@jbrowse/core 4.3.0 → 5.0.0-beta.2

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 (1140) hide show
  1. package/README.md +822 -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 +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  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 +62 -93
  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/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
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  1022. package/esm/util/useMeasure.d.ts +11 -1
  1023. package/esm/util/useMeasure.js +20 -6
  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1,38 +1,167 @@
1
+ import type { Pin } from '../configuration/promotablePin.ts';
2
+ /** #menuItem divider | a horizontal rule; not clickable */
1
3
  export interface MenuDivider {
2
4
  priority?: number;
3
5
  type: 'divider';
4
6
  }
7
+ /** #menuItem subHeader | a text label for a section of a menu; not clickable */
5
8
  export interface MenuSubHeader {
6
9
  type: 'subHeader';
7
10
  priority?: number;
8
11
  label: string;
9
12
  }
13
+ export type MenuItemClickHandler = (...args: any[]) => void;
10
14
  export interface BaseMenuItem {
15
+ /** #menuField stable identifier, for tests and for finding a row again */
11
16
  id?: string;
17
+ /** #menuField the row's text */
12
18
  label: React.ReactNode;
19
+ /** #menuField sort weight within the menu; higher sorts earlier */
13
20
  priority?: number;
21
+ /**
22
+ * #menuField secondary text under the label; prefer `withHint` in the label
23
+ *
24
+ * Renders as a second line under the label, which makes the row two lines
25
+ * tall. Nothing in this repo uses it any more: a menu whose rows are each two
26
+ * lines is harder to scan than the labels it buried, so a short clarifier
27
+ * goes in the label (`withHint` where it is conditional) and real prose goes
28
+ * in `helpText`. Kept because it renders and plugins may pass one.
29
+ */
14
30
  subLabel?: string;
31
+ /** #menuField any [MUI icon](https://mui.com/material-ui/material-icons/) component */
15
32
  icon?: React.ElementType;
33
+ /** #menuField renders the row unclickable */
16
34
  disabled?: boolean;
35
+ /** #menuField tooltip shown from a help icon at the trailing edge */
17
36
  helpText?: string;
37
+ /** #menuField tooltip shown when the item is disabled, in place of helpText */
38
+ disabledHelpText?: string;
39
+ /**
40
+ * #menuField override the dismiss-on-click rule; see `staysOpenOnClick`
41
+ *
42
+ * Override whether the menu stays open after this row is clicked. Leave it
43
+ * unset and the row TYPE decides: a `checkbox`/`radio` is a setting, so the
44
+ * menu stays put (users flip several in one visit, and the menu content is an
45
+ * observer, so its checked marks update live), while every other row is an
46
+ * action and dismisses.
47
+ *
48
+ * Set `false` on a checkbox/radio whose click is really terminal — it opens a
49
+ * dialog ("Custom...", "Solid color...") or swaps the display out from under
50
+ * the menu. Set `true` on a non-checkbox row that should survive its click.
51
+ */
52
+ keepMenuOpen?: boolean;
53
+ /**
54
+ * #menuField arbitrary trailing content; prefer `pin`
55
+ *
56
+ * Extra content rendered at the trailing (right) edge of the row, after the
57
+ * checkbox/radio decoration and help icon — e.g. a secondary toggle. The
58
+ * content must `stopPropagation` on its own click so it doesn't fire the row's
59
+ * onClick or dismiss the menu.
60
+ *
61
+ * An **element**, so a module that sets it drags React and whatever it renders
62
+ * into its own graph. That is fine for the one-off it exists for (synteny's
63
+ * color swatch) and wrong for the common case, which is why the pin below is
64
+ * a description instead. Prefer `pin`; reach for this only when the
65
+ * content is genuinely arbitrary.
66
+ */
67
+ endAdornment?: React.ReactNode;
68
+ /**
69
+ * #menuField the "apply this to all open tracks of this type" pin; set it with a promotable builder
70
+ *
71
+ * The trailing "default for all tracks of this type" pin, as a **description**
72
+ * rather than an element — the renderer builds `PinAdornment` from
73
+ * it. Same rule as a `TrackControlProps` icon name (reference/DISPLAYCHROME.md):
74
+ * menu-item builders are called from state models and menu modules, which are
75
+ * eager, so an element here puts MUI's `ToggleButton`, `Tooltip` and two icons
76
+ * into every host's first paint. It did, until 2026-08-05; see
77
+ * reference/EAGER_BUNDLE.md.
78
+ *
79
+ * Set it through `promotableToggleItem` / `promotableRadioItems` (or
80
+ * `promotableRadioItem` for a lone row), not by hand.
81
+ *
82
+ * A `type: 'custom'` row (`makePromotableSizeMenu`) draws its own pin inside
83
+ * its rendered content and still sets this — the declaration is what lets a
84
+ * built menu be asked which promotable slots it offers a pin for at all. Such
85
+ * a row is excluded from the trailing-column reservation; see
86
+ * `hasMenuItemAdornment`.
87
+ */
88
+ pin?: MenuItemPin;
18
89
  }
90
+ /**
91
+ * A row's pin declaration: the {@link Pin} `makePin` built, plus the one thing
92
+ * the row knows and the pin doesn't — what to call the setting.
93
+ *
94
+ * **`control` holds the pin by reference; don't flatten this into
95
+ * `interface MenuItemPin extends Pin`.** That was tried, to save the hop every
96
+ * reader spells (`item.pin.control.active`), and it turns the declaration into a
97
+ * *copy* of the control — so a `Pin` whose `toggle` resolves anything through
98
+ * `this` silently mutates the copy and the real control never changes. Nothing in
99
+ * `Pin` promises copy-safety: `makePin` happens to close over what it needs, but
100
+ * the interface is a plain object a plugin can build by hand, and the failure is
101
+ * a pin that draws correctly and does nothing. Two hops in `pinnedSlots` and
102
+ * `menuItemAdornment` is the whole cost of not having that.
103
+ */
104
+ export interface MenuItemPin {
105
+ control: Pin;
106
+ /**
107
+ * Names the setting in the pin's tooltip and aria-label. Carried here rather
108
+ * than read off the row's `label`, which is a `ReactNode` and may not be a
109
+ * string; a pin that can't name what it promotes reads as a bug.
110
+ */
111
+ label: string;
112
+ }
113
+ /** #menuItem normal | an action row; the default when `type` is omitted */
19
114
  export interface NormalMenuItem extends BaseMenuItem {
20
115
  type?: 'normal';
21
- onClick: (...args: any[]) => void;
116
+ onClick: MenuItemClickHandler;
22
117
  }
118
+ /** #menuItem checkbox | a setting row with a checkbox; leaves the menu open */
23
119
  export interface CheckboxMenuItem extends BaseMenuItem {
24
120
  type: 'checkbox';
25
121
  checked: boolean;
26
- onClick: (...args: any[]) => void;
122
+ onClick: MenuItemClickHandler;
27
123
  }
124
+ /** #menuItem radio | a setting row with a radio button; leaves the menu open */
28
125
  export interface RadioMenuItem extends BaseMenuItem {
29
126
  type: 'radio';
30
127
  checked: boolean;
31
- onClick: (...args: any[]) => void;
128
+ onClick: MenuItemClickHandler;
32
129
  }
130
+ /**
131
+ * #menuItem subMenu | nests another `MenuItem[]`, or a function building one, to any depth
132
+ *
133
+ * The function form is called when the submenu opens (or a walker asks for its
134
+ * rows), not when the parent menu is built — for a submenu whose rows cost a
135
+ * scan of the display's data to name. Read the field through `resolveSubMenu`
136
+ * rather than by hand, so the two forms stay one thing to the renderer, the
137
+ * pin-coverage walk and every test helper that flattens a menu.
138
+ */
33
139
  export interface SubMenuItem extends BaseMenuItem {
34
140
  type?: 'subMenu';
35
- subMenu: MenuItem[];
141
+ subMenu: MenuItem[] | (() => MenuItem[]);
142
+ }
143
+ export declare function resolveSubMenu(item: SubMenuItem): MenuItem[];
144
+ /**
145
+ * #menuItem custom | renders arbitrary React content inline, e.g. a slider
146
+ *
147
+ * The menu is not dismissed when interacting with it, so a control can be
148
+ * dragged live; `onClose` is passed for content that wants to close the menu
149
+ * explicitly. `label` is used only as a React key/testid.
150
+ */
151
+ export interface CustomMenuItem extends BaseMenuItem {
152
+ type: 'custom';
153
+ render: (onClose: () => void) => React.ReactNode;
36
154
  }
37
- export type MenuItem = MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem;
155
+ export type ClickableMenuItem = NormalMenuItem | CheckboxMenuItem | RadioMenuItem;
156
+ export type MenuItem = MenuDivider | MenuSubHeader | NormalMenuItem | CheckboxMenuItem | RadioMenuItem | SubMenuItem | CustomMenuItem;
157
+ /**
158
+ * Whether clicking a row leaves the menu up — the rule `CascadingMenu` applies,
159
+ * exported so a display's menu-shape test asserts the behavior a user gets
160
+ * rather than re-deriving it from the flag (each test that spelled out
161
+ * `keepMenuOpen === true` had to be revisited when the default moved here).
162
+ *
163
+ * Defaulted by row TYPE: a checkbox/radio is a setting and stays put, every
164
+ * other row is an action and dismisses. `keepMenuOpen` overrides either way.
165
+ */
166
+ export declare function staysOpenOnClick(item: ClickableMenuItem): boolean;
38
167
  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 +1,9 @@
1
+ import type { TextFieldProps } from '@mui/material';
2
+ export default function MonospaceTextField({ value, onChange, error, label, children, style, className, readOnly, 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
+ } & Omit<TextFieldProps, 'value' | 'onChange' | 'error' | 'slotProps'>): import("react").JSX.Element;
@@ -0,0 +1,37 @@
1
+ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { InputLabel, TextField, alpha } from '@mui/material';
3
+ import { makeStyles } from '../util/tss-react/index.js';
4
+ 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';
5
+ const useStyles = makeStyles()(theme => ({
6
+ error: {
7
+ color: theme.palette.error.main,
8
+ fontSize: '0.8em',
9
+ },
10
+ container: {
11
+ width: '100%',
12
+ overflowX: 'auto',
13
+ },
14
+ field: {
15
+ fontFamily: monospaceFontFamily,
16
+ },
17
+ errorField: {
18
+ background: alpha(theme.palette.error.main, 0.15),
19
+ },
20
+ }));
21
+ // Monospace multiline TextField for code/jexl/JSON/sequence content. Turns red
22
+ // on a parse error, renders an optional error banner above and an InputLabel,
23
+ // and applies the shared monospace font stack to the input slot. `children`
24
+ // render below the field (e.g. a description or help button).
25
+ export default function MonospaceTextField({ value, onChange, error, label, children, style, className, readOnly, variant = 'outlined', ...rest }) {
26
+ const { classes, cx } = useStyles();
27
+ return (_jsxs(_Fragment, { children: [error ? _jsx("p", { className: classes.error, children: `${error}` }) : null, _jsxs("div", { className: classes.container, children: [label ? _jsx(InputLabel, { shrink: true, children: label }) : null, _jsx(TextField, { ...rest, variant: variant, multiline: true, value: value, onChange: event => {
28
+ onChange?.(event.target.value);
29
+ }, className: cx(className, error ? classes.errorField : undefined), style: style, slotProps: {
30
+ input: {
31
+ readOnly,
32
+ classes: {
33
+ input: classes.field,
34
+ },
35
+ },
36
+ } }), children] })] }));
37
+ }
@@ -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 +1,92 @@
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
+ * How the host knows its own mode is the host's business — an attribute on
43
+ * `<html>`, a design-system context, a toggle in its own state. Pass no mode
44
+ * and JBrowse follows `prefers-color-scheme` instead, tracking OS changes; a
45
+ * host whose mode is only ever the OS preference has nothing to write.
46
+ *
47
+ * **Both halves are load-bearing, which is why the pairing is published as a
48
+ * component.** The palette is what *React* draws with; the config `theme` slot
49
+ * this writes is also what ships to the RPC worker, where feature labels are
50
+ * baked into the rendered image. Mount `PaletteProvider` on a palette from
51
+ * somewhere else and those labels stay in the old mode — light text on a light
52
+ * image, and no error anywhere. `setThemeMode` writes the one slot both are
53
+ * derived from, which is why this returns the palette rather than taking one.
54
+ *
55
+ * The write lands in an effect, so the first paint after a mode change uses
56
+ * the previous palette. That is a frame on a canvas that is about to be
57
+ * redrawn anyway; it is not somewhere to add a suspense boundary.
58
+ */
59
+ export declare function useSessionPalette(session: ThemeModeSession, mode?: 'light' | 'dark'): JBrowsePalette;
60
+ /**
61
+ * #api
62
+ * Make JBrowse follow the host's light/dark state — the whole of it, in one
63
+ * mount:
64
+ *
65
+ * ```tsx
66
+ * <SessionPaletteProvider session={session} mode={myAppIsDark ? 'dark' : 'light'}>
67
+ * {tracks}
68
+ * </SessionPaletteProvider>
69
+ * ```
70
+ *
71
+ * `mode` is optional. Left out, JBrowse follows `prefers-color-scheme` and
72
+ * re-themes when the OS preference changes, through the same session write an
73
+ * explicit mode takes — so a host whose dark mode *is* the OS preference mounts
74
+ * this with a session and nothing else. Pass a mode as soon as the host has a
75
+ * toggle of its own, since the media query cannot see it.
76
+ *
77
+ * A component rather than a documented pair of calls because the pair has a
78
+ * half that can be left out with nothing to show for it. `PaletteProvider` is
79
+ * the name a host reaches for, and it colors the React side alone; the session
80
+ * write is what reaches the RPC worker, which bakes feature labels into the
81
+ * rendered image. So a host that mounts only the provider gets light-mode
82
+ * labels on a dark page, from a canvas whose every other pixel is right, and
83
+ * nothing errors. See {@link useSessionPalette} for the mechanism.
84
+ *
85
+ * The session is the only thing that resolves a palette here, so a host
86
+ * supplying colors of its own mounts `PaletteProvider` directly instead.
87
+ */
88
+ export declare function SessionPaletteProvider({ session, mode, children, }: {
89
+ session: ThemeModeSession;
90
+ mode?: 'light' | 'dark';
91
+ children: ReactNode;
92
+ }): import("react").JSX.Element;
@@ -0,0 +1,133 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { createContext, use, useEffect, useMemo, useSyncExternalStore, } from 'react';
3
+ import { defaultStyleTheme } from './styleTheme.js';
4
+ /**
5
+ * How a React component asks for JBrowse's design tokens.
6
+ *
7
+ * This is the toolkit-free counterpart to Material UI's `useTheme`, and it is
8
+ * the seam that lets a display component render without Material UI at all: a
9
+ * display reads `usePalette()` for its content colors, an embedding app
10
+ * supplies them by mounting `PaletteProvider` rather than a `ThemeProvider`,
11
+ * and `makeStyles` reads the whole thing through `useStyleTheme`.
12
+ *
13
+ * JBrowse's own products mount both, from the same session, so the Material UI
14
+ * chrome and the display content cannot disagree.
15
+ *
16
+ * With no provider above it this falls back to the default style theme,
17
+ * mirroring `useTheme`'s fall back to the default theme. That keeps a bare
18
+ * display mountable in a test or a minimal host without ceremony.
19
+ */
20
+ const StyleThemeContext = createContext(undefined);
21
+ /**
22
+ * Supply the whole style theme — colors plus spacing and type scale. This is
23
+ * what JBrowse's own products mount, from `session.styleTheme`, so a config
24
+ * `theme` that sets `spacing` or `typography` reaches `makeStyles` and Material
25
+ * UI alike.
26
+ */
27
+ export function StyleThemeProvider({ theme, children, }) {
28
+ return _jsx(StyleThemeContext, { value: theme, children: children });
29
+ }
30
+ /**
31
+ * Supply colors only, leaving JBrowse's default sizing in place. The narrower
32
+ * of the two, and what a host that already holds a palette mounts: it is saying
33
+ * what JBrowse should draw *with*, not restating its type scale.
34
+ *
35
+ * **A host following its own light/dark state wants
36
+ * {@link SessionPaletteProvider} instead**, which is this plus the session
37
+ * write that the worker-side half of the rendering derives from. This one
38
+ * colors React and nothing else.
39
+ */
40
+ export function PaletteProvider({ palette, children, }) {
41
+ const theme = useMemo(() => ({ ...defaultStyleTheme, palette }), [palette]);
42
+ return _jsx(StyleThemeProvider, { theme: theme, children: children });
43
+ }
44
+ export function useStyleTheme() {
45
+ return use(StyleThemeContext) ?? defaultStyleTheme;
46
+ }
47
+ export function usePalette() {
48
+ return useStyleTheme().palette;
49
+ }
50
+ function darkSchemeQuery() {
51
+ return typeof window.matchMedia === 'function'
52
+ ? window.matchMedia('(prefers-color-scheme: dark)')
53
+ : undefined;
54
+ }
55
+ function subscribeToColorScheme(onChange) {
56
+ const media = darkSchemeQuery();
57
+ media?.addEventListener('change', onChange);
58
+ return () => {
59
+ media?.removeEventListener('change', onChange);
60
+ };
61
+ }
62
+ function readColorScheme() {
63
+ return darkSchemeQuery()?.matches ? 'dark' : 'light';
64
+ }
65
+ const alwaysLight = () => 'light';
66
+ const subscribeToNothing = () => () => { };
67
+ function useResolvedMode(mode) {
68
+ const systemMode = useSyncExternalStore(mode === undefined ? subscribeToColorScheme : subscribeToNothing, mode === undefined ? readColorScheme : alwaysLight, alwaysLight);
69
+ return mode === undefined ? systemMode : mode;
70
+ }
71
+ /**
72
+ * Point a session at light or dark and get back the palette it resolves to,
73
+ * for a host that wants the palette itself — to read a color out of, or to
74
+ * hand somewhere other than a provider. A host that only wants JBrowse to
75
+ * follow its dark mode mounts {@link SessionPaletteProvider}, which is this
76
+ * hook and the provider in one.
77
+ *
78
+ * How the host knows its own mode is the host's business — an attribute on
79
+ * `<html>`, a design-system context, a toggle in its own state. Pass no mode
80
+ * and JBrowse follows `prefers-color-scheme` instead, tracking OS changes; a
81
+ * host whose mode is only ever the OS preference has nothing to write.
82
+ *
83
+ * **Both halves are load-bearing, which is why the pairing is published as a
84
+ * component.** The palette is what *React* draws with; the config `theme` slot
85
+ * this writes is also what ships to the RPC worker, where feature labels are
86
+ * baked into the rendered image. Mount `PaletteProvider` on a palette from
87
+ * somewhere else and those labels stay in the old mode — light text on a light
88
+ * image, and no error anywhere. `setThemeMode` writes the one slot both are
89
+ * derived from, which is why this returns the palette rather than taking one.
90
+ *
91
+ * The write lands in an effect, so the first paint after a mode change uses
92
+ * the previous palette. That is a frame on a canvas that is about to be
93
+ * redrawn anyway; it is not somewhere to add a suspense boundary.
94
+ */
95
+ export function useSessionPalette(session, mode) {
96
+ const resolved = useResolvedMode(mode);
97
+ useEffect(() => {
98
+ session.setThemeMode(resolved);
99
+ }, [session, resolved]);
100
+ return session.palette;
101
+ }
102
+ /**
103
+ * #api
104
+ * Make JBrowse follow the host's light/dark state — the whole of it, in one
105
+ * mount:
106
+ *
107
+ * ```tsx
108
+ * <SessionPaletteProvider session={session} mode={myAppIsDark ? 'dark' : 'light'}>
109
+ * {tracks}
110
+ * </SessionPaletteProvider>
111
+ * ```
112
+ *
113
+ * `mode` is optional. Left out, JBrowse follows `prefers-color-scheme` and
114
+ * re-themes when the OS preference changes, through the same session write an
115
+ * explicit mode takes — so a host whose dark mode *is* the OS preference mounts
116
+ * this with a session and nothing else. Pass a mode as soon as the host has a
117
+ * toggle of its own, since the media query cannot see it.
118
+ *
119
+ * A component rather than a documented pair of calls because the pair has a
120
+ * half that can be left out with nothing to show for it. `PaletteProvider` is
121
+ * the name a host reaches for, and it colors the React side alone; the session
122
+ * write is what reaches the RPC worker, which bakes feature labels into the
123
+ * rendered image. So a host that mounts only the provider gets light-mode
124
+ * labels on a dark page, from a canvas whose every other pixel is right, and
125
+ * nothing errors. See {@link useSessionPalette} for the mechanism.
126
+ *
127
+ * The session is the only thing that resolves a palette here, so a host
128
+ * supplying colors of its own mounts `PaletteProvider` directly instead.
129
+ */
130
+ export function SessionPaletteProvider({ session, mode, children, }) {
131
+ const palette = useSessionPalette(session, mode);
132
+ return _jsx(PaletteProvider, { palette: palette, children: children });
133
+ }
@@ -0,0 +1,5 @@
1
+ import type { MenuItemPin } from './MenuTypes.ts';
2
+ export declare function PinAdornment({ pin, disabled, }: {
3
+ pin: MenuItemPin;
4
+ disabled?: boolean;
5
+ }): import("react").JSX.Element;
@@ -0,0 +1,85 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import PushPinIcon from '@mui/icons-material/PushPin';
3
+ import PushPinOutlinedIcon from '@mui/icons-material/PushPinOutlined';
4
+ import { ToggleButton, Tooltip } from '@mui/material';
5
+ import { makeStyles } from '../util/tss-react/index.js';
6
+ const useStyles = makeStyles()(theme => ({
7
+ // compact enough to sit inline with the value check: drop the default
8
+ // ToggleButton border/padding so it's ~icon-sized, but keep the selected
9
+ // background tint (an unmistakable on/off signal, unlike a hollow-vs-filled
10
+ // icon alone)
11
+ button: {
12
+ border: 0,
13
+ padding: theme.spacing(0.25),
14
+ },
15
+ // the Tooltip listens on this rather than on the button, which fires no
16
+ // events once the row disables it
17
+ wrapper: {
18
+ display: 'inline-flex',
19
+ },
20
+ }));
21
+ // How the pin names what it acts on. Two shapes, decided by the on-value:
22
+ //
23
+ // - **A boolean on-value carries a state**, and the row's label names the
24
+ // setting rather than a value ("Show legend", "Show soft clipping"). A pin on
25
+ // an unchecked such row applies the setting *off*, so the value-shaped copy
26
+ // below stated the opposite of what the click does — and then, once filled,
27
+ // claimed the setting was on by default when it had just been turned off.
28
+ // - **Everything else IS what the label says**: a radio option ("Compact"), a
29
+ // size row whose caller folds the value into the label ("Line width (2px)").
30
+ //
31
+ // One `typeof` rather than a flag on the row, because the two forms of
32
+ // `makePin` are exactly this distinction: a symmetric pin over a `maybeBoolean`
33
+ // slot is the only way a pin's value and its label can disagree.
34
+ function pinPredicate(onValue) {
35
+ return typeof onValue === 'boolean'
36
+ ? `${onValue ? 'on' : 'off'} by default`
37
+ : 'the default';
38
+ }
39
+ // The click, which is not the state the pin draws: an outline pin applies the
40
+ // value to the open tracks, a filled one clears the default it stands for.
41
+ //
42
+ // The aria-label carries "of this type" wherever the tooltip does: it used to
43
+ // stop at "for all open tracks", stating a wider blast radius than the control
44
+ // has.
45
+ function pinCopy(label, onValue, isDefault) {
46
+ return isDefault
47
+ ? {
48
+ title: `${label} is ${pinPredicate(onValue)} for all tracks of this type (click to clear)`,
49
+ ariaLabel: `clear the default for ${label} for all tracks of this type`,
50
+ }
51
+ : typeof onValue === 'boolean'
52
+ ? {
53
+ title: `Turn ${label} ${onValue ? 'on' : 'off'} for all open tracks of this type`,
54
+ ariaLabel: `turn ${label} ${onValue ? 'on' : 'off'} for all open tracks of this type`,
55
+ }
56
+ : {
57
+ title: `Apply ${label} to all open tracks of this type`,
58
+ ariaLabel: `apply ${label} to all open tracks of this type`,
59
+ };
60
+ }
61
+ // Trailing pin for a promotable setting, drawn beside the value check from the
62
+ // row's `pin` declaration (`menuItemAdornment` builds this; a row never
63
+ // constructs it, which is what keeps MUI out of the eager menu-builder graph). A
64
+ // ToggleButton (native button a11y + a clear selected tint) with a pin —
65
+ // distinct from the value checkbox.
66
+ //
67
+ // **The click and the state are two different things.** One click writes the
68
+ // value into every open track of this display type and raises a snackbar
69
+ // offering to keep it as the display type's default; the filled pin means that
70
+ // default is in place, so a click on a filled pin clears it and touches no
71
+ // track. A default therefore takes two deliberate clicks, which is what it costs
72
+ // to govern every track of the type opened later (ADR-048). Always shown so the
73
+ // capability is discoverable. stopPropagation keeps the click off the row value
74
+ // / menu dismissal. "of this type" because a promoted default is scoped to the
75
+ // display type (e.g. every LinearAlignmentsDisplay), not literally all tracks.
76
+ export function PinAdornment({ pin, disabled, }) {
77
+ const { classes } = useStyles();
78
+ const { label, control } = pin;
79
+ const isDefault = control.active;
80
+ const { title, ariaLabel } = pinCopy(label, control.onValue, isDefault);
81
+ return (_jsx(Tooltip, { title: title, children: _jsx("span", { className: classes.wrapper, children: _jsx(ToggleButton, { className: classes.button, value: "default", disabled: disabled, selected: isDefault, color: "primary", size: "small", "aria-label": ariaLabel, onChange: e => {
82
+ e.stopPropagation();
83
+ control.toggle();
84
+ }, children: isDefault ? (_jsx(PushPinIcon, { fontSize: "small" })) : (_jsx(PushPinOutlinedIcon, { fontSize: "small" })) }) }) }));
85
+ }
@@ -0,0 +1,10 @@
1
+ import type PluginManager from '../PluginManager';
2
+ import type { ExtensionPointName, ExtensionPointProps } from '../PluginManager';
3
+ import type React from 'react';
4
+ declare const PluggableComponent: <N extends ExtensionPointName, P extends object>({ pluginManager, name, component: DefaultComponent, props, }: {
5
+ pluginManager: PluginManager;
6
+ name: N;
7
+ component: React.ComponentType<P> | React.LazyExoticComponent<React.ComponentType<P>>;
8
+ props: P & ExtensionPointProps<N>;
9
+ }) => React.JSX.Element;
10
+ export default PluggableComponent;
@@ -0,0 +1,19 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { observer } from 'mobx-react';
3
+ // A point rendered here is a single-component fold: its registry entry declares
4
+ // `args`/`result` as the component type and `props` as that component's prop
5
+ // bag (see Core-replaceWidget for the canonical shape). Taking the name as a
6
+ // registry key rather than a bare string is what checks the default component
7
+ // and the props against the contract, instead of trusting the call site.
8
+ //
9
+ // observer so that observable reads inside evaluateExtensionPoint callbacks
10
+ // (e.g. model.trackAdapterType) are tracked here — re-evaluates when they
11
+ // change without relying on the parent being an observer
12
+ const PluggableComponent = observer(function PluggableComponent({ pluginManager, name, component: DefaultComponent, props, }) {
13
+ // the result is the point's declared component type, and `props` satisfies
14
+ // the point's declared props by the signature above. TS can't narrow either
15
+ // through the generic key, so both are restated here
16
+ const Component = pluginManager.evaluateComponentExtensionPoint(name, DefaultComponent, ...[props]);
17
+ return _jsx(Component, { ...props });
18
+ });
19
+ export default PluggableComponent;