@jbrowse/core 4.3.0 → 5.0.0-beta.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1124) hide show
  1. package/README.md +783 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +84 -65
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
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  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1,7 +1,17 @@
1
- export default function ArrayValue({ name, value, description, formatter, prefix, }: {
1
+ import type { FeatureFormatter } 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, 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;
6
15
  prefix?: string[];
7
- }): import("react/jsx-runtime").JSX.Element;
16
+ width?: number;
17
+ }): import("react").JSX.Element;
@@ -1,11 +1,15 @@
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 FieldName from './FieldName.js';
8
8
  const MAX_ARRAY_LENGTH = 100;
9
+ // Numeric arrays (e.g. base-modification probabilities, per-base scores) are
10
+ // rarely read element-by-element and can be thousands long, so only a handful
11
+ // are shown until expanded
12
+ const MAX_NUMERIC_ARRAY_LENGTH = 5;
9
13
  const useStyles = makeStyles()(theme => ({
10
14
  field: {
11
15
  display: 'flex',
@@ -20,22 +24,29 @@ const useStyles = makeStyles()(theme => ({
20
24
  overflow: 'auto',
21
25
  },
22
26
  }));
23
- export default function ArrayValue({ name, value, description, formatter, prefix = [], }) {
27
+ /**
28
+ * An array of objects renders each element as its own `Attributes` block and
29
+ * draws no label row at this level; anything else is one labelled row like any
30
+ * other field, and so takes its place in the card's shared label column.
31
+ * Exported because `Attributes` measures that column before rendering and has
32
+ * to make the same call.
33
+ */
34
+ export function isObjectArray(value) {
35
+ return value.every(isObject);
36
+ }
37
+ export default function ArrayValue({ name, value, description, formatter, prefix = [], width, }) {
24
38
  const { classes } = useStyles();
25
39
  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 ${value.length}. Show all...` })) : null] }));
40
- }
40
+ const limit = value.every(v => typeof v === 'number')
41
+ ? MAX_NUMERIC_ARRAY_LENGTH
42
+ : MAX_ARRAY_LENGTH;
43
+ const needsTruncation = value.length > limit;
44
+ const displayedValues = needsTruncation && !showAll ? value.slice(0, limit) : value;
45
+ return isObjectArray(value) ? (value.length === 1 ? (_jsx(Attributes, { formatter: formatter, attributes: value[0], prefix: [...prefix, name] })) : (_jsx(_Fragment, { children: value.map((val, i) => (_jsx(Attributes
46
+ // eslint-disable-next-line @eslint-react/no-array-index-key -- static positional list of attribute objects, no unique field available
47
+ , { formatter: formatter, attributes: val, prefix: [...prefix, `${name}-${i}`] }, i))) }))) : (_jsxs("div", { className: classes.field, children: [_jsx(FieldName, { prefix: prefix, description: description, name: name, width: width }), value.length === 1 ? (_jsx(BasicValue, { value: formatter ? formatter(value[0], name, 0) : value[0] })) : (_jsxs(_Fragment, { children: [displayedValues.map((val, i) => (_jsx("div", { className: classes.fieldSubvalue, children: _jsx(BasicValue, { value: formatter ? formatter(val, name, i) : val }) }, `${String(val)}-${i}`))), needsTruncation ? (_jsx("button", { type: "button", onClick: () => {
48
+ setShowAll(v => !v);
49
+ }, children: showAll
50
+ ? 'Show less'
51
+ : `Showing ${limit} of ${value.length}. Show all...` })) : null] }))] }));
41
52
  }
@@ -1,4 +1,4 @@
1
- import type { Descriptors } from '../types.tsx';
1
+ import type { Descriptors, FeatureFormatter } from '../types.tsx';
2
2
  export default function Attributes(props: {
3
3
  attributes: {
4
4
  [key: string]: unknown;
@@ -6,8 +6,13 @@ export default function Attributes(props: {
6
6
  };
7
7
  omit?: string[];
8
8
  omitSingleLevel?: string[];
9
- formatter?: (val: unknown, key: string) => React.ReactNode;
9
+ formatter?: FeatureFormatter;
10
10
  descriptions?: Descriptors;
11
11
  prefix?: string[];
12
12
  hideUris?: boolean;
13
- }): import("react/jsx-runtime").JSX.Element;
13
+ /**
14
+ * The label column's width, measured once for the whole card and threaded
15
+ * down the recursion. Set by `Attributes` itself; a caller leaves it alone.
16
+ */
17
+ labelWidth?: number;
18
+ }): import("react").JSX.Element;
@@ -1,11 +1,31 @@
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 UriAttribute from './UriField.js';
7
+ import { accessNested, applyFeatureFormatting } 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
30
  '__jbrowsefmt',
11
31
  'length',
@@ -13,31 +33,109 @@ const globalOmit = [
13
33
  'subfeatures',
14
34
  'uniqueId',
15
35
  'exonFrames',
36
+ '_exonFrames',
16
37
  'parentId',
17
38
  'thickStart',
18
39
  'thickEnd',
19
- '_lineHash',
40
+ // BED12/bigGenePred parsing internals (block/CDS-shape bookkeeping, not
41
+ // meaningful feature attributes)
42
+ 'chromStarts',
43
+ 'blockStarts',
44
+ 'blockSizes',
45
+ 'blockCount',
46
+ 'reserved',
47
+ 'cdsStartStat',
48
+ 'cdsEndStat',
20
49
  ];
50
+ /**
51
+ * The widest label `Attributes` will actually render under `attributes`, in
52
+ * text units — the padding is added once by `widestLabel`, not per level.
53
+ *
54
+ * Follows the same branches the render below does: a flat array is one labelled
55
+ * row (`rendersOwnFieldRow`), an array of objects renders each element as its
56
+ * own block with no label at this level, a data grid heads its own grid rather
57
+ * than sharing a row, a `UriLocation` is one field, any other object recurses.
58
+ * Kept next to the render for that reason — the two agree by being read
59
+ * together, and `Attributes.test.tsx` fails if they stop.
60
+ */
61
+ function measureLabels(attributes, opts) {
62
+ const { omits, deepOmits, hideUris, prefix } = opts;
63
+ let widest = 0;
64
+ const measure = (key) => measureText([...prefix, key].join('.'), FIELD_NAME_FONT_SIZE);
65
+ for (const [key, value] of Object.entries(applyFeatureFormatting(attributes))) {
66
+ if (value == null || omits.has(key)) {
67
+ continue;
68
+ }
69
+ if (Array.isArray(value)) {
70
+ // a data grid's FieldName is a heading above the grid, not a cell beside
71
+ // a value, so it takes no part in the column either
72
+ if (!isHomogeneousObjectArray(value) && !isObjectArray(value)) {
73
+ widest = Math.max(widest, measure(key));
74
+ }
75
+ }
76
+ else if (isObject(value)) {
77
+ if (hideUris && (isUriLocation(value) || isLocalPathLocation(value))) {
78
+ continue;
79
+ }
80
+ widest = Math.max(widest, isUriLocation(value)
81
+ ? measure(key)
82
+ : measureLabels(value, {
83
+ omits: deepOmits,
84
+ deepOmits,
85
+ hideUris,
86
+ prefix: [...prefix, key],
87
+ }));
88
+ }
89
+ else {
90
+ widest = Math.max(widest, measure(key));
91
+ }
92
+ }
93
+ return widest;
94
+ }
95
+ function widestLabel(attributes, opts) {
96
+ return Math.ceil(measureLabels(attributes, opts)) + FIELD_NAME_PADDING;
97
+ }
21
98
  export default function Attributes(props) {
22
- const { attributes, omit = [], omitSingleLevel = [], descriptions, formatter, hideUris, prefix = [], } = props;
99
+ const { attributes, omit = [], omitSingleLevel = [], descriptions, formatter, hideUris, prefix = [], labelWidth, } = props;
23
100
  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);
101
+ const filteredFormattedAttributes = Object.entries(applyFeatureFormatting(attributes)).filter(([k, v]) => v != null && !omits.has(k));
102
+ // Measured over the whole subtree on the outermost call, then handed down, so
103
+ // one card has one label column. Per-level measurement put `type`/`trackId` in
104
+ // a narrow column, `adapter.type` in a wider one and `adapter.craiLocation` in
105
+ // a wider one still — three ragged steps down a single card.
106
+ const width = Math.min(labelWidth ??
107
+ widestLabel(attributes, {
108
+ omits,
109
+ // `omitSingleLevel` is what its name says: the recursive call below
110
+ // passes only `omit` on, so the measurement must stop honoring it at
111
+ // the same depth or it measures a label that isn't there
112
+ deepOmits: omitSingleLevel.length
113
+ ? new Set([...omit, ...globalOmit])
114
+ : omits,
115
+ hideUris,
116
+ prefix,
117
+ }), MAX_FIELD_NAME_WIDTH);
30
118
  return (_jsx(_Fragment, { children: filteredFormattedAttributes.map(([key, value]) => {
31
119
  const description = accessNested([...prefix, key], descriptions);
32
120
  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));
121
+ // Only use the data grid when schemas are homogeneous enough;
122
+ // heterogeneous arrays fall through to ArrayValue which renders
123
+ // each object as individual field sections instead of disappearing
124
+ 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, description: description, prefix: prefix, width: width }, key));
34
125
  }
35
126
  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));
127
+ // hideUris means "don't show where the data sits". A LocalPathLocation
128
+ // says that as plainly as a UriLocation does — it is what desktop and
129
+ // `jbrowse add-track --load copy` write — and it used to fall through
130
+ // to the recursive branch below and print the path in full
131
+ if (hideUris &&
132
+ (isUriLocation(value) || isLocalPathLocation(value))) {
133
+ return null;
134
+ }
135
+ return isUriLocation(value) ? (_jsx(UriAttribute, { name: key, prefix: prefix, value: value, width: width }, key)) : (_jsx(Attributes, { attributes: value, omit: omit, descriptions: descriptions, formatter: formatter, hideUris: hideUris, prefix: [...prefix, key], labelWidth: width }, key));
38
136
  }
39
137
  else {
40
- return (_jsx(SimpleField, { name: key, formatter: formatter, value: value, description: description, prefix: prefix, width: Math.min(maxLabelWidth, MAX_FIELD_NAME_WIDTH) }, key));
138
+ return (_jsx(SimpleField, { name: key, formatter: formatter, value: value, description: description, prefix: prefix, width: width }, key));
41
139
  }
42
140
  }) }));
43
141
  }
@@ -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;
@@ -1,7 +1,7 @@
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',
@@ -13,5 +13,5 @@ const useStyles = makeStyles()(theme => ({
13
13
  }));
14
14
  export default function BaseCard({ children, title, defaultExpanded = true, }) {
15
15
  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 })] }));
16
+ return (_jsxs(Accordion, { defaultExpanded: defaultExpanded, slotProps: { transition: { unmountOnExit: true } }, "data-testid": `BaseCard-${title}`, children: [_jsx(AccordionSummary, { expandIcon: _jsx(ExpandMore, { className: classes.icon }), children: _jsx(Typography, { variant: "button", children: title }) }), _jsx(AccordionDetails, { className: classes.expansionPanelDetails, children: children })] }));
17
17
  }
@@ -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 +1,3 @@
1
1
  export default function BasicValue({ value }: {
2
2
  value: unknown;
3
- }): import("react/jsx-runtime").JSX.Element;
3
+ }): 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',
@@ -15,6 +15,13 @@ const useStyles = makeStyles()(theme => ({
15
15
  }));
16
16
  export default function BasicValue({ value }) {
17
17
  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: `${value}` })) : (_jsx(SanitizedHTML, { html: isObject(value) ? JSON.stringify(value) : String(value) })) }));
18
+ // a value that is nothing but a URL is a link, whether it came from the file
19
+ // or from a formatDetails callback -- the same courtesy `linkify` does for a
20
+ // URL sitting inside a longer string, one layer down in SanitizedHTML.
21
+ //
22
+ // New tab, matching `rewriteExternalAnchors` on that other path. Navigating
23
+ // in place discards the session, and in an embedded JBrowse it takes the host
24
+ // page with it.
25
+ const isLink = /^https?:\/\//.test(`${value}`);
26
+ return (_jsx("div", { className: classes.fieldValue, children: isValidElement(value) ? (value) : isLink ? (_jsx(Link, { href: `${value}`, target: "_blank", rel: "noopener noreferrer", children: `${value}` })) : (_jsx(SanitizedHTML, { html: isObject(value) ? JSON.stringify(value) : String(value) })) }));
20
27
  }
@@ -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(props: BaseProps): import("react").JSX.Element;
@@ -1,24 +1,35 @@
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";
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { toLocale } from '../../util/index.js';
3
+ import Position from './Position.js';
4
+ import SimpleField from './SimpleField.js';
5
+ import { applyFeatureFormatting, isFormattedField } from './util.js';
5
6
  export default function CoreDetails(props) {
6
7
  const { feature } = props;
7
- const obj = feature;
8
- const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
8
+ const formattedFeat = applyFeatureFormatting(feature);
9
9
  const { start, end } = formattedFeat;
10
10
  const displayedDetails = {
11
11
  ...formattedFeat,
12
- length: toLocale(end - start),
12
+ // Length is derived, so it is computed rather than read off the feature --
13
+ // but a formatDetails callback that names `length` still wins (and
14
+ // `length: null` hides the row), like every other core field. The raw
15
+ // feature's own `length`, if any, stays ignored: it is in Attributes'
16
+ // globalOmit precisely because adapters use it as bookkeeping.
17
+ length: isFormattedField(feature, 'length')
18
+ ? formattedFeat.length
19
+ : toLocale(end - start),
13
20
  };
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)))] }));
21
+ // array (not object) so the display order is explicit, not reliant on JS key
22
+ // insertion order
23
+ const coreRenderedDetails = [
24
+ ['name', 'Name'],
25
+ ['description', 'Description'],
26
+ ['length', 'Length'],
27
+ ['type', 'Type'],
28
+ ];
29
+ return (_jsxs(_Fragment, { children: [_jsx(SimpleField, { name: "Position", value: _jsx(Position, { ...props, feature: formattedFeat }) }), coreRenderedDetails
30
+ .filter(([key]) => displayedDetails[key] != null)
31
+ .map(([key, name]) => {
32
+ const value = displayedDetails[key];
33
+ return (_jsx(SimpleField, { name: name, value: Array.isArray(value) ? value.join(', ') : value }, name));
34
+ })] }));
24
35
  }
@@ -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 +1,13 @@
1
1
  import type { SimpleFeatureSerialized } from '../../util/index.ts';
2
- import type { Descriptors } from '../types.tsx';
2
+ import type { Descriptors, FeatureFormatter } from '../types.tsx';
3
3
  import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
4
- export default function FeatureDetails(props: {
4
+ interface FeatureDetailsProps {
5
5
  model: IAnyStateTreeNode;
6
6
  feature: 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
+ }
12
+ declare const FeatureDetails: (props: FeatureDetailsProps) => import("react").JSX.Element;
13
+ export default FeatureDetails;