88
+ widest = Math.max(widest, measure(key));
89
+ }
90
+ }
91
+ else if (isObject(value)) {
92
+ widest = Math.max(widest, isUriLocation(value)
93
+ ? measure(key)
94
+ : measureLabels(value, {
95
+ omits: deepOmits,
96
+ deepOmits,
97
+ prefix: [...prefix, key],
98
+ }));
99
+ }
100
+ else {
101
+ widest = Math.max(widest, measure(key));
102
+ }
103
+ }
104
+ return widest;
105
+ }
106
+ function widestLabel(attributes, opts) {
107
+ return Math.ceil(measureLabels(attributes, opts)) + FIELD_NAME_PADDING;
108
+ }
21
109
  export default function Attributes(props) {
22
- const { attributes, omit = [], omitSingleLevel = [], descriptions, formatter, hideUris, prefix = [], } = props;
110
+ const { omit = [], omitSingleLevel = [], descriptions, formatter, fieldActions, hideUris, prefix = [], labelWidth, } = props;
111
+ const attributes = hideUris
112
+ ? withoutLocations(props.attributes)
113
+ : props.attributes;
23
114
  const omits = new Set([...omit, ...globalOmit, ...omitSingleLevel]);
24
- const { __jbrowsefmt, ...rest } = attributes;
25
- const filteredFormattedAttributes = Object.entries({
26
- ...rest,
27
- ...__jbrowsefmt,
28
- }).filter(([k, v]) => v != null && !omits.has(k));
29
- const maxLabelWidth = generateMaxWidth(filteredFormattedAttributes, prefix);
30
- return (_jsx(_Fragment, { children: filteredFormattedAttributes.map(([key, value]) => {
115
+ const shown = Object.entries(attributes).filter(([k, v]) => v != null && !omits.has(k));
116
+ // Measured over the whole subtree on the outermost call, then handed down, so
117
+ // one card has one label column. Per-level measurement put `type`/`trackId` in
118
+ // a narrow column, `adapter.type` in a wider one and `adapter.craiLocation` in
119
+ // a wider one still — three ragged steps down a single card.
120
+ const width = Math.min(labelWidth ??
121
+ widestLabel(attributes, {
122
+ omits,
123
+ // `omitSingleLevel` is what its name says: the recursive call below
124
+ // passes only `omit` on, so the measurement must stop honoring it at
125
+ // the same depth or it measures a label that isn't there
126
+ deepOmits: omitSingleLevel.length
127
+ ? new Set([...omit, ...globalOmit])
128
+ : omits,
129
+ prefix,
130
+ }), MAX_FIELD_NAME_WIDTH);
131
+ return (_jsx(_Fragment, { children: shown.map(([key, value]) => {
31
132
  const description = accessNested([...prefix, key], descriptions);
32
133
  if (Array.isArray(value)) {
33
- return value.length > 1 && value.every(val => isObject(val)) ? (_jsx(DataGridDetails, { name: key, prefix: prefix, value: value }, key)) : (_jsx(ArrayValue, { name: key, value: value, formatter: formatter, description: description, prefix: prefix }, key));
134
+ // Only use the data grid when schemas are homogeneous enough;
135
+ // heterogeneous arrays fall through to ArrayValue which renders
136
+ // each object as individual field sections instead of disappearing
137
+ return isHomogeneousObjectArray(value) ? (_jsx(Suspense, { fallback: null, children: _jsx(DataGridDetails, { name: key, prefix: prefix, value: value }) }, key)) : (_jsx(ArrayValue, { name: key, value: value, formatter: formatter, fieldActions: fieldActions, description: description, prefix: prefix, width: width }, key));
34
138
  }
35
139
  else if (isObject(value)) {
36
- const { omitSingleLevel, ...rest } = props;
37
- return isUriLocation(value) ? (hideUris ? null : (_jsx(UriAttribute, { name: key, prefix: prefix, value: value }, key))) : (_jsx(Attributes, { ...rest, formatter: formatter, attributes: value, descriptions: descriptions, prefix: [...prefix, key] }, key));
140
+ return isUriLocation(value) ? (_jsx(UriField, { name: key, prefix: prefix, value: value, width: width }, key)) : (_jsx(Attributes, { attributes: value, omit: omit, descriptions: descriptions, formatter: formatter, fieldActions: fieldActions, prefix: [...prefix, key], labelWidth: width }, key));
38
141
  }
39
142
  else {
40
- return (_jsx(SimpleField, { name: key, formatter: formatter, value: value, description: description, prefix: prefix, width: Math.min(maxLabelWidth, MAX_FIELD_NAME_WIDTH) }, key));
143
+ return (_jsx(SimpleField, { name: key, formatter: formatter, fieldActions: fieldActions, value: value, description: description, prefix: prefix, width: width }, key));
41
144
  }
42
145
  }) }));
43
146
  }
@@ -1,8 +1,2 @@
1
- import type { BaseCardProps, BaseProps } from '../types.tsx';
2
- export interface BaseInputProps extends BaseCardProps {
3
- omit?: string[];
4
- model: any;
5
- descriptions?: Record<string, React.ReactNode>;
6
- formatter?: (val: unknown, key: string) => React.ReactNode;
7
- }
8
- export default function BaseAttributes(props: BaseProps): import("react/jsx-runtime").JSX.Element;
1
+ import type { BaseProps } from '../types.tsx';
2
+ export default function BaseAttributes(props: BaseProps): import("react").JSX.Element;
@@ -1,7 +1,7 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import Attributes from "./Attributes.js";
3
- import BaseCard from "./BaseCard.js";
2
+ import Attributes from './Attributes.js';
3
+ import BaseCard from './BaseCard.js';
4
4
  export default function BaseAttributes(props) {
5
- const { title = 'Attributes', feature } = props;
6
- return (_jsx(BaseCard, { ...props, title: title, children: _jsx(Attributes, { ...props, attributes: feature }) }));
5
+ const { title = 'Attributes', defaultExpanded, feature } = props;
6
+ return (_jsx(BaseCard, { title: title, defaultExpanded: defaultExpanded, children: _jsx(Attributes, { ...props, attributes: feature }) }));
7
7
  }
@@ -1,2 +1,2 @@
1
1
  import type { BaseCardProps } from '../types.tsx';
2
- export default function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): import("react/jsx-runtime").JSX.Element;
2
+ export default function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): import("react").JSX.Element;
@@ -1,17 +1,14 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import ExpandMore from '@mui/icons-material/ExpandMore';
3
3
  import { Accordion, AccordionDetails, AccordionSummary, Typography, } from '@mui/material';
4
- import { makeStyles } from "../../util/tss-react/index.js";
4
+ import { makeStyles } from '../../util/tss-react/index.js';
5
5
  const useStyles = makeStyles()(theme => ({
6
6
  expansionPanelDetails: {
7
7
  display: 'block',
8
8
  padding: theme.spacing(1),
9
9
  },
10
- icon: {
11
- color: theme.palette.tertiary.contrastText || '#fff',
12
- },
13
10
  }));
14
11
  export default function BaseCard({ children, title, defaultExpanded = true, }) {
15
12
  const { classes } = useStyles();
16
- return (_jsxs(Accordion, { defaultExpanded: defaultExpanded, children: [_jsx(AccordionSummary, { expandIcon: _jsx(ExpandMore, { className: classes.icon }), children: _jsx(Typography, { variant: "button", children: title }) }), _jsx(AccordionDetails, { className: classes.expansionPanelDetails, children: children })] }));
13
+ return (_jsxs(Accordion, { defaultExpanded: defaultExpanded, slotProps: { transition: { unmountOnExit: true } }, "data-testid": `BaseCard-${title}`, children: [_jsx(AccordionSummary, { expandIcon: _jsx(ExpandMore, {}), children: _jsx(Typography, { variant: "button", children: title }) }), _jsx(AccordionDetails, { className: classes.expansionPanelDetails, children: children })] }));
17
14
  }
@@ -1,2 +1,2 @@
1
1
  import type { BaseProps } from '../types.tsx';
2
- export default function BaseCoreDetails(props: BaseProps): import("react/jsx-runtime").JSX.Element;
2
+ export default function BaseCoreDetails(props: BaseProps): import("react").JSX.Element;
@@ -1,7 +1,7 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import BaseCard from "./BaseCard.js";
3
- import CoreDetails from "./CoreDetails.js";
2
+ import BaseCard from './BaseCard.js';
3
+ import CoreDetails from './CoreDetails.js';
4
4
  export default function BaseCoreDetails(props) {
5
- const { title = 'Primary data' } = props;
6
- return (_jsx(BaseCard, { ...props, title: title, children: _jsx(CoreDetails, { ...props }) }));
5
+ const { title = 'Primary data', defaultExpanded } = props;
6
+ return (_jsx(BaseCard, { title: title, defaultExpanded: defaultExpanded, children: _jsx(CoreDetails, { ...props }) }));
7
7
  }
@@ -1,3 +1,14 @@
1
+ export declare function isBareUrl(text: string): boolean;
2
+ export declare function valueText(value: unknown): string;
3
+ /**
4
+ * A value that is nothing but a URL is a link; anything else goes through
5
+ * SanitizedHTML, which renders markup and links URLs inside longer text. Both
6
+ * open in a new tab: navigating in place discards the session, and in an
7
+ * embedded JBrowse it takes the host page with it.
8
+ */
9
+ export declare function ValueText({ text }: {
10
+ text: string;
11
+ }): import("react").JSX.Element;
1
12
  export default function BasicValue({ value }: {
2
13
  value: unknown;
3
- }): import("react/jsx-runtime").JSX.Element;
14
+ }): import("react").JSX.Element;
@@ -1,9 +1,9 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
2
  import { isValidElement } from 'react';
3
3
  import { Link } from '@mui/material';
4
- import { SanitizedHTML } from "../../ui/index.js";
5
- import { isObject } from "../../util/index.js";
6
- import { makeStyles } from "../../util/tss-react/index.js";
4
+ import { SanitizedHTML } from '../../ui/index.js';
5
+ import { isObject } from '../../util/index.js';
6
+ import { makeStyles } from '../../util/tss-react/index.js';
7
7
  const useStyles = makeStyles()(theme => ({
8
8
  fieldValue: {
9
9
  wordBreak: 'break-word',
@@ -13,8 +13,22 @@ const useStyles = makeStyles()(theme => ({
13
13
  overflow: 'auto',
14
14
  },
15
15
  }));
16
+ export function isBareUrl(text) {
17
+ return /^https?:\/\/\S+$/.test(text);
18
+ }
19
+ export function valueText(value) {
20
+ return isObject(value) ? JSON.stringify(value) : String(value);
21
+ }
22
+ /**
23
+ * A value that is nothing but a URL is a link; anything else goes through
24
+ * SanitizedHTML, which renders markup and links URLs inside longer text. Both
25
+ * open in a new tab: navigating in place discards the session, and in an
26
+ * embedded JBrowse it takes the host page with it.
27
+ */
28
+ export function ValueText({ text }) {
29
+ return isBareUrl(text) ? (_jsx(Link, { href: text, target: "_blank", rel: "noopener noreferrer", children: text })) : (_jsx(SanitizedHTML, { html: text }));
30
+ }
16
31
  export default function BasicValue({ value }) {
17
32
  const { classes } = useStyles();
18
- const isLink = /^https?:\/\//.exec(`${value}`);
19
- return (_jsx("div", { className: classes.fieldValue, children: isValidElement(value) ? (value) : isLink ? (_jsx(Link, { href: `${value}`, children: `${value}` })) : (_jsx(SanitizedHTML, { html: isObject(value) ? JSON.stringify(value) : String(value) })) }));
33
+ return (_jsx("div", { className: classes.fieldValue, children: isValidElement(value) ? value : _jsx(ValueText, { text: valueText(value) }) }));
20
34
  }
@@ -1,2 +1,2 @@
1
1
  import type { BaseProps } from '../types.tsx';
2
- export default function CoreDetails(props: BaseProps): import("react/jsx-runtime").JSX.Element;
2
+ export default function CoreDetails({ feature }: BaseProps): import("react").JSX.Element;
@@ -1,24 +1,19 @@
1
- import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
2
- import Position from "./Position.js";
3
- import SimpleField from "./SimpleField.js";
4
- import { toLocale } from "../../util/index.js";
5
- export default function CoreDetails(props) {
6
- const { feature } = props;
7
- const obj = feature;
8
- const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
9
- const { start, end } = formattedFeat;
10
- const displayedDetails = {
11
- ...formattedFeat,
12
- length: toLocale(end - start),
13
- };
14
- const coreRenderedDetails = {
15
- description: 'Description',
16
- name: 'Name',
17
- length: 'Length',
18
- type: 'Type',
19
- };
20
- return (_jsxs(_Fragment, { children: [_jsx(SimpleField, { name: "Position", value: _jsx(Position, { ...props, feature: formattedFeat }) }), Object.entries(coreRenderedDetails)
21
- .map(([key, name]) => [name, displayedDetails[key]])
22
- .filter(([, value]) => value != null)
23
- .map(([name, value]) => (_jsx(SimpleField, { name: name, value: Array.isArray(value) ? value.join(', ') : value }, name)))] }));
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { assembleLocString, toLocale } from '../../util/index.js';
3
+ import { getStrandStr } from '../util.js';
4
+ import SimpleField from './SimpleField.js';
5
+ export default function CoreDetails({ feature }) {
6
+ const { name, description, type, start, end, strand } = feature;
7
+ // only a formatDetails callback sets `length`, to rewrite or hide the row:
8
+ // an adapter's own field of that name is in Attributes' globalOmit
9
+ const length = 'length' in feature ? feature.length : end - start;
10
+ const rows = [
11
+ ['Name', name],
12
+ ['Description', description],
13
+ ['Length', typeof length === 'number' ? toLocale(length) : length],
14
+ ['Type', type],
15
+ ];
16
+ return (_jsxs(_Fragment, { children: [_jsx(SimpleField, { name: "Position", value: [assembleLocString(feature), getStrandStr(strand)]
17
+ .filter(Boolean)
18
+ .join(' ') }), rows.map(([label, value]) => (_jsx(SimpleField, { name: label, value: Array.isArray(value) ? value.join(', ') : value }, label)))] }));
24
19
  }
@@ -2,4 +2,4 @@ export default function DataGridDetails({ value, prefix, name, }: {
2
2
  name: string;
3
3
  prefix?: string[];
4
4
  value: Record<string, unknown>[];
5
- }): import("react/jsx-runtime").JSX.Element | null;
5
+ }): import("react").JSX.Element;
@@ -1,12 +1,12 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import { useState } from 'react';
3
- import { Checkbox, FormControlLabel, Typography } from '@mui/material';
3
+ import { Typography } from '@mui/material';
4
4
  import { DataGrid } from '@mui/x-data-grid';
5
- import FieldName from "./FieldName.js";
6
- import DataGridFlexContainer from "../../ui/DataGridFlexContainer.js";
7
- import { SanitizedHTML } from "../../ui/index.js";
8
- import { getStr, measureGridWidth } from "../../util/index.js";
9
- import { makeStyles } from "../../util/tss-react/index.js";
5
+ import DataGridFlexContainer from '../../ui/DataGridFlexContainer.js';
6
+ import { LabeledCheckbox, SanitizedHTML } from '../../ui/index.js';
7
+ import { getStr, measureGridWidth } from '../../util/index.js';
8
+ import { makeStyles } from '../../util/tss-react/index.js';
9
+ import FieldName from './FieldName.js';
10
10
  const useStyles = makeStyles()(theme => ({
11
11
  margin: {
12
12
  marginBottom: theme.spacing(4),
@@ -20,38 +20,17 @@ const useStyles = makeStyles()(theme => ({
20
20
  export default function DataGridDetails({ value, prefix, name, }) {
21
21
  const { classes } = useStyles();
22
22
  const [checked, setChecked] = useState(false);
23
- const keys = Object.keys(value[0]).sort();
24
- const unionKeys = new Set(keys);
25
- const rows = Object.entries(value).map(([k, val]) => {
26
- const { id, ...rest } = val;
27
- return {
28
- id: k,
29
- identifier: id,
30
- ...rest,
31
- };
32
- });
33
- for (const val of value) {
34
- for (const k of Object.keys(val)) {
35
- unionKeys.add(k);
36
- }
37
- }
38
- let colNames;
39
- if (unionKeys.has('id')) {
40
- unionKeys.delete('id');
41
- colNames = ['identifier', ...unionKeys];
42
- }
43
- else {
44
- colNames = [...unionKeys];
45
- }
46
- const widths = colNames.map(e => measureGridWidth(rows.map(r => r[e])));
47
- if (unionKeys.size < keys.length + 5) {
48
- return (_jsxs("div", { className: classes.margin, children: [_jsx(FieldName, { prefix: prefix, name: name }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: checked, onChange: event => {
49
- setChecked(event.target.checked);
50
- } }), label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { disableRowSelectionOnClick: true, rows: rows, rowHeight: 20, columnHeaderHeight: 35, hideFooter: rows.length < 25, showToolbar: checked, columns: colNames.map((val, index) => ({
51
- field: val,
52
- width: widths[index],
53
- renderCell: ({ value }) => (_jsx("div", { className: classes.cell, children: _jsx(SanitizedHTML, { html: getStr(value || '') }) })),
54
- })) }) })] }));
55
- }
56
- return null;
23
+ // DataGrid needs a unique row id; rather than commandeering any 'id' field
24
+ // the feature itself carries, tag each row with the array index and point
25
+ // getRowId at it, leaving the feature's own keys (including 'id') untouched
26
+ const rows = value.map((val, k) => ({ ...val, __dataGridRowId: k }));
27
+ const cols = [...new Set(value.flatMap(Object.keys))];
28
+ const widths = cols.map(col => measureGridWidth(value.map(r => r[col])));
29
+ return (_jsxs("div", { className: classes.margin, children: [_jsx(FieldName, { prefix: prefix, name: name }), _jsx(LabeledCheckbox, { checked: checked, onChange: val => {
30
+ setChecked(val);
31
+ }, label: _jsx(Typography, { variant: "body2", children: "Show options" }) }), _jsx(DataGridFlexContainer, { children: _jsx(DataGrid, { disableRowSelectionOnClick: true, rows: rows, getRowId: row => row.__dataGridRowId, rowHeight: 20, columnHeaderHeight: 35, hideFooter: rows.length < 25, showToolbar: checked, columns: cols.map((field, index) => ({
32
+ field,
33
+ width: widths[index],
34
+ renderCell: ({ value }) => (_jsx("div", { className: classes.cell, children: _jsx(SanitizedHTML, { html: getStr(value ?? '') }) })),
35
+ })) }) })] }));
57
36
  }
@@ -1,11 +1,14 @@
1
1
  import type { SimpleFeatureSerialized } from '../../util/index.ts';
2
- import type { Descriptors } from '../types.tsx';
3
- import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
4
- export default function FeatureDetails(props: {
5
- model: IAnyStateTreeNode;
2
+ import type { Descriptors, FeatureDetailsModel, FeatureFormatter, FieldActions } from '../types.tsx';
3
+ interface FeatureDetailsProps {
4
+ model: FeatureDetailsModel;
6
5
  feature: SimpleFeatureSerialized;
6
+ unformatted?: SimpleFeatureSerialized;
7
7
  depth?: number;
8
8
  omit?: string[];
9
9
  descriptions?: Descriptors;
10
- formatter?: (val: unknown, key: string) => React.ReactNode;
11
- }): import("react/jsx-runtime").JSX.Element;
10
+ formatter?: FeatureFormatter;
11
+ fieldActions?: FieldActions;
12
+ }
13
+ declare const FeatureDetails: (props: FeatureDetailsProps) => import("react").JSX.Element;
14
+ export default FeatureDetails;