@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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  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
@@ -1,15 +1,12 @@
1
- export declare const PopoverPicker: ({ color, onChange, }: {
2
- color: string;
3
- onChange: (color: string) => void;
4
- }) => import("react/jsx-runtime").JSX.Element;
5
- export declare function ColorPopover({ anchorEl, onChange, onClose, color, }: {
1
+ export declare function ColorPopover({ anchorEl, onChange, onClose, color, presetAlpha, }: {
6
2
  color: string;
7
3
  anchorEl: HTMLElement | null;
8
4
  onChange: (val: string) => void;
9
5
  onClose: () => void;
10
- }): import("react/jsx-runtime").JSX.Element;
11
- export declare function ColorPicker({ onChange, color, }: {
6
+ presetAlpha?: number;
7
+ }): import("react").JSX.Element;
8
+ export default function ColorPicker({ onChange, color, presetAlpha, }: {
12
9
  color: string;
13
10
  onChange: (val: string) => void;
14
- }): import("react/jsx-runtime").JSX.Element;
15
- export default PopoverPicker;
11
+ presetAlpha?: number;
12
+ }): import("react").JSX.Element;
@@ -1,62 +1,59 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
2
  import { useState } from 'react';
3
- import { colord } from '@jbrowse/core/util/colord';
4
- import { makeStyles } from '@jbrowse/core/util/tss-react';
5
3
  import { MenuItem, Popover, Select, TextField } from '@mui/material';
6
- import * as paletteColors from "./colors.js";
7
- import { RgbaStringColorPicker } from "./react-colorful.js";
8
- import { useDebounce, useLocalStorage } from "../util/index.js";
4
+ import { colord } from '../util/colord.js';
5
+ import { useDebounce, useLocalStorage } from '../util/hooks.js';
6
+ import { makeStyles } from '../util/tss-react/index.js';
7
+ import { swatchStyle } from './colorSwatchStyle.js';
8
+ import { paletteColors } from './colors.js';
9
+ import { RgbaStringColorPicker } from './react-colorful.js';
10
+ // note: we are using a vendored copy of react-colorful because the default
11
+ // uses pure-ESM which is difficult to make pass with jest e.g.
12
+ // https://stackoverflow.com/questions/58613492/how-to-resolve-cannot-use-import-statement-outside-a-module-in-jest
9
13
  const useStyles = makeStyles()({
10
- picker: { position: 'relative' },
14
+ root: {
15
+ display: 'flex',
16
+ padding: 10,
17
+ },
18
+ column: {
19
+ width: 200,
20
+ margin: 5,
21
+ },
11
22
  swatches: {
12
23
  display: 'flex',
13
24
  padding: 12,
14
25
  flexWrap: 'wrap',
15
26
  },
16
- swatch: {
17
- width: 24,
18
- height: 24,
19
- margin: 4,
20
- border: 'none',
21
- padding: 0,
22
- cursor: 'pointer',
23
- outline: 'none',
24
- },
27
+ swatch: swatchStyle,
25
28
  });
26
- export const PopoverPicker = ({ color, onChange, }) => {
27
- const [anchorEl, setAnchorEl] = useState(null);
28
- const { classes } = useStyles();
29
- return (_jsxs("div", { className: classes.picker, children: [_jsx("div", { className: classes.swatch, style: { backgroundColor: color }, onClick: event => {
30
- setAnchorEl(event.currentTarget);
31
- } }), _jsx(ColorPopover, { anchorEl: anchorEl, onClose: () => {
32
- setAnchorEl(null);
33
- }, color: color, onChange: onChange })] }));
34
- };
35
- export function ColorPopover({ anchorEl, onChange, onClose, color, }) {
36
- return (_jsx(Popover, { open: !!anchorEl, anchorEl: anchorEl, onClose: onClose, children: _jsx(ColorPicker, { color: color, onChange: onChange }) }));
29
+ const palettes = Object.keys(paletteColors);
30
+ function isPaletteType(s) {
31
+ return Object.hasOwn(paletteColors, s);
32
+ }
33
+ export function ColorPopover({ anchorEl, onChange, onClose, color, presetAlpha, }) {
34
+ return (_jsx(Popover, { open: !!anchorEl, anchorEl: anchorEl, onClose: onClose, children: _jsx(ColorPicker, { color: color, onChange: onChange, presetAlpha: presetAlpha }) }));
37
35
  }
38
- export function ColorPicker({ onChange, color, }) {
36
+ export default function ColorPicker({ onChange, color, presetAlpha, }) {
39
37
  const { classes } = useStyles();
40
- const [val, setVal] = useLocalStorage('colorPickerPalette', 'set1');
41
- const presetColors = paletteColors[val];
42
- const palettes = Object.keys(paletteColors);
38
+ const [storedPalette, setStoredPalette] = useLocalStorage('colorPickerPalette', 'set1');
39
+ // a stale localStorage value (e.g. a palette since renamed/removed) would
40
+ // index to undefined and crash the swatch map below
41
+ const palette = isPaletteType(storedPalette) ? storedPalette : 'set1';
42
+ const presetColors = paletteColors[palette];
43
43
  const [text, setText] = useState(color);
44
44
  const rgb = colord(color).toRgbString();
45
45
  const rgbDebounced = useDebounce(rgb, 1000);
46
46
  const handleChange = (val) => {
47
47
  setText(val);
48
- try {
49
- onChange(colord(val).toRgbString());
50
- }
51
- catch (e) { }
48
+ onChange(colord(val).toRgbString());
52
49
  };
53
- return (_jsxs("div", { style: { display: 'flex', padding: 10 }, children: [_jsx("div", { style: { width: 200, margin: 5 }, children: _jsx(RgbaStringColorPicker, { color: rgbDebounced, onChange: handleChange }) }), _jsxs("div", { style: { width: 200, margin: 5 }, children: [_jsx(Select, { value: val, onChange: event => {
54
- const pal = event.target.value;
55
- setVal(pal);
50
+ return (_jsxs("div", { className: classes.root, children: [_jsx("div", { className: classes.column, children: _jsx(RgbaStringColorPicker, { color: rgbDebounced, onChange: handleChange }) }), _jsxs("div", { className: classes.column, children: [_jsx(Select, { value: palette, onChange: event => {
51
+ setStoredPalette(event.target.value);
56
52
  }, children: palettes.map(p => (_jsx(MenuItem, { value: p, children: p }, p))) }), _jsx("div", { className: classes.swatches, children: presetColors.map((presetColor, idx) => (_jsx("button", { type: "button", className: classes.swatch, style: { background: presetColor }, onClick: () => {
57
- handleChange(presetColor);
53
+ handleChange(presetAlpha === undefined
54
+ ? presetColor
55
+ : colord(presetColor).alpha(presetAlpha).toRgbString());
58
56
  } }, `${presetColor}-${idx}`))) }), _jsx(TextField, { helperText: 'Manually set color (hex, rgb, or css color name)', value: text, onChange: event => {
59
57
  handleChange(event.target.value);
60
58
  } })] })] }));
61
59
  }
62
- export default PopoverPicker;
@@ -1,10 +1,3 @@
1
- import type { DialogProps } from '@mui/material';
2
- interface Props extends DialogProps {
3
- header?: React.ReactNode;
4
- onCancel: () => void;
5
- onSubmit: () => void;
6
- cancelText?: string;
7
- submitText?: string;
8
- }
9
- declare const ConfirmDialog: (props: Props) => import("react/jsx-runtime").JSX.Element;
1
+ import type { SubmitDialogProps } from './SubmitDialog.tsx';
2
+ declare const ConfirmDialog: (props: SubmitDialogProps) => import("react").JSX.Element;
10
3
  export default ConfirmDialog;
@@ -1,13 +1,10 @@
1
- import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
- import { Button, DialogActions, DialogContent } from '@mui/material';
1
+ import { jsx as _jsx } from "react/jsx-runtime";
3
2
  import { observer } from 'mobx-react';
4
- import Dialog from "./Dialog.js";
3
+ import SubmitDialog from './SubmitDialog.js';
4
+ // ConfirmDialog is a SubmitDialog framed as a yes/no confirmation: the action
5
+ // button defaults to "OK" instead of "Submit". Enter submits, Escape/Cancel
6
+ // dismisses.
5
7
  const ConfirmDialog = observer(function ConfirmDialog(props) {
6
- const { onSubmit, onCancel, cancelText = 'Cancel', submitText = 'OK', children, } = props;
7
- return (_jsxs(Dialog, { onClose: onCancel, ...props, children: [_jsx(DialogContent, { children: children }), _jsxs(DialogActions, { children: [_jsx(Button, { color: "secondary", variant: "contained", onClick: () => {
8
- onCancel();
9
- }, children: cancelText }), _jsx(Button, { color: "primary", variant: "contained", onClick: () => {
10
- onSubmit();
11
- }, children: submitText })] })] }));
8
+ return _jsx(SubmitDialog, { submitText: "OK", ...props });
12
9
  });
13
10
  export default ConfirmDialog;
@@ -0,0 +1,50 @@
1
+ import type { MenuItemsGetter } from './MenuTypes.ts';
2
+ /**
3
+ * Where the menu opens, in viewport coordinates — i.e. an event's
4
+ * `clientX`/`clientY`, whatever produced it (a right-click, the release of a
5
+ * drag-selection). `undefined` is the closed state: displays keep the click
6
+ * point and the menu's open-ness as one value rather than two that can
7
+ * disagree.
8
+ */
9
+ export interface ContextMenuAnchor {
10
+ clientX: number;
11
+ clientY: number;
12
+ }
13
+ /**
14
+ * The popup menu every display raises from a click point: right-click menus,
15
+ * and the dotplot's drag-release menu.
16
+ *
17
+ * Its own observer, and the one place `menuItems` is resolved: a display passes
18
+ * the getter rather than a built array, so rebuilding the items re-renders this
19
+ * component alone. Built inline in a display body instead, the per-mousemove
20
+ * coordinate state there re-ran the whole menu build — with fresh item
21
+ * identities — on every move while a menu was open.
22
+ *
23
+ * Its events do not stop at the portal — React bubbles them through the
24
+ * component tree to whatever rendered the menu, which on a display is the
25
+ * element that hit-tests the pointer. `DisplayStatusChromeBase` is where that
26
+ * element refuses the events that did not happen over it, for every portalled
27
+ * overlay rather than for menus alone.
28
+ *
29
+ * Mounts only while open, and only with something to show: MUI keeps a Paper
30
+ * that fades out on close, so an anchored-but-empty menu flashes an empty box
31
+ * at the cursor. `onClose` is the single close path — Menu's
32
+ * `closeAfterItemClick` default already fires it ahead of the clicked item's
33
+ * callback, so an item's `onClick` must not read state that closing clears
34
+ * (capture it when the items are built).
35
+ *
36
+ * Being the single close path is also why the display's tracked pointer is
37
+ * dropped here rather than by each display: this menu is portalled, so the
38
+ * display under it is never sent the `mouseleave` its overlays clear on. See
39
+ * `useClearTrackedPointer`.
40
+ */
41
+ declare const ContextMenu: ({ anchor, menuItems, onClose, offset, }: {
42
+ anchor: ContextMenuAnchor | undefined;
43
+ menuItems: MenuItemsGetter;
44
+ onClose: () => void;
45
+ offset?: {
46
+ x: number;
47
+ y: number;
48
+ };
49
+ }) => import("react").JSX.Element | null;
50
+ export default ContextMenu;
@@ -0,0 +1,55 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { observer } from 'mobx-react';
3
+ import Menu from './CascadingMenu.js';
4
+ import { useClearTrackedPointer } from './useMouseTracking.js';
5
+ import { CONTEXT_MENU_Z_INDEX } from './zIndexes.js';
6
+ /**
7
+ * Nudge off the click point, so the pixel that was right-clicked — a mismatch
8
+ * column, a variant cell — stays visible beside the menu instead of under it.
9
+ */
10
+ const DEFAULT_OFFSET = { x: 12, y: 0 };
11
+ /**
12
+ * The popup menu every display raises from a click point: right-click menus,
13
+ * and the dotplot's drag-release menu.
14
+ *
15
+ * Its own observer, and the one place `menuItems` is resolved: a display passes
16
+ * the getter rather than a built array, so rebuilding the items re-renders this
17
+ * component alone. Built inline in a display body instead, the per-mousemove
18
+ * coordinate state there re-ran the whole menu build — with fresh item
19
+ * identities — on every move while a menu was open.
20
+ *
21
+ * Its events do not stop at the portal — React bubbles them through the
22
+ * component tree to whatever rendered the menu, which on a display is the
23
+ * element that hit-tests the pointer. `DisplayStatusChromeBase` is where that
24
+ * element refuses the events that did not happen over it, for every portalled
25
+ * overlay rather than for menus alone.
26
+ *
27
+ * Mounts only while open, and only with something to show: MUI keeps a Paper
28
+ * that fades out on close, so an anchored-but-empty menu flashes an empty box
29
+ * at the cursor. `onClose` is the single close path — Menu's
30
+ * `closeAfterItemClick` default already fires it ahead of the clicked item's
31
+ * callback, so an item's `onClick` must not read state that closing clears
32
+ * (capture it when the items are built).
33
+ *
34
+ * Being the single close path is also why the display's tracked pointer is
35
+ * dropped here rather than by each display: this menu is portalled, so the
36
+ * display under it is never sent the `mouseleave` its overlays clear on. See
37
+ * `useClearTrackedPointer`.
38
+ */
39
+ const ContextMenu = observer(function ContextMenu({ anchor, menuItems, onClose, offset = DEFAULT_OFFSET, }) {
40
+ const clearTrackedPointer = useClearTrackedPointer();
41
+ if (!anchor) {
42
+ return null;
43
+ }
44
+ const items = Array.isArray(menuItems) ? menuItems : menuItems();
45
+ return items.length > 0 ? (_jsx(Menu, { open: true, onMenuItemClick: callback => {
46
+ callback();
47
+ }, onClose: () => {
48
+ clearTrackedPointer();
49
+ onClose();
50
+ }, anchorReference: "anchorPosition", anchorPosition: {
51
+ top: anchor.clientY + offset.y,
52
+ left: anchor.clientX + offset.x,
53
+ }, style: { zIndex: CONTEXT_MENU_Z_INDEX }, menuItems: items })) : null;
54
+ });
55
+ export default ContextMenu;
@@ -0,0 +1,10 @@
1
+ import type { ButtonProps } from '@mui/material';
2
+ /**
3
+ * A Button that copies `value` to the clipboard and briefly swaps its label to
4
+ * `copiedLabel` as feedback. `value` may be a function so callers can defer
5
+ * computing large strings (e.g. JSON.stringify) until the click happens.
6
+ */
7
+ export default function CopyToClipboardButton({ value, children, copiedLabel, ...rest }: {
8
+ value: string | (() => string);
9
+ copiedLabel?: string;
10
+ } & Omit<ButtonProps, 'value'>): import("react").JSX.Element;
@@ -0,0 +1,14 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Button } from '@mui/material';
3
+ import { useCopyToClipboard } from './useCopyToClipboard.js';
4
+ /**
5
+ * A Button that copies `value` to the clipboard and briefly swaps its label to
6
+ * `copiedLabel` as feedback. `value` may be a function so callers can defer
7
+ * computing large strings (e.g. JSON.stringify) until the click happens.
8
+ */
9
+ export default function CopyToClipboardButton({ value, children, copiedLabel = 'Copied to clipboard!', ...rest }) {
10
+ const { copied, copy } = useCopyToClipboard();
11
+ return (_jsx(Button, { ...rest, onClick: () => {
12
+ void copy(typeof value === 'function' ? value() : value);
13
+ }, children: copied ? copiedLabel : children }));
14
+ }
@@ -0,0 +1,10 @@
1
+ declare const Crosshairs: ({ width, height, mouseX, mouseY, top, zIndex, minLeft, }: {
2
+ width: number;
3
+ height: number;
4
+ mouseX: number;
5
+ mouseY?: number;
6
+ top?: number;
7
+ zIndex?: number;
8
+ minLeft?: number;
9
+ }) => import("react").JSX.Element;
10
+ export default Crosshairs;
@@ -0,0 +1,15 @@
1
+ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
+ const Crosshairs = ({ width, height, mouseX, mouseY, top = 0, zIndex,
3
+ // The vertical (genomic-position) guide is dropped when the cursor is left of
4
+ // this, e.g. over a tree sidebar where it has no meaning and clutters the
5
+ // resize handle. The horizontal row guide is kept.
6
+ minLeft = 0, }) => (_jsxs("svg", { style: {
7
+ position: 'absolute',
8
+ top,
9
+ left: 0,
10
+ width,
11
+ height,
12
+ pointerEvents: 'none',
13
+ zIndex,
14
+ }, children: [mouseY === undefined ? null : (_jsx("line", { x1: 0, x2: width, y1: mouseY, y2: mouseY, stroke: "currentColor" })), mouseX >= minLeft ? (_jsx("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "currentColor" })) : null] }));
15
+ export default Crosshairs;
@@ -1,4 +1,4 @@
1
1
  export default function DOMPurifySanitizedHTML({ value, className, }: {
2
2
  value: string;
3
3
  className?: string;
4
- }): import("react/jsx-runtime").JSX.Element;
4
+ }): import("react").JSX.Element;
@@ -1,16 +1,16 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
2
  import { useLayoutEffect, useRef } from 'react';
3
3
  import dompurify from 'dompurify';
4
+ import { rewriteExternalAnchors } from './rewriteExternalAnchors.js';
4
5
  export default function DOMPurifySanitizedHTML({ value, className, }) {
5
6
  const spanRef = useRef(null);
6
7
  useLayoutEffect(() => {
7
8
  const el = spanRef.current;
8
9
  if (el) {
9
- for (const a of el.querySelectorAll('a')) {
10
- a.setAttribute('rel', 'noopener noreferrer');
11
- a.setAttribute('target', '_blank');
12
- }
10
+ rewriteExternalAnchors(el);
13
11
  }
14
12
  }, [value]);
15
- return (_jsx("span", { ref: spanRef, className: className, dangerouslySetInnerHTML: { __html: dompurify.sanitize(value) } }));
13
+ return (_jsx("span", { ref: spanRef, className: className,
14
+ // eslint-disable-next-line @eslint-react/dom-no-dangerously-set-innerhtml
15
+ dangerouslySetInnerHTML: { __html: dompurify.sanitize(value) } }));
16
16
  }
@@ -1,5 +1,12 @@
1
1
  import type { CSSProperties } from 'react';
2
- export default function DataGridFlexContainer({ children, style, }: {
2
+ export default function DataGridFlexContainer({ children, className, style, }: {
3
3
  children: React.ReactNode;
4
+ /**
5
+ * merged with the flex-column base. A caller that wants the grid to FILL its
6
+ * parent rather than size to its rows passes `flex: 1; min-height: 0` here —
7
+ * worth doing, because a content-sized DataGrid draws its horizontal
8
+ * scrollbar as an overlay on top of its own last row.
9
+ */
10
+ className?: string;
4
11
  style?: CSSProperties;
5
- }): import("react/jsx-runtime").JSX.Element;
12
+ }): import("react").JSX.Element;
@@ -1,12 +1,13 @@
1
1
  import { jsx as _jsx } from "react/jsx-runtime";
2
- import { makeStyles } from "../util/tss-react/index.js";
2
+ import { cx, makeStyles } from '../util/tss-react/index.js';
3
3
  const useStyles = makeStyles()({
4
4
  flexContainer: {
5
5
  display: 'flex',
6
6
  flexDirection: 'column',
7
7
  },
8
8
  });
9
- export default function DataGridFlexContainer({ children, style, }) {
9
+ // https://mui.com/x/react-data-grid/layout/#flex-parent-container
10
+ export default function DataGridFlexContainer({ children, className, style, }) {
10
11
  const { classes } = useStyles();
11
- return (_jsx("div", { className: classes.flexContainer, style: style, children: children }));
12
+ return (_jsx("div", { className: cx(classes.flexContainer, className), style: style, children: children }));
12
13
  }
@@ -1,7 +1,10 @@
1
1
  import type { DialogProps } from '@mui/material';
2
- export interface Props extends DialogProps {
2
+ export interface Props extends Omit<DialogProps, 'onClose'> {
3
3
  header?: React.ReactNode;
4
4
  titleNode?: React.ReactNode;
5
+ onClose?: {
6
+ bivarianceHack(event: object, reason: 'backdropClick' | 'escapeKeyDown' | 'closeButtonClick'): void;
7
+ }['bivarianceHack'] | undefined;
5
8
  }
6
- declare const Dialog: (props: Props) => import("react/jsx-runtime").JSX.Element;
9
+ declare function Dialog(props: Props): import("react").JSX.Element;
7
10
  export default Dialog;
package/esm/ui/Dialog.js CHANGED
@@ -1,12 +1,11 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
- import { isValidElement } from 'react';
2
+ import { useMemo } from 'react';
3
3
  import CloseIcon from '@mui/icons-material/Close';
4
- import { Dialog as MUIDialog, DialogTitle, Divider, IconButton, ScopedCssBaseline, ThemeProvider, createTheme, useTheme, } from '@mui/material';
5
- import { observer } from 'mobx-react';
6
- import { ErrorBoundary } from "./ErrorBoundary.js";
7
- import ErrorMessage from "./ErrorMessage.js";
8
- import SanitizedHTML from "./SanitizedHTML.js";
9
- import { makeStyles } from "../util/tss-react/index.js";
4
+ import { DialogTitle, Divider, IconButton, Dialog as MUIDialog, ScopedCssBaseline, ThemeProvider, createTheme, useTheme, } from '@mui/material';
5
+ import { makeStyles } from '../util/tss-react/index.js';
6
+ import ErrorBanner from './ErrorBanner.js';
7
+ import { ErrorBoundary } from './ErrorBoundary.js';
8
+ import SanitizedHTML from './SanitizedHTML.js';
10
9
  const useStyles = makeStyles()(theme => ({
11
10
  closeButton: {
12
11
  position: 'absolute',
@@ -15,31 +14,40 @@ const useStyles = makeStyles()(theme => ({
15
14
  color: theme.palette.grey[500],
16
15
  },
17
16
  errorBox: {
18
- width: 800,
19
- margin: 40,
17
+ maxWidth: 800,
18
+ margin: theme.spacing(5),
20
19
  },
21
20
  }));
22
21
  function DialogError({ error }) {
23
22
  const { classes } = useStyles();
24
- return (_jsx("div", { className: classes.errorBox, children: _jsx(ErrorMessage, { error: error }) }));
23
+ return (_jsx("div", { className: classes.errorBox, children: _jsx(ErrorBanner, { error: error }) }));
25
24
  }
26
- const Dialog = observer(function Dialog(props) {
25
+ function Dialog(props) {
27
26
  const { classes } = useStyles();
28
- const { titleNode, ...rest } = props;
29
- const { title, header, children, onClose } = rest;
27
+ const { titleNode, header, title, ...rest } = props;
28
+ const { children, onClose } = rest;
30
29
  const theme = useTheme();
31
- return (_jsx(MUIDialog, { ...rest, children: _jsxs(ScopedCssBaseline, { children: [isValidElement(header) ? (header) : (_jsxs(DialogTitle, { children: [titleNode || _jsx(SanitizedHTML, { html: title || '' }), onClose ? (_jsx(IconButton, { className: classes.closeButton, onClick: event => {
32
- onClose(event, 'backdropClick');
33
- }, children: _jsx(CloseIcon, {}) })) : null] })), _jsx(Divider, {}), _jsx(ErrorBoundary, { FallbackComponent: DialogError, children: _jsx(ThemeProvider, { theme: createTheme(theme, {
34
- components: {
35
- MuiInputBase: {
36
- styleOverrides: {
37
- input: {
38
- boxSizing: 'content-box!important',
39
- },
40
- },
41
- },
42
- },
43
- }), children: children }) })] }) }));
44
- });
30
+ // content-box override xref https://github.com/GMOD/jbrowse-components/pull/3666
31
+ const dialogTheme = useMemo(() => createTheme(theme, {
32
+ components: {
33
+ MuiInputBase: {
34
+ styleOverrides: {
35
+ input: {
36
+ boxSizing: 'content-box!important',
37
+ },
38
+ },
39
+ },
40
+ },
41
+ }), [theme]);
42
+ return (_jsx(MUIDialog, { ...rest, children: _jsxs(ScopedCssBaseline, { children: [header ? (header) : (_jsxs(DialogTitle, { children: [titleNode ?? _jsx(SanitizedHTML, { html: title ?? '' }), onClose ? (_jsx(IconButton
43
+ // The one handle on a dialog's (×), for a driver that cannot use
44
+ // Escape: MUI delivers Escape through the modal, so a press
45
+ // while focus sits on the body — where clicking an action button
46
+ // that then disables itself leaves it — closes nothing, and a
47
+ // screenshot spec's later actions all keep succeeding under the
48
+ // panel they were meant to dismiss
49
+ , { "data-testid": "dialog-close", className: classes.closeButton, onClick: event => {
50
+ onClose(event, 'closeButtonClick');
51
+ }, children: _jsx(CloseIcon, {}) })) : null] })), _jsx(Divider, {}), _jsx(ErrorBoundary, { FallbackComponent: DialogError, children: _jsx(ThemeProvider, { theme: dialogTheme, children: children }) })] }) }));
52
+ }
45
53
  export default Dialog;
@@ -1,5 +1,5 @@
1
- import type { DialogProps } from '@mui/material';
2
- declare const DraggableDialog: (props: DialogProps & {
1
+ import type { Props as DialogProps } from './Dialog.tsx';
2
+ declare const DraggableDialog: (props: Omit<DialogProps, 'slotProps'> & {
3
3
  title: string;
4
- }) => import("react/jsx-runtime").JSX.Element;
4
+ }) => import("react").JSX.Element;
5
5
  export default DraggableDialog;
@@ -1,10 +1,10 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
- import { useRef } from 'react';
3
- import { makeStyles } from '@jbrowse/core/util/tss-react';
2
+ import { useEffect, useRef, useState } from 'react';
4
3
  import CloseIcon from '@mui/icons-material/Close';
5
- import { Dialog, DialogTitle, Divider, IconButton, Paper, ScopedCssBaseline, } from '@mui/material';
4
+ import { DialogTitle, IconButton } from '@mui/material';
6
5
  import { observer } from 'mobx-react';
7
- import Draggable from 'react-draggable';
6
+ import { makeStyles } from '../util/tss-react/index.js';
7
+ import Dialog from './Dialog.js';
8
8
  const useStyles = makeStyles()(theme => ({
9
9
  closeButton: {
10
10
  position: 'absolute',
@@ -12,16 +12,54 @@ const useStyles = makeStyles()(theme => ({
12
12
  top: theme.spacing(1),
13
13
  color: theme.palette.grey[500],
14
14
  },
15
+ title: {
16
+ cursor: 'move',
17
+ },
15
18
  }));
16
- function PaperComponent(props) {
17
- const ref = useRef(null);
18
- return (_jsx(Draggable, { nodeRef: ref, cancel: '[class*="MuiDialogContent-root"]', onStart: arg => `${arg.target?.className}`.includes('MuiDialogTitle'), children: _jsx(Paper, { ref: ref, ...props }) }));
19
- }
19
+ // A drag-repositionable dialog. Renders the shared Dialog so it inherits the
20
+ // content-box input fix and the error boundary, and supplies a draggable title
21
+ // bar as Dialog's `header`. `slotProps` is not offered: the paper slot carries
22
+ // the drag transform, so a caller's would be dropped rather than merged.
20
23
  const DraggableDialog = observer(function DraggableDialog(props) {
21
24
  const { classes } = useStyles();
22
- const { title, children, onClose } = props;
23
- return (_jsx(Dialog, { ...props, PaperComponent: PaperComponent, children: _jsxs(ScopedCssBaseline, { children: [_jsxs(DialogTitle, { style: { cursor: 'move' }, children: [title, onClose ? (_jsx(IconButton, { className: classes.closeButton, onClick: () => {
24
- onClose();
25
- }, children: _jsx(CloseIcon, {}) })) : null] }), _jsx(Divider, {}), children] }) }));
25
+ const { title, children, onClose, ...rest } = props;
26
+ const [pos, setPos] = useState({ x: 0, y: 0 });
27
+ const [dragging, setDragging] = useState(false);
28
+ const originRef = useRef({ mouseX: 0, mouseY: 0, x: 0, y: 0 });
29
+ useEffect(() => {
30
+ if (dragging) {
31
+ function move(event) {
32
+ event.preventDefault();
33
+ const { mouseX, mouseY, x, y } = originRef.current;
34
+ setPos({
35
+ x: x + event.clientX - mouseX,
36
+ y: y + event.clientY - mouseY,
37
+ });
38
+ }
39
+ function up() {
40
+ setDragging(false);
41
+ }
42
+ window.addEventListener('mousemove', move);
43
+ window.addEventListener('mouseup', up);
44
+ return () => {
45
+ window.removeEventListener('mousemove', move);
46
+ window.removeEventListener('mouseup', up);
47
+ };
48
+ }
49
+ return undefined;
50
+ }, [dragging]);
51
+ return (_jsx(Dialog, { ...rest, onClose: onClose, slotProps: {
52
+ paper: { style: { transform: `translate(${pos.x}px, ${pos.y}px)` } },
53
+ }, header: _jsxs(DialogTitle, { className: classes.title, onMouseDown: event => {
54
+ originRef.current = {
55
+ mouseX: event.clientX,
56
+ mouseY: event.clientY,
57
+ x: pos.x,
58
+ y: pos.y,
59
+ };
60
+ setDragging(true);
61
+ }, children: [title, onClose ? (_jsx(IconButton, { className: classes.closeButton, onClick: event => {
62
+ onClose(event, 'closeButtonClick');
63
+ }, children: _jsx(CloseIcon, {}) })) : null] }), children: children }));
26
64
  });
27
65
  export default DraggableDialog;
@@ -1,6 +1,8 @@
1
1
  import type { MenuItem } from './Menu.tsx';
2
- declare const DropDownMenu: ({ menuTitle, menuItems, }: {
2
+ import type { MenuItemClickHandler } from './MenuTypes.ts';
3
+ declare const DropDownMenu: ({ menuTitle, menuItems, onMenuItemClick, }: {
3
4
  menuTitle: string;
4
5
  menuItems: MenuItem[] | (() => MenuItem[]);
5
- }) => import("react/jsx-runtime").JSX.Element;
6
+ onMenuItemClick?: (callback: MenuItemClickHandler) => void;
7
+ }) => import("react").JSX.Element;
6
8
  export default DropDownMenu;
@@ -1,9 +1,9 @@
1
1
  import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
2
- import { makeStyles } from '@jbrowse/core/util/tss-react';
3
2
  import ArrowDropDown from '@mui/icons-material/ArrowDropDown';
4
3
  import { Button, alpha } from '@mui/material';
5
4
  import { observer } from 'mobx-react';
6
- import CascadingMenuButton from "./CascadingMenuButton.js";
5
+ import { makeStyles } from '../util/tss-react/index.js';
6
+ import CascadingMenuButton from './CascadingMenuButton.js';
7
7
  const useStyles = makeStyles()(theme => ({
8
8
  buttonRoot: {
9
9
  '&:hover': {
@@ -18,7 +18,7 @@ function ButtonComponent(props) {
18
18
  const { classes } = useStyles();
19
19
  return (_jsx(Button, { ...props, className: classes.buttonRoot, children: props.children }));
20
20
  }
21
- const DropDownMenu = observer(function DropDownMenu({ menuTitle, menuItems, }) {
22
- return (_jsxs(CascadingMenuButton, { menuItems: menuItems, color: "inherit", ButtonComponent: ButtonComponent, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, children: [menuTitle, _jsx(ArrowDropDown, {})] }));
21
+ const DropDownMenu = observer(function DropDownMenu({ menuTitle, menuItems, onMenuItemClick, }) {
22
+ return (_jsxs(CascadingMenuButton, { menuItems: menuItems, onMenuItemClick: onMenuItemClick, color: "inherit", ButtonComponent: ButtonComponent, children: [menuTitle, _jsx(ArrowDropDown, {})] }));
23
23
  });
24
24
  export default DropDownMenu;
@@ -1,4 +1,5 @@
1
1
  import type { TypographyProps } from '@mui/material';
2
+ import type { Ref } from 'react';
2
3
  type Variant = TypographyProps['variant'];
3
4
  type EditableTypographyClassKey = 'input' | 'inputBase' | 'inputRoot' | 'inputFocused';
4
5
  interface Props {
@@ -6,6 +7,7 @@ interface Props {
6
7
  setValue: (value: string) => void;
7
8
  variant: Variant;
8
9
  classes?: Partial<Record<EditableTypographyClassKey, string>>;
10
+ ref?: Ref<HTMLDivElement>;
9
11
  }
10
- declare const EditableTypography: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
12
+ declare function EditableTypography(props: Props): import("react").JSX.Element;
11
13
  export default EditableTypography;