@jbrowse/core 4.3.0 → 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 +195 -35
  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 +1,38 @@
1
+ import type { Pin } from '../configuration/promotablePin.ts';
2
+ import type { MenuItem } from './MenuTypes.ts';
3
+ /**
4
+ * The "Show legend" checkbox, which seven displays build by hand — Hi-C, LD,
5
+ * alignments, LGVSynteny, multi-wiggle, multi-row features, both multi-sample
6
+ * variant displays and the Manhattan plot.
7
+ *
8
+ * Takes the value and the toggle rather than a `{ showLegend, setShowLegend }`
9
+ * model, because the Manhattan plot's pair is named for the LD legend it draws
10
+ * and would otherwise need an adapter object at the call site. Same argument
11
+ * order as `checkboxItem`, which is all this adds a label to.
12
+ *
13
+ * The `showLegend` **config slots** stay per display: their `promotedBase`
14
+ * values legitimately differ (a Hi-C color scale is off by default, a variant
15
+ * genotype key on), and their descriptions describe genuinely different legends.
16
+ * What they now share is being *promotable* — pass `opts.pin` and the row gains
17
+ * the pin that makes the current state this display type's session-wide
18
+ * default. Every display whose legend is backed by a config slot passes one,
19
+ * and gets it from `LegendMixin`'s `showLegendDisplayTypeDefault` rather than
20
+ * calling `makePin` itself: the slot is the per-display half, the accessors
21
+ * over it are not.
22
+ *
23
+ * `pin` is optional because two callers have no slot to promote: the Manhattan
24
+ * plot's LD legend and `LinearBasicDisplay`'s color key are a volatile and a
25
+ * per-legend `dismissed` flag respectively, neither of which is config at all.
26
+ * They get the plain row, which is what `checkboxItem` builds either way — the
27
+ * promotable form is that same row plus the pin, per `promotableToggleItem`.
28
+ *
29
+ * Deliberately not used by `synteny-core`'s "Show color legend", which sits
30
+ * inside a "Color by..." submenu where the bare word would not say which legend.
31
+ */
32
+ /** #menuBuilder showLegendCheckboxItem | the shared "Show legend" checkbox */
33
+ export declare function showLegendCheckboxItem(checked: boolean, onToggle: () => void, opts?: {
34
+ helpText?: string;
35
+ disabled?: boolean;
36
+ disabledHelpText?: string;
37
+ pin?: Pin;
38
+ }): MenuItem;
@@ -0,0 +1,44 @@
1
+ import { promotableToggleItem } from './promotableMenuItems.js';
2
+ import { checkboxItem } from './toggleMenuItems.js';
3
+ /**
4
+ * The "Show legend" checkbox, which seven displays build by hand — Hi-C, LD,
5
+ * alignments, LGVSynteny, multi-wiggle, multi-row features, both multi-sample
6
+ * variant displays and the Manhattan plot.
7
+ *
8
+ * Takes the value and the toggle rather than a `{ showLegend, setShowLegend }`
9
+ * model, because the Manhattan plot's pair is named for the LD legend it draws
10
+ * and would otherwise need an adapter object at the call site. Same argument
11
+ * order as `checkboxItem`, which is all this adds a label to.
12
+ *
13
+ * The `showLegend` **config slots** stay per display: their `promotedBase`
14
+ * values legitimately differ (a Hi-C color scale is off by default, a variant
15
+ * genotype key on), and their descriptions describe genuinely different legends.
16
+ * What they now share is being *promotable* — pass `opts.pin` and the row gains
17
+ * the pin that makes the current state this display type's session-wide
18
+ * default. Every display whose legend is backed by a config slot passes one,
19
+ * and gets it from `LegendMixin`'s `showLegendDisplayTypeDefault` rather than
20
+ * calling `makePin` itself: the slot is the per-display half, the accessors
21
+ * over it are not.
22
+ *
23
+ * `pin` is optional because two callers have no slot to promote: the Manhattan
24
+ * plot's LD legend and `LinearBasicDisplay`'s color key are a volatile and a
25
+ * per-legend `dismissed` flag respectively, neither of which is config at all.
26
+ * They get the plain row, which is what `checkboxItem` builds either way — the
27
+ * promotable form is that same row plus the pin, per `promotableToggleItem`.
28
+ *
29
+ * Deliberately not used by `synteny-core`'s "Show color legend", which sits
30
+ * inside a "Color by..." submenu where the bare word would not say which legend.
31
+ */
32
+ /** #menuBuilder showLegendCheckboxItem | the shared "Show legend" checkbox */
33
+ export function showLegendCheckboxItem(checked, onToggle, opts) {
34
+ const { pin, ...rest } = opts ?? {};
35
+ return pin
36
+ ? promotableToggleItem({
37
+ label: 'Show legend',
38
+ checked,
39
+ onToggle,
40
+ pin,
41
+ ...rest,
42
+ })
43
+ : checkboxItem('Show legend', checked, onToggle, rest);
44
+ }
@@ -0,0 +1,62 @@
1
+ import type { ReactNode } from 'react';
2
+ export type LegendMark = 'fill' | 'line' | 'curve';
3
+ export interface LegendSwatch {
4
+ color: string;
5
+ mark?: LegendMark;
6
+ }
7
+ export interface ColorLegendEntry {
8
+ key: string;
9
+ label: string;
10
+ color?: string;
11
+ swatches?: LegendSwatch[];
12
+ hidden?: boolean;
13
+ marker?: ReactNode;
14
+ }
15
+ export interface LegendItem {
16
+ color?: string;
17
+ mark?: LegendMark;
18
+ swatches?: LegendSwatch[];
19
+ label: string;
20
+ hidden?: boolean;
21
+ }
22
+ export declare function legendSwatches(item: LegendItem): LegendSwatch[];
23
+ export interface LegendSection {
24
+ id: string;
25
+ title?: string;
26
+ items: LegendItem[];
27
+ }
28
+ export interface LegendSpec {
29
+ title?: string;
30
+ items?: LegendItem[];
31
+ sections?: LegendSection[];
32
+ }
33
+ export declare function nonEmptyLegendSections({ items, sections }: LegendSpec): LegendSection[];
34
+ export declare function legendEntries(spec: LegendSpec): ColorLegendEntry[];
35
+ /**
36
+ * How many rows a color key may have and still be one. Past this it is a list
37
+ * of every row, which is the thing a key exists instead of.
38
+ */
39
+ export declare const MAX_LEGEND_ITEMS = 20;
40
+ /**
41
+ * Whether a key built from these items is worth the rows it costs, for a
42
+ * display that has to *decide* — one whose key is only sometimes the thing
43
+ * naming its colors, and which therefore asks before drawing.
44
+ *
45
+ * Two questions, and both have drawn a useless key on a real track:
46
+ *
47
+ * - **Short enough to read?** A list longer than a reader can scan is worse
48
+ * than whatever it was going to explain. Ask this of the collapsed items, not
49
+ * of the row count — a cohort track's key is one row per group, so 4,390
50
+ * cells in nine cell types is nine rows and passes, while the same cells
51
+ * ungrouped are 4,390 and do not.
52
+ * - **Does it distinguish anything?** A key maps colors to names, so it needs
53
+ * more than one color to map. Items that all share one — every swatch having
54
+ * resolved to the same fallback, which is what a track carrying no identity
55
+ * color produces — spend rows over the plot to say nothing. This is why
56
+ * `LegendItem.color` should be resolved before it gets here: an unresolved
57
+ * `undefined` compares equal to every other `undefined` only by accident.
58
+ *
59
+ * Displays whose key is unconditional (alignments, variants) don't need this;
60
+ * their vocabulary is always worth naming.
61
+ */
62
+ export declare function legendIsReadable(items: LegendItem[], maxItems?: number): boolean;
@@ -0,0 +1,78 @@
1
+ // The marks a row draws: its explicit list, else its single color/mark pair,
2
+ // else nothing at all (a heading).
3
+ export function legendSwatches(item) {
4
+ return (item.swatches ??
5
+ (item.color === undefined ? [] : [{ color: item.color, mark: item.mark }]));
6
+ }
7
+ // Drop sections with nothing in them, so a heading can never end up with no
8
+ // swatches under it.
9
+ export function nonEmptyLegendSections({ items, sections }) {
10
+ return (sections ?? (items ? [{ id: 'items', items }] : [])).filter(s => s.items.length > 0);
11
+ }
12
+ // Flatten a legend spec into `SvgColorLegend` rows: a color-less row reads as a
13
+ // heading rather than a swatch. Section titles appear only when more than one
14
+ // section survives — a lone vocabulary needs no title above it — which is the
15
+ // rule `FloatingLegend` applies on screen, so an export and the live legend
16
+ // agree about when headings show. A box-level `title` is unconditional, like its
17
+ // on-screen counterpart.
18
+ export function legendEntries(spec) {
19
+ const sections = nonEmptyLegendSections(spec);
20
+ const titled = sections.length > 1;
21
+ return [
22
+ ...(spec.title === undefined
23
+ ? []
24
+ : [{ key: 'legend-title', label: spec.title }]),
25
+ ...sections.flatMap(section => [
26
+ ...(titled && section.title !== undefined
27
+ ? [{ key: `${section.id}-title`, label: section.title }]
28
+ : []),
29
+ ...section.items.map((item, idx) => ({
30
+ key: `${section.id}-${idx}`,
31
+ label: item.label,
32
+ color: item.color,
33
+ swatches: exportSwatches(item),
34
+ hidden: item.hidden,
35
+ })),
36
+ ]),
37
+ ];
38
+ }
39
+ // A single filled swatch is what `color` alone already draws, so only a row
40
+ // that says something more — several marks, or one that isn't a fill — carries
41
+ // the list into the export. Keeps the common entry the three fields it has
42
+ // always been.
43
+ function exportSwatches(item) {
44
+ const swatches = legendSwatches(item);
45
+ return swatches.length > 1 || swatches.some(s => s.mark && s.mark !== 'fill')
46
+ ? swatches
47
+ : undefined;
48
+ }
49
+ /**
50
+ * How many rows a color key may have and still be one. Past this it is a list
51
+ * of every row, which is the thing a key exists instead of.
52
+ */
53
+ export const MAX_LEGEND_ITEMS = 20;
54
+ /**
55
+ * Whether a key built from these items is worth the rows it costs, for a
56
+ * display that has to *decide* — one whose key is only sometimes the thing
57
+ * naming its colors, and which therefore asks before drawing.
58
+ *
59
+ * Two questions, and both have drawn a useless key on a real track:
60
+ *
61
+ * - **Short enough to read?** A list longer than a reader can scan is worse
62
+ * than whatever it was going to explain. Ask this of the collapsed items, not
63
+ * of the row count — a cohort track's key is one row per group, so 4,390
64
+ * cells in nine cell types is nine rows and passes, while the same cells
65
+ * ungrouped are 4,390 and do not.
66
+ * - **Does it distinguish anything?** A key maps colors to names, so it needs
67
+ * more than one color to map. Items that all share one — every swatch having
68
+ * resolved to the same fallback, which is what a track carrying no identity
69
+ * color produces — spend rows over the plot to say nothing. This is why
70
+ * `LegendItem.color` should be resolved before it gets here: an unresolved
71
+ * `undefined` compares equal to every other `undefined` only by accident.
72
+ *
73
+ * Displays whose key is unconditional (alignments, variants) don't need this;
74
+ * their vocabulary is always worth naming.
75
+ */
76
+ export function legendIsReadable(items, maxItems = MAX_LEGEND_ITEMS) {
77
+ return items.length <= maxItems && new Set(items.map(i => i.color)).size > 1;
78
+ }
@@ -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 +1,30 @@
1
+ import type { ResolvableDisplay } from '../configuration/promotableResolve.ts';
2
+ import type { AnyConfigurationModel, ConfigurationSchemaForModel, ConfigurationSlotName } from '../configuration/types.ts';
3
+ import type { MenuItem } from './MenuTypes.ts';
4
+ import type { SliderScale } from './sliderScale.ts';
5
+ interface SizeMenuOptions {
6
+ label: string;
7
+ title: string;
8
+ help?: string;
9
+ getValue: () => number;
10
+ min?: number;
11
+ max?: number;
12
+ step?: number;
13
+ unit?: string;
14
+ scale?: SliderScale;
15
+ format?: (n: number) => string;
16
+ commitOnRelease?: boolean;
17
+ onChange: (n: number) => void;
18
+ onReset: () => void;
19
+ }
20
+ export declare function makeSizeMenu(opts: SizeMenuOptions & {
21
+ isDefault: boolean;
22
+ }): MenuItem;
23
+ export declare function makeSizeSubMenu(opts: SizeMenuOptions & {
24
+ isDefault: boolean;
25
+ }): MenuItem;
26
+ export declare function makePromotableSizeMenu<CONFMODEL extends AnyConfigurationModel, SLOT extends ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>>>(opts: SizeMenuOptions & {
27
+ display: ResolvableDisplay<CONFMODEL>;
28
+ slot: SLOT;
29
+ }): MenuItem;
30
+ export {};
@@ -0,0 +1,82 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { Suspense, lazy } from 'react';
3
+ import { isSlotCustomized, makePin, } from '../configuration/promotableDefaults.js';
4
+ import { INLINE_MENU_ROW_WIDTH } from './inlineMenuRowWidth.js';
5
+ // The row's drawn half is `lazy()` for the reason the promotable pin is a
6
+ // description rather than an element: this builder is called from state models
7
+ // and menu modules, which are eager, and the row is the only route by which MUI
8
+ // `Slider` — the largest single Material component in the eager graph — reached
9
+ // a host's first paint. `type: 'custom'` already made `render` a thunk, so the
10
+ // laziness is free at call time; it is the module edge that had to go.
11
+ //
12
+ // The fallback holds the row's footprint so the open menu doesn't reflow when
13
+ // the chunk lands. Height is the row's natural one (caption line + slider); it
14
+ // is approximate on purpose, since being a few px out for one frame is
15
+ // invisible where a collapse to zero is not.
16
+ const SizeSliderRow = lazy(() => import('./SizeSliderRow.js').then(m => ({ default: m.SizeSliderRow })));
17
+ const sizeRowFallbackHeight = 46;
18
+ // Shared inline "size" control as a single menu row (was a submenu of
19
+ // slider/reset/default). Callers own their config slot/semantics and wire the
20
+ // accessors + a title (which also derives the slider's test id). Used by wiggle
21
+ // point-size/line-width, GWAS Manhattan point-size, arc width, the alignments
22
+ // modification threshold and GC-content window/step sizes, so the
23
+ // slider/reset/pin behavior can't drift. Pass `scale: 'log'` for values spanning
24
+ // orders of magnitude, and `format` to label non-`px` units.
25
+ //
26
+ // For a row over a promotable slot use `makePromotableSizeMenu`.
27
+ export function makeSizeMenu(opts) {
28
+ return sizeMenu(opts, opts.isDefault);
29
+ }
30
+ // The same control one hop down: a plain submenu row whose only child is the
31
+ // size row above.
32
+ //
33
+ // For a menu where a slider drawn inline is the odd one out. Every other row
34
+ // there is `label + [?] + (checkbox | chevron)` and a size row is a two-line
35
+ // block with a widget of its own, so a menu holding several reads as a form to
36
+ // fill in rather than a list to pick from — and the comparative views' settings
37
+ // menus hold three each. Behind a chevron the row shape is uniform top to
38
+ // bottom, and the value moves inside next to the slider that sets it, which is
39
+ // where the radio submenus already keep their state.
40
+ //
41
+ // `help` lands on the submenu row, which is the row a reader sees: the size row
42
+ // behind the chevron never reaches the menu's shared trailing column, and a "?"
43
+ // of its own would only be a second one for the same setting, a hover away.
44
+ export function makeSizeSubMenu(opts) {
45
+ return {
46
+ label: opts.title,
47
+ helpText: opts.help,
48
+ subMenu: [makeSizeMenu(opts)],
49
+ };
50
+ }
51
+ // The same row over a **promotable** slot, which derives both halves the plain
52
+ // form takes by hand — the reset button's enablement (`isSlotCustomized`) and
53
+ // the "default for all tracks of this type" pin — from the one slot name. A
54
+ // slider has no fixed on-value, so the pin promotes whatever the track is
55
+ // currently showing.
56
+ //
57
+ // Naming the slot once is the point: the call sites used to spell it twice, in
58
+ // `isDefault` and again in the pin, with nothing checking the two agreed.
59
+ export function makePromotableSizeMenu(opts) {
60
+ const { display, slot } = opts;
61
+ return sizeMenu(opts, !isSlotCustomized(display, slot), makePin(display, slot));
62
+ }
63
+ function sizeMenu(opts, isDefault, pin) {
64
+ const { label, title, getValue, min = 0.5, max = 12, step = 0.5, unit = 'px', scale = 'linear', format = (n) => `${n}${unit}`, commitOnRelease, onChange, onReset, } = opts;
65
+ return {
66
+ label,
67
+ type: 'custom',
68
+ // Declared even though `SizeSliderRow` below is what draws it: a custom row
69
+ // never reaches the shared trailing column, so without this the pin exists
70
+ // on screen and is invisible to `pinnedSlots` — which is the difference
71
+ // between a promotable slot that is genuinely unreachable and one that just
72
+ // renders its own control. See `hasMenuItemAdornment` for why declaring it
73
+ // costs no layout.
74
+ ...(pin && {
75
+ pin: { control: pin, label: title },
76
+ }),
77
+ render: () => (_jsx(Suspense, { fallback: _jsx("div", { style: {
78
+ width: INLINE_MENU_ROW_WIDTH,
79
+ height: sizeRowFallbackHeight,
80
+ } }), children: _jsx(SizeSliderRow, { title: title, getValue: getValue, min: min, max: max, step: step, scale: scale, format: format, isDefault: isDefault, commitOnRelease: commitOnRelease, onChange: onChange, onReset: onReset, pin: pin }) })),
81
+ };
82
+ }
@@ -0,0 +1,8 @@
1
+ export interface StackFrame {
2
+ name: string;
3
+ uri: string;
4
+ line: number;
5
+ column: number;
6
+ }
7
+ export declare function parseStackLine(line: string): StackFrame | undefined;
8
+ export declare function mapStackTrace(stack: string): Promise<string>;
@@ -0,0 +1,108 @@
1
+ import { SourceMapConsumer } from 'source-map-js';
2
+ const sourceMappingUrlRe = /\/\/# sourceMappingURL=(.*)/g;
3
+ // blob: urls (worker scripts) embed a second scheme, so blob: has to be part of
4
+ // the match: without it the uri truncates to a script that doesn't exist
5
+ const protocolRe = /(?:blob:)?(?:https?|file):\/\//;
6
+ const digitsRe = /^\d+$/;
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/index.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 +1,33 @@
1
+ import type { MenuItem } from './MenuTypes.ts';
2
+ /**
3
+ * The trailing control a menu row draws, resolved at the point of drawing.
4
+ *
5
+ * Two fields feed it and they are not equivalent. `endAdornment` is an element
6
+ * the builder already made — the escape hatch, for content nothing else can
7
+ * describe. `pin` is a *description* of the "default for all tracks of
8
+ * this type" pin, and turning it into `PinAdornment` here is the whole
9
+ * point: the builders that set it (`promotableToggleItem`,
10
+ * `promotableRadioItem`) are called from state models and menu modules, which
11
+ * are eager, so a module that constructs the element instead puts MUI's
12
+ * `ToggleButton`, `Tooltip` and two icons into every host's first paint.
13
+ *
14
+ * Live in one place rather than at each of the four render sites, because the
15
+ * "does any row have one?" predicates and the rendering have to agree — a row
16
+ * that draws a pin the column-reservation pass didn't count is a misaligned
17
+ * menu, not a crash.
18
+ */
19
+ export declare function menuItemAdornment(item: MenuItem): string | number | bigint | true | import("react").JSX.Element | Iterable<import("react").ReactNode> | Promise<string | number | bigint | boolean | Iterable<import("react").ReactNode> | import("react").ReactElement<unknown, string | import("react").JSXElementConstructor<any>> | import("react").ReactPortal | null | undefined> | undefined;
20
+ /**
21
+ * Whether this row draws something in the shared trailing column — the question
22
+ * `getMenuColumnFlags` asks to decide whether to reserve that column on every
23
+ * row of the menu.
24
+ *
25
+ * **Not the same question as "does this row offer a pin"** (`pinnedSlots`, which
26
+ * counts a `pin` wherever it appears). A `type: 'custom'` row renders
27
+ * its own content edge to edge and never reaches `menuItemAdornment`, so it
28
+ * cannot draw in that column however it is declared — counting it would reserve
29
+ * a spacer on its siblings for a control that never appears. It still declares
30
+ * `pin` when it draws a pin of its own (`makePromotableSizeMenu`),
31
+ * which is what keeps the pin findable. Don't "fix" the two into agreement.
32
+ */
33
+ export declare function hasMenuItemAdornment(item: MenuItem): boolean;
@@ -0,0 +1,50 @@
1
+ import { jsx as _jsx } from "react/jsx-runtime";
2
+ import { PinAdornment } from './PinAdornment.js';
3
+ /**
4
+ * The trailing control a menu row draws, resolved at the point of drawing.
5
+ *
6
+ * Two fields feed it and they are not equivalent. `endAdornment` is an element
7
+ * the builder already made — the escape hatch, for content nothing else can
8
+ * describe. `pin` is a *description* of the "default for all tracks of
9
+ * this type" pin, and turning it into `PinAdornment` here is the whole
10
+ * point: the builders that set it (`promotableToggleItem`,
11
+ * `promotableRadioItem`) are called from state models and menu modules, which
12
+ * are eager, so a module that constructs the element instead puts MUI's
13
+ * `ToggleButton`, `Tooltip` and two icons into every host's first paint.
14
+ *
15
+ * Live in one place rather than at each of the four render sites, because the
16
+ * "does any row have one?" predicates and the rendering have to agree — a row
17
+ * that draws a pin the column-reservation pass didn't count is a misaligned
18
+ * menu, not a crash.
19
+ */
20
+ export function menuItemAdornment(item) {
21
+ if ('endAdornment' in item && item.endAdornment) {
22
+ return item.endAdornment;
23
+ }
24
+ // A disabled row is `pointer-events: none` (see `DisabledTooltip`, which
25
+ // exists because that also swallows a Tooltip's hover), so a pin drawn in one
26
+ // takes no click while looking exactly like a live one. Greying it is what
27
+ // the help "?" does on such a row by not rendering at all; the pin stays
28
+ // drawn so the trailing column keeps its alignment.
29
+ return 'pin' in item && item.pin ? (_jsx(PinAdornment, { pin: item.pin, disabled: item.disabled })) : undefined;
30
+ }
31
+ /**
32
+ * Whether this row draws something in the shared trailing column — the question
33
+ * `getMenuColumnFlags` asks to decide whether to reserve that column on every
34
+ * row of the menu.
35
+ *
36
+ * **Not the same question as "does this row offer a pin"** (`pinnedSlots`, which
37
+ * counts a `pin` wherever it appears). A `type: 'custom'` row renders
38
+ * its own content edge to edge and never reaches `menuItemAdornment`, so it
39
+ * cannot draw in that column however it is declared — counting it would reserve
40
+ * a spacer on its siblings for a control that never appears. It still declares
41
+ * `pin` when it draws a pin of its own (`makePromotableSizeMenu`),
42
+ * which is what keeps the pin findable. Don't "fix" the two into agreement.
43
+ */
44
+ export function hasMenuItemAdornment(item) {
45
+ if (item.type === 'custom') {
46
+ return false;
47
+ }
48
+ return (('endAdornment' in item && !!item.endAdornment) ||
49
+ ('pin' in item && !!item.pin));
50
+ }
@@ -0,0 +1,28 @@
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
+ * The other half of keeping that true is `MenuItemPin`: a row's pin is
18
+ * described here and built by the renderer, because an element in a descriptor
19
+ * pulls its whole component graph back in.
20
+ */
21
+ export { checkboxItem, radioItem, radioItems, toggleItem, withSubHeader, } from './toggleMenuItems.ts';
22
+ export { withHint } from './menuLabels.ts';
23
+ export { makeRadioSubMenu } from './radioSubMenu.ts';
24
+ export { showLegendCheckboxItem } from './legendMenuItem.ts';
25
+ export { promotableRadioItem, promotableRadioItems, promotableToggleItem, } from './promotableMenuItems.ts';
26
+ export type { RadioOption, SettingRowOptions } from './toggleMenuItems.ts';
27
+ export { staysOpenOnClick } from './MenuTypes.ts';
28
+ export type { BaseMenuItem, CheckboxMenuItem, ClickableMenuItem, CustomMenuItem, MenuDivider, MenuItem, MenuItemClickHandler, MenuItemPin, MenuItemsGetter, MenuSubHeader, NormalMenuItem, RadioMenuItem, SubMenuItem, } from './MenuTypes.ts';
@@ -0,0 +1,26 @@
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
+ * The other half of keeping that true is `MenuItemPin`: a row's pin is
18
+ * described here and built by the renderer, because an element in a descriptor
19
+ * pulls its whole component graph back in.
20
+ */
21
+ export { checkboxItem, radioItem, radioItems, toggleItem, withSubHeader, } from './toggleMenuItems.js';
22
+ export { withHint } from './menuLabels.js';
23
+ export { makeRadioSubMenu } from './radioSubMenu.js';
24
+ export { showLegendCheckboxItem } from './legendMenuItem.js';
25
+ export { promotableRadioItem, promotableRadioItems, promotableToggleItem, } from './promotableMenuItems.js';
26
+ export { staysOpenOnClick } from './MenuTypes.js';