@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
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  1024. package/esm/util/rpc.d.ts +16 -1
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  1044. package/esm/util/sessionSharing.d.ts +40 -0
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  1052. package/esm/util/shapeNames.d.ts +7 -0
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  1056. package/esm/util/springAnimate.d.ts +20 -0
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  1091. package/esm/util/tss-react/index.d.ts +11 -2
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  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
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  1123. package/esm/util/useEventCallback.d.ts +1 -0
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  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
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  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
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  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
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  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1155. package/esm/util/wheelZoom.d.ts +65 -0
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  1157. package/esm/util/whenViewSettled.d.ts +74 -0
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  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
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  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
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  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
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  1243. package/esm/util/map-obj/index.d.ts +0 -13
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  1247. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
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  1250. package/esm/util/offscreenCanvasUtils.js +0 -19
  1251. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,16 @@
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { progressLabel } from '../util/progress.js';
3
+ import LoadingEllipses from './LoadingEllipses.js';
4
+ import StatusProgressBar from './StatusProgressBar.js';
5
+ /**
6
+ * The shared "labelled ellipses + optional determinate bar" body used by the
7
+ * loading/refetch indicators. Renders a {@link LoadingEllipses} label — with the
8
+ * rounded percent appended via {@link progressLabel} when `fraction` is
9
+ * determinate — and a determinate {@link StatusProgressBar} only when a
10
+ * `fraction` is present (an indeterminate phase shows just the animated label,
11
+ * no bar). Callers own the surrounding layout and supply `barClassName` for the
12
+ * bar width.
13
+ */
14
+ export default function LoadingProgress({ message, fraction, variant, barClassName, }) {
15
+ return (_jsxs(_Fragment, { children: [_jsx(LoadingEllipses, { variant: variant, message: progressLabel(message || 'Loading', fraction) }), fraction === undefined ? null : (_jsx(StatusProgressBar, { className: barClassName, fraction: fraction }))] }));
16
+ }
package/esm/ui/Logo.d.ts CHANGED
@@ -2,6 +2,6 @@ type LogoVariant = 'color' | 'black' | 'white';
2
2
  interface LogoProps {
3
3
  variant?: LogoVariant;
4
4
  }
5
- export declare function Logomark({ variant }: LogoProps): import("react/jsx-runtime").JSX.Element;
6
- export declare function LogoFull({ variant }: LogoProps): import("react/jsx-runtime").JSX.Element;
5
+ export declare function Logomark({ variant }: LogoProps): import("react").JSX.Element;
6
+ export declare function LogoFull({ variant }: LogoProps): import("react").JSX.Element;
7
7
  export {};
package/esm/ui/Logo.js CHANGED
@@ -1,30 +1,29 @@
1
- import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
2
- function getColors(variant) {
3
- if (variant === 'black') {
4
- return {
5
- midnight: '#808080',
6
- forrest: '#666666',
7
- grape: '#4d4d4d',
8
- mandarin: '#333333',
9
- gray: '#1a1a1a',
10
- };
11
- }
12
- if (variant === 'white') {
13
- return {
14
- midnight: '#ffffff',
15
- forrest: '#e6e6e6',
16
- grape: '#cccccc',
17
- mandarin: '#b3b3b3',
18
- gray: '#999999',
19
- };
20
- }
21
- return {
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ const colorSets = {
3
+ black: {
4
+ midnight: '#808080',
5
+ forest: '#666666',
6
+ grape: '#4d4d4d',
7
+ mandarin: '#333333',
8
+ gray: '#1a1a1a',
9
+ },
10
+ white: {
11
+ midnight: '#ffffff',
12
+ forest: '#e6e6e6',
13
+ grape: '#cccccc',
14
+ mandarin: '#b3b3b3',
15
+ gray: '#999999',
16
+ },
17
+ color: {
22
18
  midnight: '#0d233f',
23
- forrest: '#135560',
19
+ forest: '#135560',
24
20
  grape: '#721e63',
25
21
  mandarin: '#ffb11d',
26
22
  gray: '#dadada',
27
- };
23
+ },
24
+ };
25
+ function getColors(variant = 'color') {
26
+ return colorSets[variant];
28
27
  }
29
28
  export function Logomark({ variant }) {
30
29
  return (_jsx("svg", { viewBox: "0 0 175 175", children: _jsx(Icon, { variant: variant }) }));
@@ -34,7 +33,7 @@ export function LogoFull({ variant }) {
34
33
  }
35
34
  function Icon({ variant }) {
36
35
  const colors = getColors(variant);
37
- return (_jsxs(_Fragment, { children: [_jsx("path", { style: { fill: colors.midnight }, d: "M120.5,57.5c.168,0,.333.012.5.013V40.506c-.167,0-.333-.006-.5-.006a98.325,98.325,0,0,0-77.4,37.565q-2.664,3.378-5.023,6.994l14.206,9.327Q54.043,91.709,56,89.179A81.363,81.363,0,0,1,120.5,57.5Z" }), _jsx("path", { style: { fill: colors.forrest }, d: "M148.668,86.223c.308.133.6.283.908.42l6.746-15.618c-.153-.067-.3-.143-.454-.21a81.36,81.36,0,0,0-71.777,3.5q-2.8,1.544-5.469,3.309l9.249,14.054A63.93,63.93,0,0,1,148.668,86.223Z" }), _jsx("path", { style: { fill: colors.grape }, d: "M170.894,109.37A63.929,63.929,0,0,0,113.4,88.861l2.336,15.474a48.456,48.456,0,0,1,44.322,15.42c.111.125.214.255.324.381l11.16-10C171.323,109.879,171.118,109.62,170.894,109.37Z" }), _jsx("path", { style: { fill: colors.mandarin }, d: "M150.921,150.314c.04.163.07.326.107.489l16.509-4.058c-.039-.163-.067-.326-.107-.489A48.457,48.457,0,0,0,135.575,111.8l-5.515,15.591A32.466,32.466,0,0,1,150.921,150.314Z" }), _jsx("path", { style: { fill: colors.gray }, d: "M134.1,138.129l-9.779,13.213a32.486,32.486,0,0,1,7.823,14.463l15.147.852c.012-.166.032-.331.041-.5A32.464,32.464,0,0,0,134.1,138.129Z" })] }));
36
+ return (_jsxs(_Fragment, { children: [_jsx("path", { style: { fill: colors.midnight }, d: "M120.5,57.5c.168,0,.333.012.5.013V40.506c-.167,0-.333-.006-.5-.006a98.325,98.325,0,0,0-77.4,37.565q-2.664,3.378-5.023,6.994l14.206,9.327Q54.043,91.709,56,89.179A81.363,81.363,0,0,1,120.5,57.5Z" }), _jsx("path", { style: { fill: colors.forest }, d: "M148.668,86.223c.308.133.6.283.908.42l6.746-15.618c-.153-.067-.3-.143-.454-.21a81.36,81.36,0,0,0-71.777,3.5q-2.8,1.544-5.469,3.309l9.249,14.054A63.93,63.93,0,0,1,148.668,86.223Z" }), _jsx("path", { style: { fill: colors.grape }, d: "M170.894,109.37A63.929,63.929,0,0,0,113.4,88.861l2.336,15.474a48.456,48.456,0,0,1,44.322,15.42c.111.125.214.255.324.381l11.16-10C171.323,109.879,171.118,109.62,170.894,109.37Z" }), _jsx("path", { style: { fill: colors.mandarin }, d: "M150.921,150.314c.04.163.07.326.107.489l16.509-4.058c-.039-.163-.067-.326-.107-.489A48.457,48.457,0,0,0,135.575,111.8l-5.515,15.591A32.466,32.466,0,0,1,150.921,150.314Z" }), _jsx("path", { style: { fill: colors.gray }, d: "M134.1,138.129l-9.779,13.213a32.486,32.486,0,0,1,7.823,14.463l15.147.852c.012-.166.032-.331.041-.5A32.464,32.464,0,0,0,134.1,138.129Z" })] }));
38
37
  }
39
38
  function Text({ variant }) {
40
39
  const colors = getColors(variant);
package/esm/ui/Menu.js CHANGED
@@ -1 +1 @@
1
- export { default } from "./CascadingMenu.js";
1
+ export { default } from './CascadingMenu.js';
@@ -0,0 +1,3 @@
1
+ export declare function MenuItemChevron({ hidden }: {
2
+ hidden?: boolean;
3
+ }): import("react").JSX.Element;
@@ -0,0 +1,19 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import ChevronRight from '@mui/icons-material/ChevronRight';
3
+ // The chevron a submenu row ends in, and — `hidden` — an invisible copy
4
+ // reserving the identical footprint on a clickable row that has none, so a menu
5
+ // carrying help on both kinds lands every "?" in one column.
6
+ //
7
+ // ONE COMPONENT, because "identical footprint" is the whole contract and two
8
+ // bodies can drift: a `fontSize` added to one and not the other reintroduces
9
+ // exactly the misalignment this exists to remove.
10
+ //
11
+ // A COPY, not a width. The column was a hard-coded 24, the px an MUI
12
+ // `fontSize="medium"` icon is at MUI's own defaults. This theme sets
13
+ // `typography.fontSize: 12`, which scales `pxToRem` by 12/14, so the chevron
14
+ // actually draws at ~20.6px and every clickable row's "?" sat ~3.4px inboard of
15
+ // the submenu rows'. Rendering the icon itself cannot be off by a scale factor
16
+ // nothing here gets to see.
17
+ export function MenuItemChevron({ hidden }) {
18
+ return _jsx(ChevronRight, { style: hidden ? { visibility: 'hidden' } : undefined });
19
+ }
@@ -0,0 +1,4 @@
1
+ export declare function MenuItemEndDecoration({ type, checked, }: {
2
+ type: 'checkbox' | 'radio';
3
+ checked: boolean;
4
+ }): import("react").JSX.Element;
@@ -0,0 +1,28 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import CheckBoxIcon from '@mui/icons-material/CheckBox';
3
+ import CheckBoxOutlineBlankIcon from '@mui/icons-material/CheckBoxOutlineBlank';
4
+ import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked';
5
+ import RadioButtonUncheckedIcon from '@mui/icons-material/RadioButtonUnchecked';
6
+ import { makeStyles } from '../util/tss-react/index.js';
7
+ const useStyles = makeStyles()({
8
+ menuItemEndDecoration: {
9
+ padding: 0,
10
+ margin: 0,
11
+ height: 16,
12
+ },
13
+ });
14
+ export function MenuItemEndDecoration({ type, checked, }) {
15
+ const { classes } = useStyles();
16
+ let icon;
17
+ switch (type) {
18
+ case 'checkbox': {
19
+ icon = checked ? (_jsx(CheckBoxIcon, {})) : (_jsx(CheckBoxOutlineBlankIcon, { color: "action" }));
20
+ break;
21
+ }
22
+ case 'radio': {
23
+ icon = checked ? (_jsx(RadioButtonCheckedIcon, {})) : (_jsx(RadioButtonUncheckedIcon, { color: "action" }));
24
+ break;
25
+ }
26
+ }
27
+ return _jsx("div", { className: classes.menuItemEndDecoration, children: icon });
28
+ }
@@ -0,0 +1,12 @@
1
+ import type { ClickableMenuItem, SubMenuItem } from './MenuTypes.ts';
2
+ export type DecoratedMenuItem = ClickableMenuItem | SubMenuItem;
3
+ export interface MenuColumnFlags {
4
+ hasCheckboxOrRadioWithHelp: boolean;
5
+ hasEndAdornment: boolean;
6
+ hasSubmenuWithHelp: boolean;
7
+ sharedActionColumn: boolean;
8
+ }
9
+ export declare function MenuItemTrailing({ item, columns: { hasCheckboxOrRadioWithHelp, hasEndAdornment, hasSubmenuWithHelp, sharedActionColumn, }, }: {
10
+ item: DecoratedMenuItem;
11
+ columns: MenuColumnFlags;
12
+ }): import("react").JSX.Element;
@@ -0,0 +1,42 @@
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import CascadingMenuHelpIconButton, { CascadingMenuHelpIconSpacer, } from './CascadingMenuHelpIconButton.js';
3
+ import { MenuItemChevron } from './MenuItemChevron.js';
4
+ import { MenuItemEndDecoration } from './MenuItemEndDecoration.js';
5
+ import { menuItemAdornment } from './menuItemAdornment.js';
6
+ // gap that sets the value glyph (row state) apart from the trailing help/pin
7
+ // action column, so a busy row reads as "value | actions" not one dense cluster
8
+ const valueActionGap = 8;
9
+ // fixed footprint reserved for the endAdornment column so pins right-align
10
+ const endAdornmentColumnWidth = 28;
11
+ // The checkbox/radio glyph reflecting a row's value. Held slightly apart from
12
+ // the action column when the menu has one, so state and actions don't blur.
13
+ function MenuItemValueGlyph({ type, checked, separated, }) {
14
+ return (_jsx("div", { style: { marginRight: separated ? valueActionGap : 0 }, children: _jsx(MenuItemEndDecoration, { type: type, checked: checked }) }));
15
+ }
16
+ // Fixed-width column holding an item's endAdornment (e.g. the "default for all"
17
+ // pin). Reserved on every row of a menu that has any adornment so they
18
+ // right-align into their own column.
19
+ function MenuItemEndAdornmentSlot({ children }) {
20
+ return (_jsx("div", { style: {
21
+ width: endAdornmentColumnWidth,
22
+ display: 'flex',
23
+ justifyContent: 'flex-end',
24
+ alignItems: 'center',
25
+ }, children: children }));
26
+ }
27
+ // Everything trailing a menu row's label, for a clickable row and a submenu row
28
+ // alike: a flex spacer that right-aligns the decorations, then the value glyph,
29
+ // help affordance, endAdornment column, and the chevron column. When
30
+ // `sharedActionColumn` is set, no row in the menu combines help with an
31
+ // adornment, so the two share one trailing column (whichever this row has)
32
+ // rather than each claiming its own.
33
+ export function MenuItemTrailing({ item, columns: { hasCheckboxOrRadioWithHelp, hasEndAdornment, hasSubmenuWithHelp, sharedActionColumn, }, }) {
34
+ const isSubmenu = 'subMenu' in item;
35
+ const isCheckOrRadio = item.type === 'checkbox' || item.type === 'radio';
36
+ const hasActionColumn = hasCheckboxOrRadioWithHelp || hasEndAdornment;
37
+ // a disabled row can't open the help popover (pointer-events:none), so its
38
+ // helpText is surfaced as a hover tooltip by the row instead
39
+ const helpButton = item.helpText && !item.disabled ? (_jsx(CascadingMenuHelpIconButton, { helpText: item.helpText, label: item.label })) : undefined;
40
+ return (_jsxs(_Fragment, { children: [_jsx("div", { style: { flexGrow: 1, minWidth: 10 } }), isCheckOrRadio ? (_jsx(MenuItemValueGlyph, { type: item.type, checked: item.checked, separated: hasActionColumn })) : null, sharedActionColumn ? (_jsx(MenuItemEndAdornmentSlot, { children: helpButton ?? menuItemAdornment(item) })) : (_jsxs(_Fragment, { children: [helpButton ??
41
+ (isCheckOrRadio && hasCheckboxOrRadioWithHelp ? (_jsx(CascadingMenuHelpIconSpacer, {})) : null), hasEndAdornment ? (_jsx(MenuItemEndAdornmentSlot, { children: menuItemAdornment(item) })) : null] })), isSubmenu ? (_jsx(MenuItemChevron, {})) : hasSubmenuWithHelp ? (_jsx(MenuItemChevron, { hidden: true })) : null] }));
42
+ }
@@ -1,38 +1,128 @@
1
+ /** #menuItem divider | a horizontal rule; not clickable */
1
2
  export interface MenuDivider {
2
3
  priority?: number;
3
4
  type: 'divider';
4
5
  }
6
+ /** #menuItem subHeader | a text label for a section of a menu; not clickable */
5
7
  export interface MenuSubHeader {
6
8
  type: 'subHeader';
7
9
  priority?: number;
8
10
  label: string;
9
11
  }
12
+ export type MenuItemClickHandler = (...args: any[]) => void;
10
13
  export interface BaseMenuItem {
14
+ /**
15
+ * #menuField stable identifier; keys the row, and finds it again from a test
16
+ *
17
+ * Worth setting on a row the menu cannot otherwise tell apart — one whose
18
+ * `label` is an element, or one a list may repeat the text of. A level's keys
19
+ * are unique either way (`rowKeys` suffixes a repeat), so this is what keeps a
20
+ * row's React identity when the rows around it reorder rather than something
21
+ * the menu needs to draw correctly.
22
+ */
11
23
  id?: string;
24
+ /** #menuField the row's text */
12
25
  label: React.ReactNode;
26
+ /** #menuField sort weight within the menu; higher sorts earlier */
13
27
  priority?: number;
28
+ /**
29
+ * #menuField secondary text under the label; prefer `withHint` in the label
30
+ *
31
+ * Renders as a second line under the label, which makes the row two lines
32
+ * tall. Nothing in this repo uses it any more: a menu whose rows are each two
33
+ * lines is harder to scan than the labels it buried, so a short clarifier
34
+ * goes in the label (`withHint` where it is conditional) and real prose goes
35
+ * in `helpText`. Kept because it renders and plugins may pass one.
36
+ */
14
37
  subLabel?: string;
38
+ /** #menuField any [MUI icon](https://mui.com/material-ui/material-icons/) component */
15
39
  icon?: React.ElementType;
40
+ /** #menuField renders the row unclickable */
16
41
  disabled?: boolean;
42
+ /** #menuField tooltip shown from a help icon at the trailing edge */
17
43
  helpText?: string;
44
+ /** #menuField tooltip shown when the item is disabled, in place of helpText */
45
+ disabledHelpText?: string;
46
+ /**
47
+ * #menuField override the dismiss-on-click rule; see `staysOpenOnClick`
48
+ *
49
+ * Override whether the menu stays open after this row is clicked. Leave it
50
+ * unset and the row TYPE decides: a `checkbox`/`radio` is a setting, so the
51
+ * menu stays put (users flip several in one visit, and the menu content is an
52
+ * observer, so its checked marks update live), while every other row is an
53
+ * action and dismisses.
54
+ *
55
+ * Set `false` on a checkbox/radio whose click is really terminal — it opens a
56
+ * dialog ("Custom...", "Solid color...") or swaps the display out from under
57
+ * the menu. Set `true` on a non-checkbox row that should survive its click.
58
+ */
59
+ keepMenuOpen?: boolean;
60
+ /**
61
+ * #menuField arbitrary trailing content
62
+ *
63
+ * Extra content rendered at the trailing (right) edge of the row, after the
64
+ * checkbox/radio decoration and help icon — e.g. a secondary toggle. The
65
+ * content must `stopPropagation` on its own click so it doesn't fire the row's
66
+ * onClick or dismiss the menu.
67
+ *
68
+ * An **element**, so a module that sets it drags React and whatever it renders
69
+ * into its own graph. Reach for it only when the content is genuinely
70
+ * arbitrary — synteny's and wiggle's colour swatches are what it exists for.
71
+ */
72
+ endAdornment?: React.ReactNode;
18
73
  }
74
+ /** #menuItem normal | an action row; the default when `type` is omitted */
19
75
  export interface NormalMenuItem extends BaseMenuItem {
20
76
  type?: 'normal';
21
- onClick: (...args: any[]) => void;
77
+ onClick: MenuItemClickHandler;
22
78
  }
79
+ /** #menuItem checkbox | a setting row with a checkbox; leaves the menu open */
23
80
  export interface CheckboxMenuItem extends BaseMenuItem {
24
81
  type: 'checkbox';
25
82
  checked: boolean;
26
- onClick: (...args: any[]) => void;
83
+ onClick: MenuItemClickHandler;
27
84
  }
85
+ /** #menuItem radio | a setting row with a radio button; leaves the menu open */
28
86
  export interface RadioMenuItem extends BaseMenuItem {
29
87
  type: 'radio';
30
88
  checked: boolean;
31
- onClick: (...args: any[]) => void;
89
+ onClick: MenuItemClickHandler;
32
90
  }
91
+ /**
92
+ * #menuItem subMenu | nests another `MenuItem[]`, or a function building one, to any depth
93
+ *
94
+ * The function form is called when the submenu opens (or a walker asks for its
95
+ * rows), not when the parent menu is built — for a submenu whose rows cost a
96
+ * scan of the display's data to name. Read the field through `resolveSubMenu`
97
+ * rather than by hand, so the two forms stay one thing to the renderer and to
98
+ * every test helper that flattens a menu.
99
+ */
33
100
  export interface SubMenuItem extends BaseMenuItem {
34
101
  type?: 'subMenu';
35
- subMenu: MenuItem[];
102
+ subMenu: MenuItem[] | (() => MenuItem[]);
36
103
  }
37
- export type MenuItem = MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem;
104
+ export declare function resolveSubMenu(item: SubMenuItem): MenuItem[];
105
+ /**
106
+ * #menuItem custom | renders arbitrary React content inline, e.g. a slider
107
+ *
108
+ * The menu is not dismissed when interacting with it, so a control can be
109
+ * dragged live; `onClose` is passed for content that wants to close the menu
110
+ * explicitly. `label` is used only as a React key/testid.
111
+ */
112
+ export interface CustomMenuItem extends BaseMenuItem {
113
+ type: 'custom';
114
+ render: (onClose: () => void) => React.ReactNode;
115
+ }
116
+ export type ClickableMenuItem = NormalMenuItem | CheckboxMenuItem | RadioMenuItem;
117
+ export type MenuItem = MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | CustomMenuItem;
118
+ /**
119
+ * Whether clicking a row leaves the menu up — the rule `CascadingMenu` applies,
120
+ * exported so a display's menu-shape test asserts the behavior a user gets
121
+ * rather than re-deriving it from the flag (each test that spelled out
122
+ * `keepMenuOpen === true` had to be revisited when the default moved here).
123
+ *
124
+ * Defaulted by row TYPE: a checkbox/radio is a setting and stays put, every
125
+ * other row is an action and dismisses. `keepMenuOpen` overrides either way.
126
+ */
127
+ export declare function staysOpenOnClick(item: ClickableMenuItem): boolean;
38
128
  export type MenuItemsGetter = MenuItem[] | (() => MenuItem[]);
@@ -1 +1,16 @@
1
- export {};
1
+ export function resolveSubMenu(item) {
2
+ return typeof item.subMenu === 'function' ? item.subMenu() : item.subMenu;
3
+ }
4
+ // #endregion
5
+ /**
6
+ * Whether clicking a row leaves the menu up — the rule `CascadingMenu` applies,
7
+ * exported so a display's menu-shape test asserts the behavior a user gets
8
+ * rather than re-deriving it from the flag (each test that spelled out
9
+ * `keepMenuOpen === true` had to be revisited when the default moved here).
10
+ *
11
+ * Defaulted by row TYPE: a checkbox/radio is a setting and stays put, every
12
+ * other row is an action and dismisses. `keepMenuOpen` overrides either way.
13
+ */
14
+ export function staysOpenOnClick(item) {
15
+ return (item.keepMenuOpen ?? (item.type === 'checkbox' || item.type === 'radio'));
16
+ }
@@ -0,0 +1,10 @@
1
+ import type { TextFieldProps } from '@mui/material';
2
+ export default function MonospaceTextField({ value, onChange, error, label, children, style, className, readOnly, inputTestId, helperText, variant, ...rest }: {
3
+ value: string;
4
+ onChange?: (value: string) => void;
5
+ error?: unknown;
6
+ label?: React.ReactNode;
7
+ children?: React.ReactNode;
8
+ readOnly?: boolean;
9
+ inputTestId?: string;
10
+ } & Omit<TextFieldProps, 'value' | 'onChange' | 'error' | 'slotProps'>): import("react").JSX.Element;
@@ -0,0 +1,40 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { InputLabel, TextField } from '@mui/material';
3
+ import { makeStyles } from '../util/tss-react/index.js';
4
+ import { alpha } from './palette.js';
5
+ const monospaceFontFamily = 'Consolas, "Andale Mono WT", "Andale Mono", "Lucida Console", "Lucida Sans Typewriter", "DejaVu Sans Mono", "Bitstream Vera Sans Mono", "Liberation Mono", "Nimbus Mono L", Monaco, "Courier New", Courier, monospace';
6
+ const useStyles = makeStyles()(theme => ({
7
+ container: {
8
+ width: '100%',
9
+ overflowX: 'auto',
10
+ },
11
+ field: {
12
+ fontFamily: monospaceFontFamily,
13
+ },
14
+ errorField: {
15
+ background: alpha(theme.palette.error.main, 0.15),
16
+ },
17
+ }));
18
+ // Monospace multiline TextField for code/jexl/JSON/sequence content. A parse
19
+ // error turns it red and takes the helper text's place under the field, so
20
+ // the text does not move while it flips between valid and invalid. `children`
21
+ // render below the field (e.g. a description or help button).
22
+ export default function MonospaceTextField({ value, onChange, error, label, children, style, className, readOnly, inputTestId, helperText, variant = 'outlined', ...rest }) {
23
+ const { classes, cx } = useStyles();
24
+ return (_jsxs("div", { className: classes.container, children: [label ? _jsx(InputLabel, { shrink: true, children: label }) : null, _jsx(TextField, { ...rest, variant: variant, multiline: true, error: !!error, helperText: error ? `${error}` : helperText, value: value, onChange: event => {
25
+ onChange?.(event.target.value);
26
+ }, className: cx(className, error ? classes.errorField : undefined), style: style, slotProps: {
27
+ input: {
28
+ readOnly,
29
+ classes: {
30
+ input: classes.field,
31
+ },
32
+ },
33
+ htmlInput: {
34
+ 'data-testid': inputTestId,
35
+ spellCheck: false,
36
+ autoCorrect: 'off',
37
+ autoCapitalize: 'off',
38
+ },
39
+ } }), children] }));
40
+ }
@@ -0,0 +1,31 @@
1
+ import type { TextFieldProps } from '@mui/material';
2
+ interface OwnProps {
3
+ /** Initial numeric value; undefined renders as empty input. */
4
+ defaultValue?: number;
5
+ /**
6
+ * Fires on every keystroke with the parsed number, or undefined when
7
+ * the input is empty or invalid (NaN / out of bounds). The parent
8
+ * decides whether to gate submission on undefined.
9
+ */
10
+ onValueChange: (value: number | undefined) => void;
11
+ /** Optional inclusive lower bound. */
12
+ min?: number;
13
+ /** Optional inclusive upper bound. */
14
+ max?: number;
15
+ /** Shown under the input when the value is non-empty and invalid. */
16
+ errorText?: string;
17
+ }
18
+ type Props = Omit<TextFieldProps, 'value' | 'onChange' | 'type' | 'error'> & OwnProps & {
19
+ helperText?: TextFieldProps['helperText'];
20
+ };
21
+ /**
22
+ * Uncontrolled-style numeric TextField. Owns the input *text* internally;
23
+ * emits the parsed *number* (or undefined) to the parent on every change.
24
+ *
25
+ * Use over `<TextField type="number" />` — the browser number input has
26
+ * known UX problems (scroll-to-change, locale issues, browser-specific
27
+ * spinners). This component keeps a plain text input and validates with
28
+ * `Number.isFinite` + optional min/max.
29
+ */
30
+ export default function NumberTextField(props: Props): import("react").JSX.Element;
31
+ export {};
@@ -0,0 +1,33 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { useState } from 'react';
3
+ import { TextField } from '@mui/material';
4
+ /**
5
+ * Uncontrolled-style numeric TextField. Owns the input *text* internally;
6
+ * emits the parsed *number* (or undefined) to the parent on every change.
7
+ *
8
+ * Use over `<TextField type="number" />` — the browser number input has
9
+ * known UX problems (scroll-to-change, locale issues, browser-specific
10
+ * spinners). This component keeps a plain text input and validates with
11
+ * `Number.isFinite` + optional min/max.
12
+ */
13
+ export default function NumberTextField(props) {
14
+ const { defaultValue, onValueChange, min, max, errorText = 'Must be a valid number', helperText, ...rest } = props;
15
+ const [text, setText] = useState(defaultValue === undefined ? '' : `${defaultValue}`);
16
+ const parsed = parseInBounds(text, min, max);
17
+ const showError = text !== '' && parsed === undefined;
18
+ return (_jsx(TextField, { ...rest, value: text, error: showError, helperText: showError ? errorText : helperText, autoComplete: "off", onChange: event => {
19
+ const next = event.target.value;
20
+ setText(next);
21
+ onValueChange(parseInBounds(next, min, max));
22
+ } }));
23
+ }
24
+ function parseInBounds(text, min, max) {
25
+ if (text === '') {
26
+ return undefined;
27
+ }
28
+ const n = Number(text);
29
+ const ok = Number.isFinite(n) &&
30
+ (min === undefined || n >= min) &&
31
+ (max === undefined || n <= max);
32
+ return ok ? n : undefined;
33
+ }
@@ -0,0 +1,90 @@
1
+ import type { JBrowsePalette } from './palette.ts';
2
+ import type { JBrowseStyleTheme } from './styleTheme.ts';
3
+ import type { ReactNode } from 'react';
4
+ /**
5
+ * Supply the whole style theme — colors plus spacing and type scale. This is
6
+ * what JBrowse's own products mount, from `session.styleTheme`, so a config
7
+ * `theme` that sets `spacing` or `typography` reaches `makeStyles` and Material
8
+ * UI alike.
9
+ */
10
+ export declare function StyleThemeProvider({ theme, children, }: {
11
+ theme: JBrowseStyleTheme;
12
+ children: ReactNode;
13
+ }): import("react").JSX.Element;
14
+ /**
15
+ * Supply colors only, leaving JBrowse's default sizing in place. The narrower
16
+ * of the two, and what a host that already holds a palette mounts: it is saying
17
+ * what JBrowse should draw *with*, not restating its type scale.
18
+ *
19
+ * **A host following its own light/dark state wants
20
+ * {@link SessionPaletteProvider} instead**, which is this plus the session
21
+ * write that the worker-side half of the rendering derives from. This one
22
+ * colors React and nothing else.
23
+ */
24
+ export declare function PaletteProvider({ palette, children, }: {
25
+ palette: JBrowsePalette;
26
+ children: ReactNode;
27
+ }): import("react").JSX.Element;
28
+ export declare function useStyleTheme(): JBrowseStyleTheme;
29
+ export declare function usePalette(): JBrowsePalette;
30
+ /** What {@link useSessionPalette} needs of a session. */
31
+ export interface ThemeModeSession {
32
+ setThemeMode: (mode: 'light' | 'dark') => void;
33
+ readonly palette: JBrowsePalette;
34
+ }
35
+ /**
36
+ * Point a session at light or dark and get back the palette it resolves to,
37
+ * for a host that wants the palette itself — to read a color out of, or to
38
+ * hand somewhere other than a provider. A host that only wants JBrowse to
39
+ * follow its dark mode mounts {@link SessionPaletteProvider}, which is this
40
+ * hook and the provider in one.
41
+ *
42
+ * Pass no mode and JBrowse follows the page: its declared CSS `color-scheme`
43
+ * when that names one of light or dark, the OS preference otherwise, tracking
44
+ * both. A host whose mode lives somewhere a stylesheet cannot see passes it.
45
+ *
46
+ * **Both halves are load-bearing, which is why the pairing is published as a
47
+ * component.** The palette is what *React* draws with; the config `theme` slot
48
+ * this writes is also what ships to the RPC worker, where feature labels are
49
+ * baked into the rendered image. Mount `PaletteProvider` on a palette from
50
+ * somewhere else and those labels stay in the old mode — light text on a light
51
+ * image, and no error anywhere. `setThemeMode` writes the one slot both are
52
+ * derived from, which is why this returns the palette rather than taking one.
53
+ *
54
+ * The write lands in an effect, so the first paint after a mode change uses
55
+ * the previous palette. That is a frame on a canvas that is about to be
56
+ * redrawn anyway; it is not somewhere to add a suspense boundary.
57
+ */
58
+ export declare function useSessionPalette(session: ThemeModeSession, mode?: 'light' | 'dark'): JBrowsePalette;
59
+ /**
60
+ * #api
61
+ * Make JBrowse follow the host's light/dark state — the whole of it, in one
62
+ * mount:
63
+ *
64
+ * ```tsx
65
+ * <SessionPaletteProvider session={session} mode={myAppIsDark ? 'dark' : 'light'}>
66
+ * {tracks}
67
+ * </SessionPaletteProvider>
68
+ * ```
69
+ *
70
+ * `mode` is optional. Left out, JBrowse follows the page's declared
71
+ * `color-scheme` — so a host whose dark-mode toggle sets it, as most do, mounts
72
+ * this with a session and nothing else — and the OS preference where the page
73
+ * declares none.
74
+ *
75
+ * A component rather than a documented pair of calls because the pair has a
76
+ * half that can be left out with nothing to show for it. `PaletteProvider` is
77
+ * the name a host reaches for, and it colors the React side alone; the session
78
+ * write is what reaches the RPC worker, which bakes feature labels into the
79
+ * rendered image. So a host that mounts only the provider gets light-mode
80
+ * labels on a dark page, from a canvas whose every other pixel is right, and
81
+ * nothing errors. See {@link useSessionPalette} for the mechanism.
82
+ *
83
+ * The session is the only thing that resolves a palette here, so a host
84
+ * supplying colors of its own mounts `PaletteProvider` directly instead.
85
+ */
86
+ export declare function SessionPaletteProvider({ session, mode, children, }: {
87
+ session: ThemeModeSession;
88
+ mode?: 'light' | 'dark';
89
+ children: ReactNode;
90
+ }): import("react").JSX.Element;