@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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@@ -0,0 +1,45 @@
1
+ import type { AbstractSessionModel } from '../util/types/index.ts';
2
+ /**
3
+ * One element that says whether the whole app has finished, and what is open.
4
+ *
5
+ * `[data-app-phase="ready"]` is the entire readiness contract for anything
6
+ * driving JBrowse from outside — a screenshot tool, a test, an agent. Wait for
7
+ * that selector and you are done; there is no chain to assemble and no
8
+ * per-display census to take.
9
+ *
10
+ * Why it exists when `data-view-phase` and `data-display-phase` already do:
11
+ * those are per-element and NEGATIVE. Asking them "is everything finished"
12
+ * means asserting that no element carries the loading value, which is equally
13
+ * true of an app that has not started — and the gap is real, measured at about
14
+ * a second on a two-track session. A positive attribute cannot be satisfied
15
+ * early, because something has to render it.
16
+ *
17
+ * The census attributes beside it — `data-app-views`, `data-app-assemblies`,
18
+ * `data-app-tracks` (the latter two JSON arrays) — publish WHAT is open the
19
+ * same way the phase publishes whether it is done, so an outside reader asking
20
+ * "is the track I requested actually open" reads one element instead of
21
+ * walking `window.JBrowseSession` with its own copy of the view nesting. The
22
+ * walk itself is `openViews`/`openTracks` over each view's declared
23
+ * `ownViews`/`ownTracks`, so this component knows nothing about which property
24
+ * a container view keeps its children on either.
25
+ *
26
+ * Its own component, and `hidden`, for two reasons: an observer here subscribes
27
+ * to every view's phase without re-rendering the app shell around it, and a
28
+ * marker that is never drawn cannot be mistaken for UI or shift a layout. It is
29
+ * still found by `querySelector`, which is what reads it.
30
+ *
31
+ * **What it is silent about**: a display in a TERMINAL state. `error` and
32
+ * `canceled` are finished states, so this reads `ready` over a display whose
33
+ * fetch failed or that the user stopped — correctly, since nothing is still
34
+ * working, and a user's cancel is durable until Retry. A capture wants more than
35
+ * that: it wants a picture, and neither banner is one. The capture census after
36
+ * this is what draws that line: it names every `data-display-drawn="false"`,
37
+ * which the two comparative canvases publish from their stricter `settled` gate
38
+ * (see `comparativeReadiness` in `@jbrowse/synteny-core`, which holds both
39
+ * answers and says why an error separates them), and every
40
+ * `data-display-phase="canceled"`.
41
+ */
42
+ declare const AppReadyMarker: ({ session, }: {
43
+ session: AbstractSessionModel;
44
+ }) => import("react").JSX.Element;
45
+ export default AppReadyMarker;
@@ -0,0 +1,89 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { observer } from 'mobx-react';
3
+ import { openTracks, openViews } from '../util/openViews.js';
4
+ function trackLoading(track) {
5
+ return track.displays.some(d => d.displayPhase === 'loading');
6
+ }
7
+ /**
8
+ * A view whose init failed (its assembly was never found) stays uninitialized
9
+ * for good and paints its error, so like a display's terminal phase it is
10
+ * finished, not pending: without this the whole app read `loading` for as long
11
+ * as that view was open, and every settle answered false with no reason.
12
+ *
13
+ * `pendingLaunch` is the third term and the one that was missing. `initialized`
14
+ * goes true mid-launch — LGV's flips the moment displayedRegions land, while
15
+ * the same apply pass still has the spec's tracks to attach — and `showLoading`
16
+ * goes false at the same moment, deliberately, so the reader sees the
17
+ * navigated view rather than a spinner while its tracks arrive. That left a
18
+ * window, exactly as wide as attaching the tracks, in which the marker said
19
+ * `ready` over a session missing everything it had been asked for.
20
+ * `whenViewSettled` states the same rule for the callers that await a single
21
+ * view, and says why in more detail. Not shared as one predicate: that one
22
+ * requires `initialized`, while absent here means not loading, and an adapter
23
+ * between the two null rules would read as agreement it does not have.
24
+ *
25
+ * `showImportForm` excuses the `initialized` term, and only that one. The
26
+ * comparative views spell `initialized` as "every row exists and is ready" —
27
+ * LinearSyntenyView's wants `views.length > 0`, dotplot's wants regions on both
28
+ * axes — so a view clicked into existence through `Add -> Linear synteny view`
29
+ * reads uninitialized for as long as its form is up, which is until a person
30
+ * fills it in. The app sat at `loading` behind every import-form figure. The
31
+ * other two terms keep their meaning: `showLoading` is the spinner the form
32
+ * yields to, and `showImportForm` is already false while a launch is pending.
33
+ */
34
+ function viewLoading(view) {
35
+ const flags = view;
36
+ return (flags.error === undefined &&
37
+ (flags.showLoading === true ||
38
+ flags.pendingLaunch !== undefined ||
39
+ (flags.initialized === false && flags.showImportForm !== true)));
40
+ }
41
+ /**
42
+ * One element that says whether the whole app has finished, and what is open.
43
+ *
44
+ * `[data-app-phase="ready"]` is the entire readiness contract for anything
45
+ * driving JBrowse from outside — a screenshot tool, a test, an agent. Wait for
46
+ * that selector and you are done; there is no chain to assemble and no
47
+ * per-display census to take.
48
+ *
49
+ * Why it exists when `data-view-phase` and `data-display-phase` already do:
50
+ * those are per-element and NEGATIVE. Asking them "is everything finished"
51
+ * means asserting that no element carries the loading value, which is equally
52
+ * true of an app that has not started — and the gap is real, measured at about
53
+ * a second on a two-track session. A positive attribute cannot be satisfied
54
+ * early, because something has to render it.
55
+ *
56
+ * The census attributes beside it — `data-app-views`, `data-app-assemblies`,
57
+ * `data-app-tracks` (the latter two JSON arrays) — publish WHAT is open the
58
+ * same way the phase publishes whether it is done, so an outside reader asking
59
+ * "is the track I requested actually open" reads one element instead of
60
+ * walking `window.JBrowseSession` with its own copy of the view nesting. The
61
+ * walk itself is `openViews`/`openTracks` over each view's declared
62
+ * `ownViews`/`ownTracks`, so this component knows nothing about which property
63
+ * a container view keeps its children on either.
64
+ *
65
+ * Its own component, and `hidden`, for two reasons: an observer here subscribes
66
+ * to every view's phase without re-rendering the app shell around it, and a
67
+ * marker that is never drawn cannot be mistaken for UI or shift a layout. It is
68
+ * still found by `querySelector`, which is what reads it.
69
+ *
70
+ * **What it is silent about**: a display in a TERMINAL state. `error` and
71
+ * `canceled` are finished states, so this reads `ready` over a display whose
72
+ * fetch failed or that the user stopped — correctly, since nothing is still
73
+ * working, and a user's cancel is durable until Retry. A capture wants more than
74
+ * that: it wants a picture, and neither banner is one. The capture census after
75
+ * this is what draws that line: it names every `data-display-drawn="false"`,
76
+ * which the two comparative canvases publish from their stricter `settled` gate
77
+ * (see `comparativeReadiness` in `@jbrowse/synteny-core`, which holds both
78
+ * answers and says why an error separates them), and every
79
+ * `data-display-phase="canceled"`.
80
+ */
81
+ const AppReadyMarker = observer(function AppReadyMarker({ session, }) {
82
+ const views = openViews(session);
83
+ const tracks = openTracks(session);
84
+ const loading = views.some(viewLoading) || tracks.some(trackLoading);
85
+ return (_jsx("span", { hidden: true, "data-testid": "app-ready-marker", "data-app-phase": loading ? 'loading' : 'ready', "data-app-views": session.views.length, "data-app-assemblies": JSON.stringify([
86
+ ...new Set(views.flatMap(v => v.assemblyNames ?? [])),
87
+ ]), "data-app-tracks": JSON.stringify(tracks.map(t => t.configuration.trackId ?? '(unnamed)')) }));
88
+ });
89
+ export default AppReadyMarker;
@@ -1,13 +1,10 @@
1
- import type { AbstractSessionModel } from '../util/index.ts';
2
- import type { InputProps as IIP, TextFieldProps as TFP } from '@mui/material';
3
- declare const AssemblySelector: ({ session, onChange, label, selected, InputProps, TextFieldProps, localStorageKey, helperText, }: {
4
- session: AbstractSessionModel;
1
+ import type { AssemblyHost } from '../util/index.ts';
2
+ declare const AssemblySelector: ({ session, onChange, label, selected, fullWidth, helperText, }: {
3
+ session: AssemblyHost;
5
4
  label?: string;
6
5
  helperText?: string;
7
6
  onChange: (arg: string) => void;
8
7
  selected?: string;
9
- localStorageKey?: string;
10
- InputProps?: IIP;
11
- TextFieldProps?: TFP;
12
- }) => import("react/jsx-runtime").JSX.Element;
8
+ fullWidth?: boolean;
9
+ }) => import("react").JSX.Element;
13
10
  export default AssemblySelector;
@@ -1,39 +1,21 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import { useEffect } from 'react';
3
2
  import { MenuItem, TextField } from '@mui/material';
4
3
  import { observer } from 'mobx-react';
5
- import { useLocalStorage } from "../util/index.js";
6
- import { makeStyles } from "../util/tss-react/index.js";
4
+ import { makeStyles } from '../util/tss-react/index.js';
7
5
  const useStyles = makeStyles()({
8
6
  importFormEntry: {
9
7
  minWidth: 180,
10
8
  },
11
9
  });
12
- const AssemblySelector = observer(function AssemblySelector({ session, onChange, label = 'Assembly', selected, InputProps, TextFieldProps, localStorageKey, helperText = 'Select assembly to view', }) {
10
+ const AssemblySelector = observer(function AssemblySelector({ session, onChange, label = 'Assembly', selected, fullWidth, helperText = 'Select assembly to view', }) {
13
11
  const { classes } = useStyles();
14
12
  const { assemblyNames, assemblyManager } = session;
15
- const config = new URLSearchParams(window.location.search).get('config');
16
- const [lastSelected, setLastSelected] = useLocalStorage(`lastAssembly-${[
17
- window.location.host + window.location.pathname,
18
- config,
19
- localStorageKey,
20
- ].join('-')}`, selected, typeof jest === 'undefined' && Boolean(localStorageKey));
21
- const selection = assemblyNames.includes(lastSelected || '')
22
- ? lastSelected
23
- : selected;
24
- useEffect(() => {
25
- if (selection && selection !== selected) {
26
- onChange(selection);
27
- }
28
- }, [selection, onChange, selected]);
13
+ // ignore a stale/removed selection so MUI doesn't warn about an out-of-range
14
+ // select value
15
+ const value = selected && assemblyNames.includes(selected) ? selected : '';
29
16
  const error = assemblyNames.length ? '' : 'No configured assemblies';
30
- return (_jsx(TextField, { select: true, "data-testid": "assembly-selector-textfield", label: label, variant: "outlined", helperText: error || helperText, value: selection || '', onChange: event => {
31
- setLastSelected(event.target.value);
32
- }, error: !!error, disabled: !!error, className: classes.importFormEntry, ...TextFieldProps, slotProps: {
33
- input: InputProps,
34
- htmlInput: {
35
- 'data-testid': 'assembly-selector',
36
- },
37
- }, children: assemblyNames.map(name => (_jsx(MenuItem, { value: name, children: assemblyManager.get(name)?.displayName || name }, name))) }));
17
+ return (_jsx(TextField, { select: true, label: label, variant: "outlined", helperText: error || helperText, value: value, fullWidth: fullWidth, onChange: event => {
18
+ onChange(event.target.value);
19
+ }, error: !!error, disabled: !!error, className: classes.importFormEntry, children: assemblyNames.map(name => (_jsx(MenuItem, { value: name, children: assemblyManager.get(name)?.displayName || name }, name))) }));
38
20
  });
39
21
  export default AssemblySelector;
@@ -0,0 +1,16 @@
1
+ import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
2
+ export interface BaseExportSvgOptions {
3
+ rasterizeLayers: boolean;
4
+ format: 'svg' | 'png';
5
+ filename: string;
6
+ themeName: string;
7
+ fontFamily: string;
8
+ }
9
+ declare const _default: ({ model, handleClose, exportSvg, children, checkboxes, }: {
10
+ model: IAnyStateTreeNode;
11
+ handleClose: () => void;
12
+ exportSvg: (opts: BaseExportSvgOptions) => Promise<unknown>;
13
+ children?: React.ReactNode;
14
+ checkboxes?: React.ReactNode;
15
+ }) => import("react").JSX.Element;
16
+ export default _default;
@@ -0,0 +1,84 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ import { useState } from 'react';
3
+ import { CircularProgress, MenuItem, TextField, ToggleButton, ToggleButtonGroup, Typography, } from '@mui/material';
4
+ import { observer } from 'mobx-react';
5
+ import { getSession } from '../util/index.js';
6
+ import ErrorBanner from './ErrorBanner.js';
7
+ import LabeledCheckbox from './LabeledCheckbox.js';
8
+ import SubmitDialog from './SubmitDialog.js';
9
+ import { useExportSvgPreference } from './useExportSvgPreference.js';
10
+ // Generic CSS families only, so exported text resolves in any SVG renderer
11
+ // (browser, Inkscape, Illustrator) without embedding a named font like Roboto.
12
+ // The 'default' sentinel is the selected default; it maps to no font-family so
13
+ // the renderer decides (see the exportSvg call below).
14
+ const DEFAULT_FONT = 'default';
15
+ const fontFamilyOptions = [
16
+ { value: DEFAULT_FONT, label: 'Default' },
17
+ { value: 'sans-serif', label: 'Sans-serif' },
18
+ { value: 'serif', label: 'Serif' },
19
+ { value: 'monospace', label: 'Monospace' },
20
+ { value: 'system-ui, sans-serif', label: 'System UI' },
21
+ ];
22
+ export default observer(function BaseExportSvgDialog({ model, handleClose, exportSvg, children, checkboxes, }) {
23
+ const session = getSession(model);
24
+ const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
25
+ // persisted like every other option here, but still gated on the capability:
26
+ // the checkbox isn't rendered without OffscreenCanvas, so a stored `true` must
27
+ // not survive into a browser that can't rasterize
28
+ const [rasterizePreference, setRasterizePreference] = useExportSvgPreference('rasterize', true);
29
+ const rasterizeLayers = offscreenCanvas && rasterizePreference;
30
+ const [loading, setLoading] = useState(false);
31
+ const [error, setError] = useState();
32
+ const [format, setFormat] = useExportSvgPreference('format', 'svg');
33
+ const [filename, setFilename] = useExportSvgPreference('file', 'jbrowse.svg');
34
+ const [themePreference, setThemeName] = useExportSvgPreference('theme', session.themeName || 'default');
35
+ // A stored name outlives the theme it names: an admin drops an `extraThemes`
36
+ // entry, or another JBrowse on this origin writes `svg-theme`, which has no
37
+ // instance scope. Unguarded it draws a blank Select and makes
38
+ // `getActiveThemeOptions` answer undefined, so the export comes out stock.
39
+ // `session.themeName` guards the name it stores the same way.
40
+ const allThemes = session.allThemes?.();
41
+ const themeName = allThemes?.[themePreference]
42
+ ? themePreference
43
+ : session.themeName || 'default';
44
+ const [fontFamily, setFontFamily] = useExportSvgPreference('fontfamily', DEFAULT_FONT);
45
+ return (_jsxs(SubmitDialog, { open: true, title: "Export image", submitDisabled: loading, onCancel: handleClose, onSubmit: async () => {
46
+ setLoading(true);
47
+ setError(undefined);
48
+ try {
49
+ await exportSvg({
50
+ rasterizeLayers,
51
+ format,
52
+ filename,
53
+ themeName,
54
+ fontFamily: fontFamily === DEFAULT_FONT ? '' : fontFamily,
55
+ });
56
+ handleClose();
57
+ }
58
+ catch (e) {
59
+ console.error(e);
60
+ setError(e);
61
+ }
62
+ finally {
63
+ setLoading(false);
64
+ }
65
+ }, children: [error ? (_jsx(ErrorBanner, { error: error })) : loading ? (_jsxs("div", { children: [_jsx(CircularProgress, { size: 20, style: { marginRight: 20 } }), _jsxs(Typography, { sx: { display: 'inline' }, children: ["Creating ", format.toUpperCase()] })] })) : null, _jsxs("div", { style: { display: 'flex', flexDirection: 'column', gap: 12 }, children: [_jsxs("div", { style: { display: 'flex', alignItems: 'center', gap: 8 }, children: [_jsx(TextField, { label: "Filename", value: filename, onChange: event => {
66
+ setFilename(event.target.value);
67
+ } }), _jsxs(ToggleButtonGroup, { value: format, exclusive: true, onChange: (_event, value) => {
68
+ if (value) {
69
+ setFormat(value);
70
+ if (filename.endsWith('.svg') && value === 'png') {
71
+ setFilename(filename.replace(/\.svg$/, '.png'));
72
+ }
73
+ else if (filename.endsWith('.png') && value === 'svg') {
74
+ setFilename(filename.replace(/\.png$/, '.svg'));
75
+ }
76
+ }
77
+ }, size: "small", children: [_jsx(ToggleButton, { value: "svg", children: "SVG" }), _jsx(ToggleButton, { value: "png", children: "PNG" })] })] }), children, allThemes ? (_jsx(TextField, { select: true, label: "Theme", variant: "outlined", style: { minWidth: 200 }, value: themeName, onChange: event => {
78
+ setThemeName(event.target.value);
79
+ }, children: Object.entries(allThemes).map(([key, val]) => (_jsx(MenuItem, { value: key, children: val.name || '(Unknown name)' }, key))) })) : null, _jsx(TextField, { select: true, label: "Font", variant: "outlined", style: { minWidth: 200 }, value: fontFamily, onChange: event => {
80
+ setFontFamily(event.target.value);
81
+ }, children: fontFamilyOptions.map(({ value, label }) => (_jsx(MenuItem, { value: value, children: label }, value))) }), _jsxs("div", { style: { display: 'flex', flexDirection: 'column' }, children: [checkboxes, offscreenCanvas ? (_jsx(LabeledCheckbox, { checked: rasterizeLayers, onChange: val => {
82
+ setRasterizePreference(val);
83
+ }, label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (_jsx(Typography, { children: "Note: rasterizing layers not yet supported in this browser, so SVG size may be large" }))] })] })] }));
84
+ });
@@ -1,8 +1,19 @@
1
- export default function BaseTooltip({ clientPoint: clientPointCoords, children, placement, }: {
2
- placement?: 'top' | 'top-start' | 'top-end' | 'right' | 'right-start' | 'right-end' | 'bottom' | 'bottom-start' | 'bottom-end' | 'left' | 'left-start' | 'left-end';
1
+ export type TooltipPlacement = 'top' | 'top-start' | 'top-end' | 'right' | 'right-start' | 'right-end' | 'bottom' | 'bottom-start' | 'bottom-end' | 'left' | 'left-start' | 'left-end';
2
+ export default function BaseTooltip({ clientPoint: clientPointCoords, anchor, id, children, placement, }: {
3
+ placement?: TooltipPlacement;
4
+ /** Follow the pointer. The cursor-anchored mode, and the older of the two. */
3
5
  clientPoint?: {
4
6
  x: number;
5
7
  y: number;
6
8
  };
9
+ /**
10
+ * Hang off an element instead — what a control's hover label wants, where
11
+ * following the cursor across a button reads as a stray box. Mutually
12
+ * exclusive with `clientPoint`; `@jbrowse/display-ui`'s `useTooltip` is what
13
+ * drives this arm.
14
+ */
15
+ anchor?: HTMLElement;
16
+ /** For a trigger pointing at this with `aria-describedby`. */
17
+ id?: string;
7
18
  children: React.ReactNode;
8
- }): import("react/jsx-runtime").JSX.Element;
19
+ }): import("react").ReactPortal | null;
@@ -1,42 +1,159 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import { offset, useClientPoint, useFloating, useInteractions, } from '@floating-ui/react';
3
- import { Portal, alpha, useTheme } from '@mui/material';
4
- import { makeStyles } from "../util/tss-react/index.js";
5
- function round(value) {
6
- return Math.round(value * 1e5) / 1e5;
2
+ import { useEffect, useState } from 'react';
3
+ import { autoUpdate, flip, offset, shift, useClientPoint, useFloating, useInteractions, } from '@floating-ui/react';
4
+ import { createPortal } from 'react-dom';
5
+ import { useStyleTheme } from './PaletteContext.js';
6
+ import { alpha, grey } from './palette.js';
7
+ import { TOOLTIP_Z_INDEX } from './zIndexes.js';
8
+ // The hover tooltip every display shares, in both of its anchorings: following
9
+ // the pointer over a display's data (`clientPoint`, what the ten display
10
+ // tooltips use through `HoverTooltip`), or hanging off a control that was
11
+ // hovered (`anchor`, what `@jbrowse/display-ui`'s `Tooltip` drives). One
12
+ // component rather than two, because the second one only ever differed in which
13
+ // reference it positioned against — everything below this line was the part
14
+ // worth having once.
15
+ //
16
+ // Its look comes from the palette and plain inline styles rather than from a
17
+ // `makeStyles` reading the Material UI theme, and that is deliberate: an
18
+ // embedder who installs `plainChromeOverlays` + `plainTrackControl` gets stock
19
+ // displays that render no Material UI, and a tooltip carrying the MUI *default*
20
+ // theme's grey and Roboto (which is what it did, since such a host mounts no
21
+ // ThemeProvider) put a Material widget back on their screen. It was invisible
22
+ // to `jbrowse-build-your-own`'s smoke census too, which counts `Mui*`
23
+ // classnames and never sees an emotion class.
24
+ //
25
+ // The chip is dark in both palette modes, the way a tooltip conventionally is.
26
+ // It is the one thing on screen that deliberately does not match the page.
27
+ //
28
+ // `fontFamily: inherit` puts it in whatever font it is portaled into: Roboto in
29
+ // JBrowse's own products, whose `CssBaseline` sets the body font, and the
30
+ // host's font in an embed. The size is stated rather than inherited, because
31
+ // body text is a good deal larger than a tooltip should be.
32
+ const tooltipBaseStyle = {
33
+ pointerEvents: 'none',
34
+ borderRadius: 4,
35
+ fontFamily: 'inherit',
36
+ fontSize: 12,
37
+ padding: '4px 8px',
38
+ lineHeight: 1.4,
39
+ maxWidth: 300,
40
+ wordWrap: 'break-word',
41
+ };
42
+ // The gap between the reference and the tooltip, and the ONLY place it is
43
+ // decided. `offset()` applies it along the resolved placement axis, so it stays
44
+ // a gap when `flip()` puts the tooltip to the LEFT of the cursor near the right
45
+ // edge of the viewport.
46
+ //
47
+ // Callers pass the pointer's true client point. Eight of them used to add 5, 10
48
+ // or 15 to `x` themselves on top of this, so the same affordance sat 20, 25 or
49
+ // 30px from the cursor depending on which track you hovered — nobody chose
50
+ // that, and a nudge baked into the coordinate moves the reference point rather
51
+ // than the tooltip, so on a flipped placement it pushed the tooltip *toward*
52
+ // the cursor instead of away. Don't reintroduce one; change this number.
53
+ const CURSOR_GAP_PX = 15;
54
+ // Where the pointer last was, app-wide.
55
+ //
56
+ // A hover tooltip mounts BECAUSE the pointer landed on something, so the event
57
+ // that could position it has already been delivered — and floating-ui's own
58
+ // follow mode (`useClientPoint` with no x/y) registers its window listener on
59
+ // mount, so it learns nothing until the NEXT move. An unpositioned tooltip is
60
+ // `visibility: hidden` (see below), which means landing on a narrow feature and
61
+ // stopping showed no tooltip at all, indefinitely. It is why the callers that
62
+ // have a pointer in hand pass `clientPoint`; the ones that do not are hovering
63
+ // an ELEMENT (an SVG arc, a breakpoint connector), whose `onMouseOver` says
64
+ // only that it was entered.
65
+ //
66
+ // One passive listener storing two numbers, installed at import rather than per
67
+ // tooltip: the value a tooltip needs is the one from before it existed, so
68
+ // there is nothing for a listener installed with it to have recorded.
69
+ let lastPointerPoint;
70
+ if (typeof window !== 'undefined') {
71
+ window.addEventListener('pointermove', event => {
72
+ lastPointerPoint = { x: event.clientX, y: event.clientY };
73
+ }, { passive: true, capture: true });
7
74
  }
8
- const useStyles = makeStyles()(theme => ({
9
- tooltip: {
10
- position: 'absolute',
11
- pointerEvents: 'none',
12
- backgroundColor: alpha(theme.palette.grey[700], 0.9),
13
- borderRadius: theme.shape.borderRadius,
14
- color: theme.palette.common.white,
15
- fontFamily: theme.typography.fontFamily,
16
- padding: '4px 8px',
17
- fontSize: theme.typography.fontSize,
18
- lineHeight: `${round(14 / 10)}em`,
19
- maxWidth: 300,
20
- wordWrap: 'break-word',
21
- },
22
- }));
23
- export default function BaseTooltip({ clientPoint: clientPointCoords, children, placement = 'right', }) {
24
- const theme = useTheme();
25
- const popperTheme = theme.components?.MuiPopper;
26
- const { classes } = useStyles();
75
+ // An element is its own size, so the gap is measured from its edge rather than
76
+ // from a point the pointer happens to be at. 15px off a button reads as a
77
+ // tooltip belonging to nothing in particular.
78
+ const ANCHOR_GAP_PX = 6;
79
+ export default function BaseTooltip({ clientPoint: clientPointCoords, anchor, id, children, placement = anchor ? 'top' : 'right', }) {
80
+ // The style theme is read for two things and neither is a Material import:
81
+ // the colors below, and the portal container a shadow-DOM embed configures
82
+ // through `MuiPopper.defaultProps.container` — the same slot every other
83
+ // portaled thing in JBrowse honours, lifted onto the style theme by
84
+ // `resolveStyleTheme` so reading it here costs no UI toolkit.
85
+ const { palette, portalContainer } = useStyleTheme();
27
86
  const { refs, floatingStyles, context } = useFloating({
28
87
  placement,
29
88
  strategy: 'fixed',
30
- middleware: [offset(5)],
89
+ elements: { reference: anchor },
90
+ // flip/shift keep the tooltip on-screen when the reference is near a
91
+ // viewport edge instead of letting it clip off the right/bottom — and a
92
+ // control with a hover label is usually in a corner, so this arm needs it
93
+ // at least as much as the cursor one
94
+ middleware: [
95
+ offset(anchor ? ANCHOR_GAP_PX : CURSOR_GAP_PX),
96
+ flip(),
97
+ shift({ padding: 8 }),
98
+ ],
99
+ // An anchored tooltip is measured against an element that scrolls with the
100
+ // track under it, so its position is followed. A cursor-anchored one is
101
+ // remeasured by every pointer move anyway.
102
+ whileElementsMounted: anchor ? autoUpdate : undefined,
103
+ });
104
+ // Follow the pointer here, rather than handing floating-ui its own follow
105
+ // mode, so the tooltip opens AT a point instead of at nothing — see
106
+ // `lastPointerPoint`. A caller that named a point, or an element, owns the
107
+ // position outright and this stays out of the way.
108
+ const [tracked, setTracked] = useState(lastPointerPoint);
109
+ const following = !anchor && clientPointCoords === undefined;
110
+ useEffect(() => {
111
+ if (!following) {
112
+ return undefined;
113
+ }
114
+ setTracked(lastPointerPoint);
115
+ const onMove = (event) => {
116
+ setTracked({ x: event.clientX, y: event.clientY });
117
+ };
118
+ window.addEventListener('pointermove', onMove, {
119
+ passive: true,
120
+ capture: true,
121
+ });
122
+ return () => {
123
+ window.removeEventListener('pointermove', onMove, true);
124
+ };
125
+ }, [following]);
126
+ // `enabled` rather than a conditional hook: with an element reference in
127
+ // play, letting this also write one would leave the two arms fighting over
128
+ // the same slot.
129
+ const clientPoint = useClientPoint(context, {
130
+ ...(clientPointCoords ?? tracked),
131
+ enabled: !anchor,
31
132
  });
32
- const clientPoint = useClientPoint(context, clientPointCoords);
33
133
  const { getFloatingProps } = useInteractions([clientPoint]);
34
- return (_jsx(Portal, { container: popperTheme?.defaultProps?.container, children: _jsx("div", { className: classes.tooltip, ref: refs.setFloating, style: {
35
- ...floatingStyles,
36
- zIndex: 100000,
37
- visibility: floatingStyles.transform === 'translate(0px, 0px)'
38
- ? 'hidden'
39
- : undefined,
40
- pointerEvents: 'none',
41
- }, ...getFloatingProps(), children: children }) }));
134
+ // `document.body` is the default, which is what MUI's `Portal` did. Resolved
135
+ // at render rather than in an effect: a tooltip only ever mounts in response
136
+ // to a pointer, so there is no first paint to be wrong about and no
137
+ // hydration pass to mismatch — but the `document` guard stays, because this
138
+ // module is reachable from a server render even when this component is not.
139
+ const target = (typeof portalContainer === 'function'
140
+ ? portalContainer()
141
+ : portalContainer) ??
142
+ (typeof document === 'undefined' ? undefined : document.body);
143
+ if (!target) {
144
+ return null;
145
+ }
146
+ return createPortal(_jsx("div", { id: id, ref: refs.setFloating, role: "tooltip", style: {
147
+ ...tooltipBaseStyle,
148
+ backgroundColor: alpha(grey[700], 0.9),
149
+ color: palette.common.white,
150
+ // after the base style, so the strategy's `position: fixed` wins
151
+ ...floatingStyles,
152
+ zIndex: TOOLTIP_Z_INDEX,
153
+ // workaround for tooltips flashing at top left corner of screen
154
+ // when first appearing
155
+ visibility: floatingStyles.transform === 'translate(0px, 0px)'
156
+ ? 'hidden'
157
+ : undefined,
158
+ }, ...getFloatingProps(), children: children }), target);
42
159
  }
@@ -1,30 +1,21 @@
1
- import type { MenuItemsGetter } from './MenuTypes.ts';
1
+ import type { MenuItemClickHandler, MenuItemsGetter } from './MenuTypes.ts';
2
+ import type { PopoverOrigin } from '@mui/material';
2
3
  export type { MenuItemsGetter } from './MenuTypes.ts';
3
- export default function CascadingMenu({ onMenuItemClick, closeAfterItemClick, menuItems, open, onClose, anchorEl, anchorOrigin, transformOrigin, anchorReference, anchorPosition, slotProps, marginThreshold, style, }: {
4
- onMenuItemClick: (event: unknown, callback: () => void) => void;
4
+ interface CascadingMenuProps {
5
+ onMenuItemClick: (callback: MenuItemClickHandler) => void;
5
6
  closeAfterItemClick?: boolean;
6
7
  menuItems: MenuItemsGetter;
7
8
  open: boolean;
8
9
  onClose: () => void;
9
10
  anchorEl?: Element | null;
10
- anchorOrigin?: {
11
- vertical: 'top' | 'center' | 'bottom';
12
- horizontal: 'left' | 'center' | 'right';
13
- };
14
- transformOrigin?: {
15
- vertical: 'top' | 'center' | 'bottom';
16
- horizontal: 'left' | 'center' | 'right';
17
- };
11
+ anchorOrigin?: PopoverOrigin;
12
+ transformOrigin?: PopoverOrigin;
18
13
  anchorReference?: 'anchorEl' | 'anchorPosition' | 'none';
19
14
  anchorPosition?: {
20
15
  top: number;
21
16
  left: number;
22
17
  };
23
- slotProps?: {
24
- transition?: {
25
- onExit?: () => void;
26
- };
27
- };
28
- marginThreshold?: number | null;
29
18
  style?: React.CSSProperties;
30
- }): import("react/jsx-runtime").JSX.Element;
19
+ }
20
+ declare const CascadingMenu: ({ onMenuItemClick, closeAfterItemClick, menuItems, open, onClose, anchorEl, anchorOrigin, transformOrigin, anchorReference, anchorPosition, style, }: CascadingMenuProps) => import("react").JSX.Element;
21
+ export default CascadingMenu;