@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1024. package/esm/util/rpc.d.ts +16 -1
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  1099. package/esm/util/tss-react/types.d.ts +1 -1
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  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,24 @@
1
+ /**
2
+ * One launch offer, over the datasets that can serve it: nothing at all when
3
+ * none can, otherwise a submenu naming each. Which dataset a launch reads from
4
+ * changes the answer, so the name is always on screen — a single dataset gets
5
+ * the same submenu as several rather than a flat item that leaves it unsaid.
6
+ *
7
+ * Kept apart from the discovery it is fed so the shape is testable on plain
8
+ * data.
9
+ */
10
+ export function launchTargetsMenuItem({ label, icon, entries, entryLabel, onSelect, }) {
11
+ return entries.length
12
+ ? [
13
+ {
14
+ label,
15
+ icon,
16
+ type: 'subMenu',
17
+ subMenu: entries.map(entry => ({
18
+ label: entryLabel(entry),
19
+ onClick: onSelect(entry),
20
+ })),
21
+ },
22
+ ]
23
+ : [];
24
+ }
@@ -0,0 +1,4 @@
1
+ import type { MenuItem } from './MenuTypes.ts';
2
+ export declare const LAUNCH_LABEL = "Launch";
3
+ export declare function pushIntoSubMenu(items: MenuItem[], label: string, item: MenuItem): void;
4
+ export declare function pushLaunchViewMenuItem(items: MenuItem[], item: MenuItem): void;
@@ -0,0 +1,46 @@
1
+ // The submenu every "open something for this region" contribution collects
2
+ // under, in a track menu, a view menu and the rubberband menu alike. One word,
3
+ // because half of what it now launches is not a view — a consensus dialog, the
4
+ // MAF subsequence widget, a sequence readout — and the rubberband menu has
5
+ // spelled it this way all along.
6
+ export const LAUNCH_LABEL = 'Launch';
7
+ // Add `item` under the `label` submenu of `items`, creating that submenu the
8
+ // first time. What makes several plugins' contributions collect in one place
9
+ // instead of each becoming its own top-level row, whatever order they ran in.
10
+ export function pushIntoSubMenu(items, label, item) {
11
+ // `'subMenu' in i`, not `i.type === 'subMenu'`: `type` is OPTIONAL on a
12
+ // submenu row and most of the tree omits it, so the type test would miss an
13
+ // existing group and push a second top-level row under the same label — two
14
+ // rows that then share a React key and an open/closed state.
15
+ const existing = items.find((i) => 'subMenu' in i && i.label === label);
16
+ if (existing) {
17
+ const { subMenu } = existing;
18
+ if (typeof subMenu === 'function') {
19
+ existing.subMenu = () => [...subMenu(), item];
20
+ }
21
+ else {
22
+ subMenu.push(item);
23
+ }
24
+ }
25
+ else {
26
+ items.push({ label, type: 'subMenu', subMenu: [item] });
27
+ }
28
+ }
29
+ // Several independent plugins (dotplot-view, linear-comparative-view, …) each
30
+ // contribute one "open another view for this feature" context-menu item. Call
31
+ // this instead of pushing a top-level item so the contributions land in a
32
+ // single "Launch" submenu regardless of which plugin's extension runs
33
+ // first. The `group` option on `addViewMenuItems`/`addDisplayMenuItems` does the
34
+ // same thing for a contributor registered that way, and is the shorter road to
35
+ // it.
36
+ //
37
+ // The rubberband menu has its own seam for the same job —
38
+ // `rubberBandLaunchMenuItems()` on the linear genome view — because there the
39
+ // grouping is the model's, not each contributor's, to do.
40
+ //
41
+ // Keeps its name while the label loses a word: `@jbrowse/core/ui` serves it, so
42
+ // a published plugin bundle reads it off the host at module scope and a rename
43
+ // is `undefined` inside an already-shipped UMD.
44
+ export function pushLaunchViewMenuItem(items, item) {
45
+ pushIntoSubMenu(items, LAUNCH_LABEL, item);
46
+ }
@@ -0,0 +1,16 @@
1
+ import type { MenuItem } from './MenuTypes.ts';
2
+ import type { SettingRowOptions } from './toggleMenuItems.ts';
3
+ /**
4
+ * The "Show legend" checkbox behind `LegendMixin`'s row and the circular
5
+ * view's. Takes the value and the toggle, in `checkboxItem`'s order, which is
6
+ * all this adds a label to.
7
+ *
8
+ * The `showLegend` **config slots** stay per display: their default values
9
+ * legitimately differ (a Hi-C color scale is off by default, a variant genotype
10
+ * key on), and their descriptions describe genuinely different legends.
11
+ *
12
+ * `synteny-core`'s color-by legend has no toggle at all: it comes up with the
13
+ * modes that have a key and is dismissed from its own close button.
14
+ */
15
+ /** #menuBuilder showLegendCheckboxItem | the shared "Show legend" checkbox */
16
+ export declare function showLegendCheckboxItem(checked: boolean, onToggle: () => void, opts?: SettingRowOptions): MenuItem;
@@ -0,0 +1,17 @@
1
+ import { checkboxItem } from './toggleMenuItems.js';
2
+ /**
3
+ * The "Show legend" checkbox behind `LegendMixin`'s row and the circular
4
+ * view's. Takes the value and the toggle, in `checkboxItem`'s order, which is
5
+ * all this adds a label to.
6
+ *
7
+ * The `showLegend` **config slots** stay per display: their default values
8
+ * legitimately differ (a Hi-C color scale is off by default, a variant genotype
9
+ * key on), and their descriptions describe genuinely different legends.
10
+ *
11
+ * `synteny-core`'s color-by legend has no toggle at all: it comes up with the
12
+ * modes that have a key and is dismissed from its own close button.
13
+ */
14
+ /** #menuBuilder showLegendCheckboxItem | the shared "Show legend" checkbox */
15
+ export function showLegendCheckboxItem(checked, onToggle, opts) {
16
+ return checkboxItem('Show legend', checked, onToggle, opts);
17
+ }
@@ -0,0 +1,69 @@
1
+ import type { ShapeName } from '../util/markEncodingTypes.ts';
2
+ import type { RampStop } from './colorScale.ts';
3
+ export interface LegendSwatch {
4
+ color: string;
5
+ shape?: ShapeName;
6
+ }
7
+ export interface LegendGradient {
8
+ stops: RampStop[];
9
+ minLabel: string;
10
+ maxLabel: string;
11
+ }
12
+ export interface ColorLegendEntry {
13
+ key: string;
14
+ label: string;
15
+ color?: string;
16
+ swatches?: LegendSwatch[];
17
+ hidden?: boolean;
18
+ gradient?: LegendGradient;
19
+ }
20
+ export interface LegendItem {
21
+ value?: string;
22
+ color?: string;
23
+ swatches?: LegendSwatch[];
24
+ gradient?: LegendGradient;
25
+ label: string;
26
+ hidden?: boolean;
27
+ }
28
+ export declare function legendSwatches(item: LegendItem): LegendSwatch[];
29
+ export interface LegendSection {
30
+ id: string;
31
+ title?: string;
32
+ note?: string;
33
+ items: LegendItem[];
34
+ focusesRows?: boolean;
35
+ }
36
+ export interface LegendSpec {
37
+ title?: string;
38
+ sections: LegendSection[];
39
+ }
40
+ export declare function nonEmptyLegendSections(sections: readonly LegendSection[]): LegendSection[];
41
+ export declare function legendEntries(spec: LegendSpec): ColorLegendEntry[];
42
+ /**
43
+ * How many rows a color key may have and still be one. Past this it is a list
44
+ * of every row, which is the thing a key exists instead of.
45
+ */
46
+ export declare const MAX_LEGEND_ITEMS = 20;
47
+ /**
48
+ * Whether a key built from these items is worth the rows it costs, for a
49
+ * display that has to *decide* — one whose key is only sometimes the thing
50
+ * naming its colors, and which therefore asks before drawing.
51
+ *
52
+ * Two questions, and both have drawn a useless key on a real track:
53
+ *
54
+ * - **Short enough to read?** A list longer than a reader can scan is worse
55
+ * than whatever it was going to explain. Ask this of the collapsed items, not
56
+ * of the row count — a cohort track's key is one row per group, so 4,390
57
+ * cells in nine cell types is nine rows and passes, while the same cells
58
+ * ungrouped are 4,390 and do not.
59
+ * - **Does it distinguish anything?** A key maps colors to names, so it needs
60
+ * more than one color to map. Items that all share one — every swatch having
61
+ * resolved to the same fallback, which is what a track carrying no identity
62
+ * color produces — spend rows over the plot to say nothing. This is why
63
+ * `LegendItem.color` should be resolved before it gets here: an unresolved
64
+ * `undefined` compares equal to every other `undefined` only by accident.
65
+ *
66
+ * Displays whose key is unconditional (alignments, variants) don't need this;
67
+ * their vocabulary is always worth naming.
68
+ */
69
+ export declare function legendIsReadable(items: LegendItem[], maxItems?: number): boolean;
@@ -0,0 +1,69 @@
1
+ // The boxes a row draws: its explicit list, else its single color, else nothing
2
+ // at all (a heading).
3
+ export function legendSwatches(item) {
4
+ return (item.swatches ?? (item.color === undefined ? [] : [{ color: item.color }]));
5
+ }
6
+ // Drop sections with nothing in them, so a heading can never end up with no
7
+ // swatches under it.
8
+ export function nonEmptyLegendSections(sections) {
9
+ return sections.filter(s => s.items.length > 0);
10
+ }
11
+ // Flatten a legend spec into `SvgColorLegend` rows: a color-less row reads as a
12
+ // heading rather than a swatch. Section titles appear only when more than one
13
+ // section survives — a lone vocabulary needs no title above it — which is the
14
+ // rule `FloatingLegend` applies on screen, so an export and the live legend
15
+ // agree about when headings show. A box-level `title` is unconditional, like its
16
+ // on-screen counterpart, and `''` is no heading in either.
17
+ export function legendEntries(spec) {
18
+ const sections = nonEmptyLegendSections(spec.sections);
19
+ const titled = sections.length > 1;
20
+ return [
21
+ ...(spec.title ? [{ key: 'legend-title', label: spec.title }] : []),
22
+ ...sections.flatMap(section => [
23
+ ...(titled && section.title
24
+ ? [{ key: `${section.id}-title`, label: section.title }]
25
+ : []),
26
+ ...(section.note === undefined
27
+ ? []
28
+ : [{ key: `${section.id}-note`, label: section.note }]),
29
+ ...section.items.map((item, idx) => ({
30
+ key: `${section.id}-${idx}`,
31
+ label: item.label,
32
+ color: item.color,
33
+ swatches: item.swatches,
34
+ hidden: item.hidden,
35
+ gradient: item.gradient,
36
+ })),
37
+ ]),
38
+ ];
39
+ }
40
+ /**
41
+ * How many rows a color key may have and still be one. Past this it is a list
42
+ * of every row, which is the thing a key exists instead of.
43
+ */
44
+ export const MAX_LEGEND_ITEMS = 20;
45
+ /**
46
+ * Whether a key built from these items is worth the rows it costs, for a
47
+ * display that has to *decide* — one whose key is only sometimes the thing
48
+ * naming its colors, and which therefore asks before drawing.
49
+ *
50
+ * Two questions, and both have drawn a useless key on a real track:
51
+ *
52
+ * - **Short enough to read?** A list longer than a reader can scan is worse
53
+ * than whatever it was going to explain. Ask this of the collapsed items, not
54
+ * of the row count — a cohort track's key is one row per group, so 4,390
55
+ * cells in nine cell types is nine rows and passes, while the same cells
56
+ * ungrouped are 4,390 and do not.
57
+ * - **Does it distinguish anything?** A key maps colors to names, so it needs
58
+ * more than one color to map. Items that all share one — every swatch having
59
+ * resolved to the same fallback, which is what a track carrying no identity
60
+ * color produces — spend rows over the plot to say nothing. This is why
61
+ * `LegendItem.color` should be resolved before it gets here: an unresolved
62
+ * `undefined` compares equal to every other `undefined` only by accident.
63
+ *
64
+ * Displays whose key is unconditional (alignments, variants) don't need this;
65
+ * their vocabulary is always worth naming.
66
+ */
67
+ export function legendIsReadable(items, maxItems = MAX_LEGEND_ITEMS) {
68
+ return items.length <= maxItems && new Set(items.map(i => i.color)).size > 1;
69
+ }
@@ -0,0 +1,18 @@
1
+ export declare const dot1: {
2
+ name: string;
3
+ styles: string;
4
+ anim: 1;
5
+ toString: () => string;
6
+ } & string;
7
+ export declare const dot2: {
8
+ name: string;
9
+ styles: string;
10
+ anim: 1;
11
+ toString: () => string;
12
+ } & string;
13
+ export declare const dot3: {
14
+ name: string;
15
+ styles: string;
16
+ anim: 1;
17
+ toString: () => string;
18
+ } & string;
@@ -0,0 +1,17 @@
1
+ import { keyframes } from '../util/tss-react/index.js';
2
+ // Animate opacity (a compositor-offloaded property) rather than visibility so
3
+ // the animation keeps running on the GPU compositor thread while the main
4
+ // thread is busy. visibility/width/color animations run on the main thread and
5
+ // freeze during jank.
6
+ export const dot1 = keyframes `
7
+ 0%, 25% { opacity: 0; }
8
+ 25.1%, 100% { opacity: 1; }
9
+ `;
10
+ export const dot2 = keyframes `
11
+ 0%, 50% { opacity: 0; }
12
+ 50.1%, 100% { opacity: 1; }
13
+ `;
14
+ export const dot3 = keyframes `
15
+ 0%, 75% { opacity: 0; }
16
+ 75.1%, 100% { opacity: 1; }
17
+ `;
@@ -0,0 +1,24 @@
1
+ import type { MenuItem } from './MenuTypes.ts';
2
+ import type { SliderScale } from './sliderScale.ts';
3
+ interface SizeMenuOptions {
4
+ label: string;
5
+ title: string;
6
+ help?: string;
7
+ getValue: () => number;
8
+ min?: number;
9
+ max?: number;
10
+ step?: number;
11
+ unit?: string;
12
+ scale?: SliderScale;
13
+ format?: (n: number) => string;
14
+ commitOnRelease?: boolean;
15
+ onChange: (n: number) => void;
16
+ onReset: () => void;
17
+ }
18
+ export declare function makeSizeMenu(opts: SizeMenuOptions & {
19
+ isDefault: boolean;
20
+ }): MenuItem;
21
+ export declare function makeSizeSubMenu(opts: SizeMenuOptions & {
22
+ isDefault: boolean;
23
+ }): MenuItem;
24
+ export {};
@@ -0,0 +1,58 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Suspense, lazy } from 'react';
3
+ import { INLINE_MENU_ROW_WIDTH } from './inlineMenuRowWidth.js';
4
+ // The row's drawn half is `lazy()` because this builder is called from state
5
+ // models and menu modules, which are eager, and the row is the only route by
6
+ // which MUI
7
+ // `Slider` — the largest single Material component in the eager graph — reached
8
+ // a host's first paint. `type: 'custom'` already made `render` a thunk, so the
9
+ // laziness is free at call time; it is the module edge that had to go.
10
+ //
11
+ // The fallback holds the row's footprint so the open menu doesn't reflow when
12
+ // the chunk lands. Height is the row's natural one (caption line + slider); it
13
+ // is approximate on purpose, since being a few px out for one frame is
14
+ // invisible where a collapse to zero is not.
15
+ const SizeSliderRow = lazy(() => import('./SizeSliderRow.js').then(m => ({ default: m.SizeSliderRow })));
16
+ const sizeRowFallbackHeight = 46;
17
+ // Shared inline "size" control as a single menu row (was a submenu of
18
+ // slider/reset/default). Callers own their config slot/semantics and wire the
19
+ // accessors + a title (which also derives the slider's test id). Used by wiggle
20
+ // point-size/line-width, GWAS Manhattan point-size, arc width, the alignments
21
+ // modification threshold and GC-content window/step sizes, so the
22
+ // slider/reset behavior can't drift. Pass `scale: 'log'` for values spanning
23
+ // orders of magnitude, and `format` to label non-`px` units.
24
+ export function makeSizeMenu(opts) {
25
+ return sizeMenu(opts, opts.isDefault);
26
+ }
27
+ // The same control one hop down: a plain submenu row whose only child is the
28
+ // size row above.
29
+ //
30
+ // For a menu where a slider drawn inline is the odd one out. Every other row
31
+ // there is `label + [?] + (checkbox | chevron)` and a size row is a two-line
32
+ // block with a widget of its own, so a menu holding several reads as a form to
33
+ // fill in rather than a list to pick from — and the comparative views' settings
34
+ // menus hold three each. Behind a chevron the row shape is uniform top to
35
+ // bottom, and the value moves inside next to the slider that sets it, which is
36
+ // where the radio submenus already keep their state.
37
+ //
38
+ // `help` lands on the submenu row, which is the row a reader sees: the size row
39
+ // behind the chevron never reaches the menu's shared trailing column, and a "?"
40
+ // of its own would only be a second one for the same setting, a hover away.
41
+ export function makeSizeSubMenu(opts) {
42
+ return {
43
+ label: opts.title,
44
+ helpText: opts.help,
45
+ subMenu: [makeSizeMenu(opts)],
46
+ };
47
+ }
48
+ function sizeMenu(opts, isDefault) {
49
+ const { label, title, getValue, min = 0.5, max = 12, step = 0.5, unit = 'px', scale = 'linear', format = (n) => `${n}${unit}`, commitOnRelease, onChange, onReset, } = opts;
50
+ return {
51
+ label,
52
+ type: 'custom',
53
+ render: () => (_jsx(Suspense, { fallback: _jsx("div", { style: {
54
+ width: INLINE_MENU_ROW_WIDTH,
55
+ height: sizeRowFallbackHeight,
56
+ } }), children: _jsx(SizeSliderRow, { title: title, getValue: getValue, min: min, max: max, step: step, scale: scale, format: format, isDefault: isDefault, commitOnRelease: commitOnRelease, onChange: onChange, onReset: onReset }) })),
57
+ };
58
+ }
@@ -0,0 +1,8 @@
1
+ export interface StackFrame {
2
+ name: string;
3
+ uri: string;
4
+ line: number;
5
+ column: number;
6
+ }
7
+ export declare function parseStackLine(line: string): StackFrame | undefined;
8
+ export declare function mapStackTrace(stack: string): Promise<string>;
@@ -0,0 +1,108 @@
1
+ import { SourceMapConsumer } from 'source-map-js';
2
+ const sourceMappingUrlRe = /\/\/# sourceMappingURL=(.*)/g;
3
+ // blob: urls (worker scripts) embed a second scheme, so blob: has to be part of
4
+ // the match: without it the uri truncates to a script that doesn't exist
5
+ const protocolRe = /(?:blob:)?(?:https?|file):\/\//;
6
+ const digitsRe = /^\d+$/;
7
+ async function myfetchtext(uri) {
8
+ const res = await fetch(uri);
9
+ if (!res.ok) {
10
+ throw new Error(`HTTP ${res.status} fetching ${uri}: ${await res.text()}`);
11
+ }
12
+ return res.text();
13
+ }
14
+ function sourceMapUrl(script, uri) {
15
+ // the real annotation is the last one — a bundle can carry the literal
16
+ // earlier in an inlined dependency
17
+ const mapUri = [...script.matchAll(sourceMappingUrlRe)].at(-1)?.[1]?.trim();
18
+ let url;
19
+ if (mapUri) {
20
+ url = new URL(mapUri, uri);
21
+ // vite serves scripts as /foo.js?v=hash and the sibling .map needs the same
22
+ // query; never touch an inline data: map or a map url with its own query
23
+ if (!url.search && url.protocol !== 'data:') {
24
+ url.search = new URL(uri).search;
25
+ }
26
+ }
27
+ return url?.href;
28
+ }
29
+ async function loadSourceMap(uri) {
30
+ try {
31
+ const mapUrl = sourceMapUrl(await myfetchtext(uri), uri);
32
+ return mapUrl
33
+ ? new SourceMapConsumer(JSON.parse(await myfetchtext(mapUrl)))
34
+ : undefined;
35
+ }
36
+ catch {
37
+ // a frame can point at a script with no map, an unreachable url, or a
38
+ // revoked blob: worker url. Those frames stay raw instead of failing the
39
+ // whole trace
40
+ return undefined;
41
+ }
42
+ }
43
+ // one load attempt per script per session; loadSourceMap never rejects, so a
44
+ // miss is cached like a hit rather than refetched for every frame
45
+ const sourceMaps = new Map();
46
+ function getSourceMap(uri) {
47
+ const existing = sourceMaps.get(uri);
48
+ if (existing) {
49
+ return existing;
50
+ }
51
+ else {
52
+ const map = loadSourceMap(uri);
53
+ sourceMaps.set(uri, map);
54
+ return map;
55
+ }
56
+ }
57
+ // parses a frame line like " at f (file:///foo.js:12:34)", or firefox's
58
+ // "f@file:///foo.js:12:34", into its function name, source uri, line and
59
+ // column. undefined when the line has no uri:line:column reference, e.g. the
60
+ // message line that chrome puts first
61
+ export function parseStackLine(line) {
62
+ const protocolMatch = protocolRe.exec(line);
63
+ if (!protocolMatch) {
64
+ return undefined;
65
+ }
66
+ const urlStart = protocolMatch.index;
67
+ const rest = line.slice(urlStart).replace(/\)$/, '');
68
+ const lastColon = rest.lastIndexOf(':');
69
+ const secondLastColon = rest.lastIndexOf(':', lastColon - 1);
70
+ const lineStr = rest.slice(secondLastColon + 1, lastColon);
71
+ const columnStr = rest.slice(lastColon + 1);
72
+ return secondLastColon > 0 &&
73
+ digitsRe.test(lineStr) &&
74
+ digitsRe.test(columnStr)
75
+ ? {
76
+ name: line
77
+ .slice(0, urlStart)
78
+ .trim()
79
+ .replace(/^at\b\s*/, '')
80
+ .replace(/\s*\($/, '')
81
+ .replace(/@$/, ''),
82
+ uri: rest.slice(0, secondLastColon),
83
+ line: +lineStr,
84
+ column: +columnStr,
85
+ }
86
+ : undefined;
87
+ }
88
+ async function mapStackLine(line) {
89
+ const frame = parseStackLine(line);
90
+ const consumer = frame ? await getSourceMap(frame.uri) : undefined;
91
+ if (frame && consumer) {
92
+ const pos = consumer.originalPositionFor({
93
+ line: frame.line,
94
+ // stack traces report 1-based columns, source maps are 0-based
95
+ column: frame.column - 1,
96
+ });
97
+ const { source, line: origLine, column } = pos;
98
+ return source !== null && origLine !== null && column !== null
99
+ ? `${source}:${origLine}:${column + 1}${frame.name ? ` (${frame.name})` : ''}`
100
+ : line;
101
+ }
102
+ else {
103
+ return line;
104
+ }
105
+ }
106
+ export async function mapStackTrace(stack) {
107
+ return (await Promise.all(stack.split('\n').map(mapStackLine))).join('\n');
108
+ }
@@ -0,0 +1 @@
1
+ export declare function measureLegendText(str: string, fontSize: number): number;
@@ -0,0 +1,8 @@
1
+ import { measureText } from '../util/measureText.js';
2
+ // measureText uses a Helvetica width table, but SVG legend <text> nodes have no
3
+ // font-family and render in the wider app font (Roboto), so scale the estimate
4
+ // up before sizing the white paper behind a label or it clips.
5
+ const APP_FONT_WIDTH_RATIO = 1.1;
6
+ export function measureLegendText(str, fontSize) {
7
+ return measureText(str, fontSize) * APP_FONT_WIDTH_RATIO;
8
+ }
@@ -0,0 +1,22 @@
1
+ import type { MenuItem } from './MenuTypes.ts';
2
+ /**
3
+ * The trailing control a menu row draws, resolved at the point of drawing.
4
+ *
5
+ * `endAdornment` is an element the builder already made — synteny's and
6
+ * wiggle's colour swatches — so the row hands it straight through.
7
+ *
8
+ * Lives in one place rather than at each of the four render sites, because the
9
+ * "does any row have one?" predicate and the rendering have to agree — a row
10
+ * that draws an adornment the column-reservation pass didn't count is a
11
+ * misaligned menu, not a crash.
12
+ */
13
+ export declare function menuItemAdornment(item: MenuItem): import("react").ReactNode;
14
+ /**
15
+ * Whether this row draws something in the shared trailing column — the question
16
+ * `getMenuColumnFlags` asks to decide whether to reserve that column on every
17
+ * row of the menu.
18
+ *
19
+ * A `type: 'custom'` row renders its own content edge to edge and never reaches
20
+ * `menuItemAdornment`, so it cannot draw in that column however it is declared.
21
+ */
22
+ export declare function hasMenuItemAdornment(item: MenuItem): boolean;
@@ -0,0 +1,28 @@
1
+ /**
2
+ * The trailing control a menu row draws, resolved at the point of drawing.
3
+ *
4
+ * `endAdornment` is an element the builder already made — synteny's and
5
+ * wiggle's colour swatches — so the row hands it straight through.
6
+ *
7
+ * Lives in one place rather than at each of the four render sites, because the
8
+ * "does any row have one?" predicate and the rendering have to agree — a row
9
+ * that draws an adornment the column-reservation pass didn't count is a
10
+ * misaligned menu, not a crash.
11
+ */
12
+ export function menuItemAdornment(item) {
13
+ return 'endAdornment' in item ? item.endAdornment : undefined;
14
+ }
15
+ /**
16
+ * Whether this row draws something in the shared trailing column — the question
17
+ * `getMenuColumnFlags` asks to decide whether to reserve that column on every
18
+ * row of the menu.
19
+ *
20
+ * A `type: 'custom'` row renders its own content edge to edge and never reaches
21
+ * `menuItemAdornment`, so it cannot draw in that column however it is declared.
22
+ */
23
+ export function hasMenuItemAdornment(item) {
24
+ if (item.type === 'custom') {
25
+ return false;
26
+ }
27
+ return 'endAdornment' in item && !!item.endAdornment;
28
+ }
@@ -0,0 +1,23 @@
1
+ /**
2
+ * Menu-item *builders*, and nothing that draws one.
3
+ *
4
+ * These builders return plain objects, and their callers are state models
5
+ * and `menuItems.ts` / `trackMenus.ts` modules across a dozen plugins — code
6
+ * that is evaluated when a plugin installs, before any session can be read.
7
+ * Reaching them through `@jbrowse/core/ui` meant reaching them through a barrel
8
+ * that re-exports ~80 Material UI components, and the union of what those eager
9
+ * callers happened to name was most of Material UI in every host's first paint
10
+ * (reference/EAGER_BUNDLE.md).
11
+ *
12
+ * So the split is not stylistic: **import menu builders from here, components
13
+ * from `@jbrowse/core/ui`.** This entry must never reach react, @mui or
14
+ * @emotion, and `menuItems.purity.test.ts` fails if it starts to — including
15
+ * transitively, which is the only way the failure would ever show up.
16
+ */
17
+ export { checkboxItem, radioItem, radioItems, toggleItem, withSubHeader, } from './toggleMenuItems.ts';
18
+ export { withHint } from './menuLabels.ts';
19
+ export { makeRadioSubMenu } from './radioSubMenu.ts';
20
+ export { showLegendCheckboxItem } from './legendMenuItem.ts';
21
+ export type { RadioOption, SettingRowOptions } from './toggleMenuItems.ts';
22
+ export { resolveSubMenu, staysOpenOnClick } from './MenuTypes.ts';
23
+ export type { BaseMenuItem, CheckboxMenuItem, ClickableMenuItem, CustomMenuItem, MenuDivider, MenuItem, MenuItemClickHandler, MenuItemsGetter, MenuSubHeader, NormalMenuItem, RadioMenuItem, SubMenuItem, } from './MenuTypes.ts';
@@ -0,0 +1,21 @@
1
+ /**
2
+ * Menu-item *builders*, and nothing that draws one.
3
+ *
4
+ * These builders return plain objects, and their callers are state models
5
+ * and `menuItems.ts` / `trackMenus.ts` modules across a dozen plugins — code
6
+ * that is evaluated when a plugin installs, before any session can be read.
7
+ * Reaching them through `@jbrowse/core/ui` meant reaching them through a barrel
8
+ * that re-exports ~80 Material UI components, and the union of what those eager
9
+ * callers happened to name was most of Material UI in every host's first paint
10
+ * (reference/EAGER_BUNDLE.md).
11
+ *
12
+ * So the split is not stylistic: **import menu builders from here, components
13
+ * from `@jbrowse/core/ui`.** This entry must never reach react, @mui or
14
+ * @emotion, and `menuItems.purity.test.ts` fails if it starts to — including
15
+ * transitively, which is the only way the failure would ever show up.
16
+ */
17
+ export { checkboxItem, radioItem, radioItems, toggleItem, withSubHeader, } from './toggleMenuItems.js';
18
+ export { withHint } from './menuLabels.js';
19
+ export { makeRadioSubMenu } from './radioSubMenu.js';
20
+ export { showLegendCheckboxItem } from './legendMenuItem.js';
21
+ export { resolveSubMenu, staysOpenOnClick } from './MenuTypes.js';
@@ -0,0 +1,41 @@
1
+ /**
2
+ * Menu row LABELS, as opposed to the rows themselves — the builders that make a
3
+ * row live in `toggleMenuItems.ts` and its neighbours, and take a label they do
4
+ * not compose.
5
+ *
6
+ * Its own module because a label is not a row: `withHint` is reached from radio
7
+ * options and from hand-written literals as often as from a builder, so filing
8
+ * it under the checkbox builders put it behind an import that half its callers
9
+ * had no other reason to make.
10
+ *
11
+ * Same purity boundary as the rest of `menuItems.ts` — no react, @mui or
12
+ * @emotion, ever (`menuItems.purity.test.ts`).
13
+ */
14
+ /**
15
+ * #menuBuilder withHint | a row label carrying an aside that is only sometimes there
16
+ *
17
+ * `withHint('Show row separators', tooShort ? 'needs rows 4px or taller' :
18
+ * undefined)`.
19
+ *
20
+ * The rows that want this are the ones that can be on, correctly on, and doing
21
+ * nothing observable -- a band overridden by the summary tier, a separator
22
+ * below the height it draws at. The tick keeps reporting what the user chose,
23
+ * so silence would leave the setting looking broken.
24
+ *
25
+ * IN THE LABEL rather than a `subLabel`, which is what these were: a second
26
+ * line under the row is heavy for a clarifier this short, and rather than a
27
+ * `helpText`, which would reserve a "?" column across the whole menu for one
28
+ * conditional row and hide the reason behind a hover -- on a control the reader
29
+ * has no reason to hover, since from the tick it looks like it already works.
30
+ *
31
+ * AN EM DASH, NOT PARENTHESES. Two of these labels already end in a
32
+ * parenthetical of their own ("Show conservation (% identity)", "Codon changes
33
+ * (amino acids)"), and a second pair straight after the first reads as a typo.
34
+ * It also keeps the aside distinct from the ` - ` that names a permanent half of
35
+ * a label ("Square view - average bp per pixel").
36
+ *
37
+ * KEEP THE HINT SHORT -- a few words, not a sentence. A menu sizes to its widest
38
+ * row, so a long one widens every row for as long as it fires, which is the same
39
+ * cost that rules out `helpText` above.
40
+ */
41
+ export declare function withHint(label: string, hint: string | undefined): string;