@jbrowse/core 4.2.1 → 5.0.0-beta.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1124) hide show
  1. package/README.md +783 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +84 -65
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +196 -55
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
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  1024. package/esm/util/viewStatus.d.ts +58 -0
  1025. package/esm/util/viewStatus.js +20 -0
  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,44 @@
1
+ import type { CheckboxMenuItem, MenuItem, RadioMenuItem } from './MenuTypes.ts';
2
+ export interface SettingRowOptions {
3
+ helpText?: string;
4
+ disabled?: boolean;
5
+ disabledHelpText?: string;
6
+ keepMenuOpen?: boolean;
7
+ }
8
+ /** #menuBuilder checkboxItem | one checkbox setting row */
9
+ export declare function checkboxItem(label: string, checked: boolean, onToggle: () => void, opts?: SettingRowOptions): CheckboxMenuItem;
10
+ /**
11
+ * #menuBuilder toggleItem | a checkbox row whose setter takes the new value
12
+ *
13
+ * `checkboxItem` where the callback is handed the value rather than left to
14
+ * derive it. Prefer this: the derivation is `!` applied to the same expression
15
+ * the row is `checked` by, and writing it out per row is 38 chances to negate
16
+ * the wrong thing — which fails as a checkbox that ticks and does nothing, with
17
+ * nothing thrown.
18
+ *
19
+ * It is also the shape `radioItems` already takes (`setMode: (m: T) => void`),
20
+ * so the two group builders now agree about who computes the new value.
21
+ *
22
+ * MAF had this as a local wrapper, and it had already lost most of
23
+ * `SettingRowOptions` to a hand-narrowed one-field bag — the exact drift the
24
+ * comment on that interface warns about.
25
+ */
26
+ export declare function toggleItem(label: string, value: boolean, setValue: (value: boolean) => void, opts?: SettingRowOptions): CheckboxMenuItem;
27
+ /** #menuBuilder radioItem | one radio setting row; the singular of `radioItems` */
28
+ export declare function radioItem(label: string, checked: boolean, onClick: () => void, opts?: SettingRowOptions): RadioMenuItem;
29
+ export interface RadioOption<T extends string> {
30
+ value: T;
31
+ label: string;
32
+ helpText?: string;
33
+ keepMenuOpen?: boolean;
34
+ }
35
+ /** #menuBuilder radioItems | a radio group, one row per option */
36
+ export declare function radioItems<T extends string>(options: readonly RadioOption<T>[], current: T | undefined, setMode: (m: T) => void): RadioMenuItem[];
37
+ /**
38
+ * #menuBuilder withSubHeader | a section heading, present only if the section is
39
+ *
40
+ * Derived from the rows rather than from whatever gated them, so a heading
41
+ * cannot outlive its section — the rows are usually gated on data, and an empty
42
+ * section renders its heading directly above the next one's.
43
+ */
44
+ export declare function withSubHeader(label: string, rows: MenuItem[]): MenuItem[];
@@ -0,0 +1,60 @@
1
+ /** #menuBuilder checkboxItem | one checkbox setting row */
2
+ export function checkboxItem(label, checked, onToggle, opts) {
3
+ return {
4
+ label,
5
+ type: 'checkbox',
6
+ checked,
7
+ onClick: onToggle,
8
+ ...opts,
9
+ };
10
+ }
11
+ /**
12
+ * #menuBuilder toggleItem | a checkbox row whose setter takes the new value
13
+ *
14
+ * `checkboxItem` where the callback is handed the value rather than left to
15
+ * derive it. Prefer this: the derivation is `!` applied to the same expression
16
+ * the row is `checked` by, and writing it out per row is 38 chances to negate
17
+ * the wrong thing — which fails as a checkbox that ticks and does nothing, with
18
+ * nothing thrown.
19
+ *
20
+ * It is also the shape `radioItems` already takes (`setMode: (m: T) => void`),
21
+ * so the two group builders now agree about who computes the new value.
22
+ *
23
+ * MAF had this as a local wrapper, and it had already lost most of
24
+ * `SettingRowOptions` to a hand-narrowed one-field bag — the exact drift the
25
+ * comment on that interface warns about.
26
+ */
27
+ export function toggleItem(label, value, setValue, opts) {
28
+ return checkboxItem(label, value, () => {
29
+ setValue(!value);
30
+ }, opts);
31
+ }
32
+ // One radio row. The singular of `radioItems`, and what
33
+ // `promotableRadioItem` builds through, so a lone radio row and a member of a
34
+ // group are the same object plus or minus its pin.
35
+ /** #menuBuilder radioItem | one radio setting row; the singular of `radioItems` */
36
+ export function radioItem(label, checked, onClick, opts) {
37
+ return {
38
+ label,
39
+ type: 'radio',
40
+ checked,
41
+ onClick,
42
+ ...opts,
43
+ };
44
+ }
45
+ /** #menuBuilder radioItems | a radio group, one row per option */
46
+ export function radioItems(options, current, setMode) {
47
+ return options.map(({ value, label, ...opts }) => radioItem(label, current === value, () => {
48
+ setMode(value);
49
+ }, opts));
50
+ }
51
+ /**
52
+ * #menuBuilder withSubHeader | a section heading, present only if the section is
53
+ *
54
+ * Derived from the rows rather than from whatever gated them, so a heading
55
+ * cannot outlive its section — the rows are usually gated on data, and an empty
56
+ * section renders its heading directly above the next one's.
57
+ */
58
+ export function withSubHeader(label, rows) {
59
+ return rows.length > 0 ? [{ type: 'subHeader', label }, ...rows] : [];
60
+ }
@@ -0,0 +1,153 @@
1
+ import type { AbstractSessionModel } from '../util/index.ts';
2
+ export declare function instanceScopedKey(prefix: string, suffix: string): string;
3
+ /**
4
+ * Tracks the assembly chosen in an import form and resolves the outcomes the
5
+ * form renders from: `assemblyError` (failed, or nothing configured), `regions`
6
+ * (ready), or neither (still loading). The user's choice is stored as an
7
+ * override and re-resolved against the live assembly list every render, so it
8
+ * always names a currently-configured assembly even as assemblies load in, get
9
+ * removed, or when a remembered choice is no longer valid. Passing a
10
+ * `localStorageKey` persists the choice across reloads. Shared by the LGV and
11
+ * circular-view import forms.
12
+ */
13
+ export declare function useAssemblySelection(session: AbstractSessionModel, localStorageKey?: string): {
14
+ selectedAssemblyName: string | undefined;
15
+ setSelectedAssemblyName: (value: string | ((val: string | undefined) => string | undefined) | undefined) => void;
16
+ assembly: (import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
17
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
18
+ }> & {
19
+ error: unknown;
20
+ loadingP: Promise<void> | undefined;
21
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("../assemblyManager/refNameMaps.ts").RefNameAliases>>;
22
+ volatileRegions: import("../assemblyManager/assembly.ts").BasicRegion[] | undefined;
23
+ refNameAliases: import("../assemblyManager/refNameMaps.ts").RefNameAliases | undefined;
24
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
25
+ cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
26
+ loadedGeneticCodes: Record<string, number> | undefined;
27
+ lowerCaseRefNameAliases: import("../assemblyManager/refNameMaps.ts").RefNameAliases | undefined;
28
+ statusMessage: string | undefined;
29
+ statusProgress: number | undefined;
30
+ statusSource: string | undefined;
31
+ refNameMismatches: Map<string, import("../assemblyManager/refNameMismatch.ts").RefNameMismatch>;
32
+ } & {
33
+ getConf(arg: string): any;
34
+ } & {
35
+ readonly name: string;
36
+ readonly aliases: string[];
37
+ readonly displayName: string;
38
+ readonly refNameColors: string[];
39
+ } & {
40
+ readonly allAliases: string[];
41
+ hasName(name: string): boolean;
42
+ } & {
43
+ setStatus(status?: import("../util/progress.ts").RpcStatus): void;
44
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("../assemblyManager/refNameMismatch.ts").RefNameMismatch): void;
45
+ } & {
46
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("../assemblyManager/refNameMaps.ts").RefNameMaps & {
47
+ regions: import("../util/index.ts").Region[];
48
+ cytobands: import("../util/simpleFeature.ts").Feature[];
49
+ geneticCodes: Record<string, number>;
50
+ }): void;
51
+ setError(e: unknown): void;
52
+ setLoadingP(p?: Promise<void>): void;
53
+ loadPre(): Promise<void>;
54
+ } & {
55
+ load(): Promise<void>;
56
+ } & {
57
+ afterAttach(): void;
58
+ } & {
59
+ readonly initialized: boolean;
60
+ readonly regions: import("../assemblyManager/assembly.ts").BasicRegion[] | undefined;
61
+ readonly allRefNames: string[] | undefined;
62
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
63
+ readonly rpcManager: import("../rpc/RpcManager.ts").default;
64
+ } & {
65
+ readonly refNames: string[] | undefined;
66
+ } & {
67
+ readonly refNameToIndex: Map<string, number> | undefined;
68
+ } & {
69
+ getCanonicalRefName(refName: string): string | undefined;
70
+ getRefNameColor(refName: string): string | undefined;
71
+ getRegionForRefName(refName: string): import("../assemblyManager/assembly.ts").BasicRegion | undefined;
72
+ getGeneticCodeId(refName: string): number;
73
+ getSeqAdapterRefName(canonicalRefName: string): string;
74
+ } & {
75
+ getCanonicalRefName2(refName: string): string;
76
+ isValidRefName(refName: string): boolean;
77
+ } & {
78
+ getAliasesForRefName(refName: string): string[];
79
+ getRefNameMapForAdapter(adapterConf: {
80
+ [x: string]: unknown;
81
+ }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("../assemblyManager/refNameMaps.ts").RefNameAliases>;
82
+ getRefNameMismatch(adapterCacheKey: string): import("../assemblyManager/refNameMismatch.ts").RefNameMismatch | undefined;
83
+ } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
84
+ configuration: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
85
+ }, {
86
+ error: unknown;
87
+ loadingP: Promise<void> | undefined;
88
+ adapterLoads: import("@jbrowse/quick-lru").default<string, Promise<import("../assemblyManager/refNameMaps.ts").RefNameAliases>>;
89
+ volatileRegions: import("../assemblyManager/assembly.ts").BasicRegion[] | undefined;
90
+ refNameAliases: import("../assemblyManager/refNameMaps.ts").RefNameAliases | undefined;
91
+ canonicalToSeqAdapterRefNames: Record<string, string> | undefined;
92
+ cytobands: import("../util/simpleFeature.ts").Feature[] | undefined;
93
+ loadedGeneticCodes: Record<string, number> | undefined;
94
+ lowerCaseRefNameAliases: import("../assemblyManager/refNameMaps.ts").RefNameAliases | undefined;
95
+ statusMessage: string | undefined;
96
+ statusProgress: number | undefined;
97
+ statusSource: string | undefined;
98
+ refNameMismatches: Map<string, import("../assemblyManager/refNameMismatch.ts").RefNameMismatch>;
99
+ } & {
100
+ getConf(arg: string): any;
101
+ } & {
102
+ readonly name: string;
103
+ readonly aliases: string[];
104
+ readonly displayName: string;
105
+ readonly refNameColors: string[];
106
+ } & {
107
+ readonly allAliases: string[];
108
+ hasName(name: string): boolean;
109
+ } & {
110
+ setStatus(status?: import("../util/progress.ts").RpcStatus): void;
111
+ setRefNameMismatch(adapterCacheKey: string, mismatch: import("../assemblyManager/refNameMismatch.ts").RefNameMismatch): void;
112
+ } & {
113
+ setLoaded({ regions, refNameAliases, lowerCaseRefNameAliases, canonicalToSeqAdapterRefNames, cytobands, geneticCodes, }: import("../assemblyManager/refNameMaps.ts").RefNameMaps & {
114
+ regions: import("../util/index.ts").Region[];
115
+ cytobands: import("../util/simpleFeature.ts").Feature[];
116
+ geneticCodes: Record<string, number>;
117
+ }): void;
118
+ setError(e: unknown): void;
119
+ setLoadingP(p?: Promise<void>): void;
120
+ loadPre(): Promise<void>;
121
+ } & {
122
+ load(): Promise<void>;
123
+ } & {
124
+ afterAttach(): void;
125
+ } & {
126
+ readonly initialized: boolean;
127
+ readonly regions: import("../assemblyManager/assembly.ts").BasicRegion[] | undefined;
128
+ readonly allRefNames: string[] | undefined;
129
+ readonly namesByCanonicalRefName: Map<string, string[]> | undefined;
130
+ readonly rpcManager: import("../rpc/RpcManager.ts").default;
131
+ } & {
132
+ readonly refNames: string[] | undefined;
133
+ } & {
134
+ readonly refNameToIndex: Map<string, number> | undefined;
135
+ } & {
136
+ getCanonicalRefName(refName: string): string | undefined;
137
+ getRefNameColor(refName: string): string | undefined;
138
+ getRegionForRefName(refName: string): import("../assemblyManager/assembly.ts").BasicRegion | undefined;
139
+ getGeneticCodeId(refName: string): number;
140
+ getSeqAdapterRefName(canonicalRefName: string): string;
141
+ } & {
142
+ getCanonicalRefName2(refName: string): string;
143
+ isValidRefName(refName: string): boolean;
144
+ } & {
145
+ getAliasesForRefName(refName: string): string[];
146
+ getRefNameMapForAdapter(adapterConf: {
147
+ [x: string]: unknown;
148
+ }, options: import("../data_adapters/BaseAdapter/types.ts").BaseOptions): Promise<import("../assemblyManager/refNameMaps.ts").RefNameAliases>;
149
+ getRefNameMismatch(adapterCacheKey: string): import("../assemblyManager/refNameMismatch.ts").RefNameMismatch | undefined;
150
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
151
+ assemblyError: unknown;
152
+ regions: import("../assemblyManager/assembly.ts").BasicRegion[] | undefined;
153
+ };
@@ -0,0 +1,54 @@
1
+ import { useLocalStorage } from '../util/hooks.js';
2
+ // scope a localStorage key to this host/path/config so reloads (and embedded
3
+ // apps sharing a host) see their own value. Shared by the remembered-assembly
4
+ // and recent-locations persistence
5
+ //
6
+ // The near-twin is data-management's `configScopedKey`, and the two must NOT be
7
+ // merged even though they are the same idea. They disagree on every detail that
8
+ // reaches the output: this one includes the host, joins unfiltered (so a page
9
+ // with no `?config=` genuinely stores a literal `null` segment) and assumes a
10
+ // browser; that one omits the host, filters empty parts out, and answers
11
+ // `'empty'` off-window. So a "cleanup" that unified them would re-key every
12
+ // stored setting on both sides at once — remembered assembly and recent
13
+ // locations here, hidden columns and widths there — and every user would find
14
+ // their settings silently back at the defaults. Touch either spelling only as a
15
+ // deliberate migration.
16
+ export function instanceScopedKey(prefix, suffix) {
17
+ const config = new URLSearchParams(window.location.search).get('config');
18
+ return [
19
+ prefix,
20
+ window.location.host + window.location.pathname,
21
+ config,
22
+ suffix,
23
+ ].join('-');
24
+ }
25
+ /**
26
+ * Tracks the assembly chosen in an import form and resolves the outcomes the
27
+ * form renders from: `assemblyError` (failed, or nothing configured), `regions`
28
+ * (ready), or neither (still loading). The user's choice is stored as an
29
+ * override and re-resolved against the live assembly list every render, so it
30
+ * always names a currently-configured assembly even as assemblies load in, get
31
+ * removed, or when a remembered choice is no longer valid. Passing a
32
+ * `localStorageKey` persists the choice across reloads. Shared by the LGV and
33
+ * circular-view import forms.
34
+ */
35
+ export function useAssemblySelection(session, localStorageKey) {
36
+ const { assemblyNames, assemblyManager } = session;
37
+ const [override, setOverride] = useLocalStorage(instanceScopedKey('lastAssembly', localStorageKey ?? ''), undefined, Boolean(localStorageKey));
38
+ const selectedAssemblyName = assemblyNames.includes(override ?? '')
39
+ ? override
40
+ : assemblyNames[0];
41
+ const assembly = selectedAssemblyName
42
+ ? assemblyManager.get(selectedAssemblyName)
43
+ : undefined;
44
+ const assemblyError = assemblyNames.length
45
+ ? assembly?.error
46
+ : 'No configured assemblies';
47
+ return {
48
+ selectedAssemblyName,
49
+ setSelectedAssemblyName: setOverride,
50
+ assembly,
51
+ assemblyError,
52
+ regions: assembly?.regions,
53
+ };
54
+ }
@@ -0,0 +1,36 @@
1
+ /**
2
+ * Run a pointer handler at most once per frame, on the latest position.
3
+ *
4
+ * `mousemove` arrives far faster than a frame on any modern pointer, so a
5
+ * handler doing real work per raw event is spending most of it on positions the
6
+ * user never sees. The pileup's hit test measured 3.3ms of listener time per
7
+ * event on a 150px canvas — five events into a frame the frame is already gone —
8
+ * and it was the most expensive hover of any display.
9
+ *
10
+ * **Coalescing is only safe because nothing decides anything from a hover.**
11
+ * Click and right-click re-run their own hit test from their own event, which is
12
+ * already the rule (a hover recorded a frame ago must not act), so a hover
13
+ * landing one frame after the cursor is by construction invisible. A gesture
14
+ * that reads the stored hover instead would see this as a lost frame.
15
+ *
16
+ * The **first** scheduled frame is kept and the latest payload read inside it,
17
+ * rather than cancelling and rescheduling per event: both deliver one call per
18
+ * frame, and this one does no cancel churn. (`useMouseTracking` reschedules
19
+ * because it also publishes to a store that a mid-frame leave must be able to
20
+ * clear.)
21
+ *
22
+ * `cancel` is the other half, and it is not optional. A frame queued just before
23
+ * the pointer leaves lands *after* it has gone and re-lights the hover the leave
24
+ * handler just cleared, so a `mouseleave` cancels before clearing. Unmount
25
+ * cancels too — a display is detached from the MST tree before React unmounts
26
+ * it, so a frame landing in between writes onto a dead node.
27
+ *
28
+ * The payload is whatever the caller reads off the event, because where a
29
+ * display's coordinates come from is its own business: a borderless leaf canvas
30
+ * takes `offsetX`/`offsetY`, one with overlays measures a rect. Read it at event
31
+ * time — a React event's fields are gone by the frame.
32
+ */
33
+ export declare function useCoalescedPointer<T>(onFrame: (payload: T) => void): {
34
+ queue: (payload: T) => void;
35
+ cancel: () => void;
36
+ };
@@ -0,0 +1,60 @@
1
+ import { useEffect, useRef } from 'react';
2
+ import { useEventCallback } from '../util/useEventCallback.js';
3
+ /**
4
+ * Run a pointer handler at most once per frame, on the latest position.
5
+ *
6
+ * `mousemove` arrives far faster than a frame on any modern pointer, so a
7
+ * handler doing real work per raw event is spending most of it on positions the
8
+ * user never sees. The pileup's hit test measured 3.3ms of listener time per
9
+ * event on a 150px canvas — five events into a frame the frame is already gone —
10
+ * and it was the most expensive hover of any display.
11
+ *
12
+ * **Coalescing is only safe because nothing decides anything from a hover.**
13
+ * Click and right-click re-run their own hit test from their own event, which is
14
+ * already the rule (a hover recorded a frame ago must not act), so a hover
15
+ * landing one frame after the cursor is by construction invisible. A gesture
16
+ * that reads the stored hover instead would see this as a lost frame.
17
+ *
18
+ * The **first** scheduled frame is kept and the latest payload read inside it,
19
+ * rather than cancelling and rescheduling per event: both deliver one call per
20
+ * frame, and this one does no cancel churn. (`useMouseTracking` reschedules
21
+ * because it also publishes to a store that a mid-frame leave must be able to
22
+ * clear.)
23
+ *
24
+ * `cancel` is the other half, and it is not optional. A frame queued just before
25
+ * the pointer leaves lands *after* it has gone and re-lights the hover the leave
26
+ * handler just cleared, so a `mouseleave` cancels before clearing. Unmount
27
+ * cancels too — a display is detached from the MST tree before React unmounts
28
+ * it, so a frame landing in between writes onto a dead node.
29
+ *
30
+ * The payload is whatever the caller reads off the event, because where a
31
+ * display's coordinates come from is its own business: a borderless leaf canvas
32
+ * takes `offsetX`/`offsetY`, one with overlays measures a rect. Read it at event
33
+ * time — a React event's fields are gone by the frame.
34
+ */
35
+ export function useCoalescedPointer(onFrame) {
36
+ const rafRef = useRef(undefined);
37
+ const payloadRef = useRef(undefined);
38
+ const runFrame = useEventCallback(onFrame);
39
+ const cancel = useEventCallback(() => {
40
+ if (rafRef.current !== undefined) {
41
+ cancelAnimationFrame(rafRef.current);
42
+ rafRef.current = undefined;
43
+ }
44
+ payloadRef.current = undefined;
45
+ });
46
+ useEffect(() => cancel, [cancel]);
47
+ const queue = useEventCallback((payload) => {
48
+ payloadRef.current = payload;
49
+ if (rafRef.current === undefined) {
50
+ rafRef.current = requestAnimationFrame(() => {
51
+ rafRef.current = undefined;
52
+ const latest = payloadRef.current;
53
+ if (latest !== undefined) {
54
+ runFrame(latest);
55
+ }
56
+ });
57
+ }
58
+ });
59
+ return { queue, cancel };
60
+ }
@@ -0,0 +1,15 @@
1
+ /**
2
+ * Copy to the clipboard and briefly flash a "copied" confirmation. Returns the
3
+ * flag to render that confirmation from and the copy function to call from a
4
+ * click handler.
5
+ *
6
+ * The timer is what this exists for: it has to be reset on each copy, so a
7
+ * second click doesn't revert the label early, and cleared on unmount, so a
8
+ * panel closed mid-flash leaves nothing pending. `CopyToClipboardButton` and the
9
+ * feature-details `Formatter` had each grown a version of it, one of them
10
+ * without the unmount cleanup.
11
+ */
12
+ export declare function useCopyToClipboard(durationMs?: number): {
13
+ copied: boolean;
14
+ copy: (text: string) => Promise<void>;
15
+ };
@@ -0,0 +1,41 @@
1
+ import { useEffect, useRef, useState } from 'react';
2
+ import copyToClipboard from '../util/copyToClipboard.js';
3
+ /**
4
+ * Copy to the clipboard and briefly flash a "copied" confirmation. Returns the
5
+ * flag to render that confirmation from and the copy function to call from a
6
+ * click handler.
7
+ *
8
+ * The timer is what this exists for: it has to be reset on each copy, so a
9
+ * second click doesn't revert the label early, and cleared on unmount, so a
10
+ * panel closed mid-flash leaves nothing pending. `CopyToClipboardButton` and the
11
+ * feature-details `Formatter` had each grown a version of it, one of them
12
+ * without the unmount cleanup.
13
+ */
14
+ export function useCopyToClipboard(durationMs = 1000) {
15
+ const [copied, setCopied] = useState(false);
16
+ const timerRef = useRef(undefined);
17
+ useEffect(() => () => {
18
+ clearTimeout(timerRef.current);
19
+ }, []);
20
+ return {
21
+ copied,
22
+ // plain text only: a rich `text/html` copy is a menu action with no label to
23
+ // flash, so it calls copyToClipboard directly.
24
+ // The confirmation is flashed only once the write has actually landed —
25
+ // there is no session to notify from an inline button, so a failure leaves
26
+ // the label alone rather than claiming a copy that didn't happen.
27
+ copy: async (text) => {
28
+ try {
29
+ await copyToClipboard(text);
30
+ setCopied(true);
31
+ clearTimeout(timerRef.current);
32
+ timerRef.current = setTimeout(() => {
33
+ setCopied(false);
34
+ }, durationMs);
35
+ }
36
+ catch (e) {
37
+ console.error(e);
38
+ }
39
+ },
40
+ };
41
+ }
@@ -0,0 +1 @@
1
+ export declare function useExportSvgPreference<T>(key: string, val: T): readonly [T, (value: T | ((val: T) => T)) => void];
@@ -0,0 +1,4 @@
1
+ import { useLocalStorage } from '../util/hooks.js';
2
+ export function useExportSvgPreference(key, val) {
3
+ return useLocalStorage(`svg-${key}`, val);
4
+ }
@@ -0,0 +1,71 @@
1
+ export interface MouseState {
2
+ x: number;
3
+ y: number;
4
+ clientX: number;
5
+ clientY: number;
6
+ }
7
+ /**
8
+ * The pointer position, as something to read rather than something you hold.
9
+ *
10
+ * `useMouseTracking` hands this back instead of the position itself, and that
11
+ * indirection is the entire point — see there.
12
+ */
13
+ export interface MouseTracker {
14
+ subscribe: (onStoreChange: () => void) => () => void;
15
+ getSnapshot: () => MouseState | undefined;
16
+ }
17
+ export declare const ClearTrackedPointerProvider: import("react").Provider<() => void>;
18
+ export declare function useClearTrackedPointer(): () => void;
19
+ /**
20
+ * Container-relative mouse position for the overlays that follow the pointer
21
+ * (`Crosshairs`, tooltips), coalesced to one update per frame.
22
+ *
23
+ * The position is measured against the box of whatever element the handlers are
24
+ * bound to, which is what the overlays are positioned in — off `currentTarget`,
25
+ * so there is no ref to pass and no way to bind the two to different elements.
26
+ * A display that also hit-tests takes `onMove`, so its hit and its guides come
27
+ * off one measurement in one frame instead of two pointer paths that have to
28
+ * agree.
29
+ *
30
+ * **It returns a `mouseTracker` rather than the position, and that is the
31
+ * load-bearing part.** Its one caller is `DisplayChromeBase`, which owns the
32
+ * container the handlers bind to — so if the position were state here, every
33
+ * mouse move would re-render the chrome itself (re-running
34
+ * `useRenderingBackend`), the status container with a fresh inline `style`
35
+ * object, all three overlays, and only then the body that actually wanted the
36
+ * coordinate. That is a whole display's chrome repainting because the cursor
37
+ * moved a pixel over it; it cost a full document `Layout` plus three `Paint`s
38
+ * per mousemove on the wiggle displays, back when each display called this hook
39
+ * itself and every one of them had it.
40
+ *
41
+ * So the position is published instead, and whoever wants it calls
42
+ * `useMouseState(mouseTracker)` — from inside the chrome's body, where the
43
+ * overlays live. Re-rendering then starts at the component that reads it.
44
+ * Passing the tracker down a prop is free; passing `mouseState` down is the bug.
45
+ */
46
+ export declare function useMouseTracking(onMove?: (state?: MouseState) => void): {
47
+ mouseTracker: MouseTracker;
48
+ handleMouseMove: (event: React.MouseEvent) => void;
49
+ handleMouseLeave: () => void;
50
+ };
51
+ /**
52
+ * Read something derived from the tracked pointer, re-rendering only when the
53
+ * derived value changes.
54
+ *
55
+ * `useMouseState` renders once per frame the pointer moves, which is what a
56
+ * thing drawn *at* the cursor wants. A consumer that only asks a question of the
57
+ * position — "is the pointer inside this band?" — renders once per answer
58
+ * instead, because `useSyncExternalStore` compares snapshots and a boolean
59
+ * compares equal to the last one.
60
+ *
61
+ * The tracker is optional so a component can sit outside whatever bound the
62
+ * handlers (a highlight band rendered in a test, say) and read a pointer that is
63
+ * simply never there.
64
+ */
65
+ export declare function useMouseSelector<T>(tracker: MouseTracker | undefined, selector: (state: MouseState | undefined) => T): T;
66
+ /**
67
+ * Read the tracked pointer position. Call this in the component that draws the
68
+ * cursor-following thing, not in the one that bound the handlers — see
69
+ * `useMouseTracking`.
70
+ */
71
+ export declare function useMouseState(tracker: MouseTracker): MouseState | undefined;