@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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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
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  1028. package/esm/util/sameStrings.d.ts +16 -0
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  1030. package/esm/util/samplesTsv.d.ts +49 -0
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  1034. package/esm/util/scrollLatch.d.ts +5 -0
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  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
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  1042. package/esm/util/sessionServices.d.ts +29 -0
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  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
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  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
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  1058. package/esm/util/starFusion.d.ts +26 -0
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  1064. package/esm/util/stringUtils.d.ts +5 -0
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  1066. package/esm/util/svAlt.d.ts +145 -0
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  1074. package/esm/util/tags.d.ts +2 -0
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  1078. package/esm/util/thresholdScale.d.ts +91 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
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  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
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  1086. package/esm/util/tracks.d.ts +431 -30
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  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
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  1127. package/esm/util/useFetch.d.ts +55 -0
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  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
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  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1147. package/esm/util/viewHighlights.d.ts +3 -0
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  1149. package/esm/util/viewStatus.d.ts +90 -0
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  1151. package/esm/util/virtualRange.d.ts +36 -0
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  1153. package/esm/util/webStorage.d.ts +26 -0
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  1155. package/esm/util/wheelZoom.d.ts +65 -0
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  1157. package/esm/util/whenViewSettled.d.ts +74 -0
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  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
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  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,103 +1,80 @@
1
- import { getSnapshot, isStateTreeNode } from '@jbrowse/mobx-state-tree';
2
- import { BlockSet, ContentBlock, ElidedBlock, InterRegionPaddingBlock, } from "./blockTypes.js";
3
- import { assembleLocStringFast } from "./index.js";
4
- export default function calculateStaticBlocks(model, padding = true, elision = true, extra = 0, width = 800) {
5
- const { offsetPx, displayedRegions, bpPerPx, minimumBlockWidth, interRegionPaddingWidth, width: modelWidth, } = model;
1
+ import { BlockSet } from './blockTypes.js';
2
+ const blockSizeCssPx = 800;
3
+ export default function calculateStaticBlocks(model, padding = true, elision = true) {
4
+ const { offsetPx, displayedRegions, bpPerPx, minimumBlockWidth, width: modelWidth, } = model;
6
5
  const windowLeftBp = offsetPx * bpPerPx;
7
6
  const windowRightBp = (offsetPx + modelWidth) * bpPerPx;
8
- const blockSizePx = width;
9
- const blockSizeBp = Math.ceil(blockSizePx * bpPerPx);
7
+ const blockSizeBp = Math.ceil(blockSizeCssPx * bpPerPx);
10
8
  const invBpPerPx = 1 / bpPerPx;
11
9
  const invBlockSizeBp = 1 / blockSizeBp;
12
10
  let regionBpOffset = 0;
13
11
  const blocks = new BlockSet();
14
- for (let regionNumber = 0; regionNumber < displayedRegions.length; regionNumber++) {
15
- const region = displayedRegions[regionNumber];
16
- const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = region;
17
- const regionBlockCount = Math.ceil((regionEnd - regionStart) * invBlockSizeBp);
18
- const parentRegion = isStateTreeNode(region) ? getSnapshot(region) : region;
19
- let windowRightBlockNum = Math.floor((windowRightBp - regionBpOffset) * invBlockSizeBp) + extra;
20
- if (windowRightBlockNum >= regionBlockCount) {
21
- windowRightBlockNum = regionBlockCount - 1;
22
- }
23
- let windowLeftBlockNum = Math.floor((windowLeftBp - regionBpOffset) * invBlockSizeBp) - extra;
24
- if (windowLeftBlockNum < 0) {
25
- windowLeftBlockNum = 0;
12
+ for (let displayedRegionIndex = 0; displayedRegionIndex < displayedRegions.length; displayedRegionIndex++) {
13
+ // Regions are laid out left to right, so once the cursor passes the window's
14
+ // right edge nothing further can contribute a block — and the trailing
15
+ // padding block needs the last region to be in view anyway. A whole-genome
16
+ // view holds one region per refName, so without this the loop (and its five
17
+ // MST observable reads per region) runs thousands of times per zoom frame to
18
+ // emit a handful of blocks.
19
+ if (regionBpOffset > windowRightBp) {
20
+ break;
26
21
  }
22
+ const { assemblyName, refName, start: regionStart, end: regionEnd, reversed, } = displayedRegions[displayedRegionIndex];
23
+ const regionBlockCount = Math.ceil((regionEnd - regionStart) * invBlockSizeBp);
24
+ const windowRightBlockNum = Math.min(Math.floor((windowRightBp - regionBpOffset) * invBlockSizeBp), regionBlockCount - 1);
25
+ const windowLeftBlockNum = Math.max(Math.floor((windowLeftBp - regionBpOffset) * invBlockSizeBp), 0);
27
26
  const regionWidthPx = (regionEnd - regionStart) * invBpPerPx;
28
- for (let blockNum = windowLeftBlockNum; blockNum <= windowRightBlockNum; blockNum += 1) {
27
+ for (let blockNum = windowLeftBlockNum; blockNum <= windowRightBlockNum; blockNum++) {
28
+ const isLeftEndOfDisplayedRegion = blockNum === 0;
29
+ const isRightEndOfDisplayedRegion = blockNum === regionBlockCount - 1;
29
30
  let start;
30
31
  let end;
31
- let isLeftEndOfDisplayedRegion;
32
- let isRightEndOfDisplayedRegion;
33
32
  if (reversed) {
34
33
  start = Math.max(regionStart, regionEnd - (blockNum + 1) * blockSizeBp);
35
34
  end = regionEnd - blockNum * blockSizeBp;
36
- isLeftEndOfDisplayedRegion = end === regionEnd;
37
- isRightEndOfDisplayedRegion = start === regionStart;
38
35
  }
39
36
  else {
40
37
  start = regionStart + blockNum * blockSizeBp;
41
38
  end = Math.min(regionEnd, regionStart + (blockNum + 1) * blockSizeBp);
42
- isLeftEndOfDisplayedRegion = start === regionStart;
43
- isRightEndOfDisplayedRegion = end === regionEnd;
44
39
  }
45
40
  const widthPx = (end - start) * invBpPerPx;
46
- const blockData = {
41
+ const blockOffsetPx = (regionBpOffset + blockNum * blockSizeBp) * invBpPerPx;
42
+ const key = `${assemblyName}:${refName}:${start}:${end}:${displayedRegionIndex}${reversed ? ':rev' : ''}`;
43
+ if (padding && displayedRegionIndex === 0 && blockNum === 0) {
44
+ blocks.push({
45
+ type: 'InterRegionPaddingBlock',
46
+ key: `${key}-beforeFirstRegion`,
47
+ widthPx: blockSizeCssPx,
48
+ offsetPx: blockOffsetPx - blockSizeCssPx,
49
+ variant: 'boundary',
50
+ });
51
+ }
52
+ const data = {
47
53
  assemblyName,
48
54
  refName,
49
55
  start,
50
56
  end,
51
57
  reversed,
52
- offsetPx: (regionBpOffset + blockNum * blockSizeBp) * invBpPerPx,
53
- parentRegion,
54
- regionNumber,
58
+ offsetPx: blockOffsetPx,
59
+ displayedRegionIndex,
55
60
  widthPx,
56
61
  isLeftEndOfDisplayedRegion,
57
62
  isRightEndOfDisplayedRegion,
58
- key: `${assembleLocStringFast({
59
- assemblyName,
60
- refName,
61
- start,
62
- end,
63
- reversed,
64
- })}-${regionNumber}${reversed ? '-reversed' : ''}`,
63
+ key,
65
64
  };
66
- if (padding && regionNumber === 0 && blockNum === 0) {
67
- blocks.push(new InterRegionPaddingBlock({
68
- key: `${blockData.key}-beforeFirstRegion`,
69
- widthPx: width,
70
- offsetPx: blockData.offsetPx - width,
65
+ blocks.push(elision && regionWidthPx < minimumBlockWidth
66
+ ? { ...data, type: 'ElidedBlock' }
67
+ : { ...data, type: 'ContentBlock' });
68
+ if (padding &&
69
+ displayedRegionIndex === displayedRegions.length - 1 &&
70
+ isRightEndOfDisplayedRegion) {
71
+ blocks.push({
72
+ type: 'InterRegionPaddingBlock',
73
+ key: `${key}-afterLastRegion`,
74
+ widthPx: blockSizeCssPx,
75
+ offsetPx: blockOffsetPx + widthPx,
71
76
  variant: 'boundary',
72
- }));
73
- }
74
- if (elision && regionWidthPx < minimumBlockWidth) {
75
- blocks.push(new ElidedBlock(blockData));
76
- }
77
- else {
78
- blocks.push(new ContentBlock(blockData));
79
- }
80
- if (padding) {
81
- if (regionWidthPx >= minimumBlockWidth &&
82
- blockData.isRightEndOfDisplayedRegion &&
83
- regionNumber < displayedRegions.length - 1) {
84
- regionBpOffset += interRegionPaddingWidth * bpPerPx;
85
- blocks.push(new InterRegionPaddingBlock({
86
- key: `${blockData.key}-rightpad`,
87
- widthPx: interRegionPaddingWidth,
88
- offsetPx: blockData.offsetPx + blockData.widthPx,
89
- }));
90
- }
91
- if (regionNumber === displayedRegions.length - 1 &&
92
- blockData.isRightEndOfDisplayedRegion) {
93
- regionBpOffset += interRegionPaddingWidth * bpPerPx;
94
- blocks.push(new InterRegionPaddingBlock({
95
- key: `${blockData.key}-afterLastRegion`,
96
- widthPx: width,
97
- offsetPx: blockData.offsetPx + blockData.widthPx,
98
- variant: 'boundary',
99
- }));
100
- }
77
+ });
101
78
  }
102
79
  }
103
80
  regionBpOffset += regionEnd - regionStart;
@@ -0,0 +1,56 @@
1
+ /** #api */
2
+ export declare const STRAND_FIELD = "strand";
3
+ /**
4
+ * #api
5
+ * The structural-variant class `svClassOf` names. A VCF record and a BEDPE
6
+ * row carry it, and the mark display's `mate` step writes it per allele.
7
+ */
8
+ export declare const SV_TYPE_FIELD = "svType";
9
+ /**
10
+ * #api
11
+ * The row a feature with nothing in a categorical field lands on, so a key
12
+ * says why a mark is grey rather than listing a blank value.
13
+ */
14
+ export declare const NO_VALUE_LABEL = "(no value)";
15
+ /**
16
+ * #api
17
+ * One categorical field as every channel reads it — a facet's sections, a
18
+ * color's range entries, a key's rows. `key` files a value, `compare`
19
+ * orders keys (the `domain` first, the rest by `compareGroupKeys`, `''`
20
+ * after them), `label` names a key in a legend, `sectionLabel` on a chip, and
21
+ * `color` paints it. A key's color depends only on the key and the
22
+ * declaration, so every region agrees on it.
23
+ */
24
+ export interface CategoricalField {
25
+ field: string;
26
+ /** The declared order, or the field's own where none is declared. */
27
+ domain: readonly string[];
28
+ /**
29
+ * Every key a value can file under is in `domain`, as a threshold scale's
30
+ * bins are, so a key lists all of them whether or not anything painted one.
31
+ */
32
+ closed?: boolean;
33
+ key: (value: unknown) => string;
34
+ compare: (a: string, b: string) => number;
35
+ label: (key: string) => string;
36
+ sectionLabel: (key: string) => string;
37
+ color: (key: string) => string;
38
+ }
39
+ /**
40
+ * #api
41
+ * What a key names each of `keys`, from a colour object's `labels`: one each in
42
+ * order, an empty or missing entry leaving that key its own name. Every key
43
+ * that takes `labels` reads them through this, so a config means one thing by
44
+ * them everywhere.
45
+ */
46
+ export declare function keyNames(keys: readonly unknown[], labels?: readonly string[]): ReadonlyMap<string, string>;
47
+ /**
48
+ * #api
49
+ * `labels` names the `domain`'s values in a key, one each in order, where a
50
+ * config spells them for a reader rather than as the data does.
51
+ */
52
+ export declare function categoricalField(field: string, { domain, range, labels, }?: {
53
+ domain?: readonly string[];
54
+ range?: readonly string[];
55
+ labels?: readonly string[];
56
+ }): CategoricalField;
@@ -0,0 +1,73 @@
1
+ import { categoricalColorScale } from '../ui/colors.js';
2
+ import { NO_CATEGORY_COLOR } from './color/index.js';
3
+ import { universalPresetOf } from './colorScale.js';
4
+ import { groupKeyComparator, valueText } from './groupKeys.js';
5
+ /** #api */
6
+ export const STRAND_FIELD = 'strand';
7
+ /**
8
+ * #api
9
+ * The structural-variant class `svClassOf` names. A VCF record and a BEDPE
10
+ * row carry it, and the mark display's `mate` step writes it per allele.
11
+ */
12
+ export const SV_TYPE_FIELD = 'svType';
13
+ /**
14
+ * #api
15
+ * The row a feature with nothing in a categorical field lands on, so a key
16
+ * says why a mark is grey rather than listing a blank value.
17
+ */
18
+ export const NO_VALUE_LABEL = '(no value)';
19
+ /**
20
+ * #api
21
+ * What a key names each of `keys`, from a colour object's `labels`: one each in
22
+ * order, an empty or missing entry leaving that key its own name. Every key
23
+ * that takes `labels` reads them through this, so a config means one thing by
24
+ * them everywhere.
25
+ */
26
+ export function keyNames(keys, labels = []) {
27
+ const names = new Map();
28
+ keys.forEach((key, i) => {
29
+ const name = labels[i];
30
+ const text = String(key);
31
+ if (name && !names.has(text)) {
32
+ names.set(text, name);
33
+ }
34
+ });
35
+ return names;
36
+ }
37
+ /**
38
+ * #api
39
+ * `labels` names the `domain`'s values in a key, one each in order, where a
40
+ * config spells them for a reader rather than as the data does.
41
+ */
42
+ export function categoricalField(field, { domain = [], range = [], labels = [], } = {}) {
43
+ // a field with a vocabulary of its own reads it on every channel, a facet's
44
+ // sections as well as a colour's key
45
+ const vocabulary = universalPresetOf(field);
46
+ const ownOrder = vocabulary?.domain ?? [];
47
+ const order = domain.length > 0 ? domain : ownOrder;
48
+ const [paired, colors] = range.length > 0 || !vocabulary
49
+ ? [order, range]
50
+ : [ownOrder, vocabulary.range ?? []];
51
+ const declared = keyNames(order, labels);
52
+ const own = vocabulary && keyNames(ownOrder, vocabulary.labels);
53
+ const named = (key) => declared.get(key) ?? own?.get(key);
54
+ let colorOf;
55
+ return {
56
+ field,
57
+ domain: order,
58
+ key: value => {
59
+ const key = valueText(value);
60
+ return key === '' ? (vocabulary?.missing ?? key) : key;
61
+ },
62
+ compare: groupKeyComparator(order),
63
+ label: key => named(key) ?? (key === '' ? NO_VALUE_LABEL : key),
64
+ sectionLabel: key => named(key) ?? `${field}: ${key === '' ? 'none' : key}`,
65
+ color: key => {
66
+ if (key === '') {
67
+ return NO_CATEGORY_COLOR;
68
+ }
69
+ colorOf ??= categoricalColorScale(paired, colors);
70
+ return colorOf(key);
71
+ },
72
+ };
73
+ }
@@ -0,0 +1,9 @@
1
+ /**
2
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
3
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
4
+ * the gridline pitches to use.
5
+ */
6
+ export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
7
+ majorPitch: number;
8
+ minorPitch: number;
9
+ };
@@ -0,0 +1,31 @@
1
+ /**
2
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
3
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
4
+ * the gridline pitches to use.
5
+ */
6
+ export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
7
+ scale = Math.abs(scale);
8
+ const minMajorPitchBp = minMajorPitchPx * scale;
9
+ const majorMagnitude = +minMajorPitchBp.toExponential().split(/e/i, 2)[1];
10
+ let majorPitch = 10 ** majorMagnitude;
11
+ while (majorPitch < minMajorPitchBp) {
12
+ majorPitch *= 2;
13
+ if (majorPitch >= minMajorPitchBp) {
14
+ break;
15
+ }
16
+ majorPitch *= 2.5;
17
+ }
18
+ majorPitch = Math.max(majorPitch, 5);
19
+ const majorPitchPx = majorPitch / scale;
20
+ let minorPitch = 0;
21
+ if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
22
+ minorPitch = majorPitch / 10;
23
+ }
24
+ else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
25
+ minorPitch = majorPitch / 5;
26
+ }
27
+ else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
28
+ minorPitch = majorPitch / 2;
29
+ }
30
+ return { majorPitch, minorPitch };
31
+ }
@@ -0,0 +1,43 @@
1
+ import type { Assembly } from '../assemblyManager/assembly.ts';
2
+ import type { Region } from './types/data.ts';
3
+ /**
4
+ * Clamp a span to the extents of the contig it names, resolving the refName to
5
+ * canonical on the way. Returns undefined when the clamp leaves nothing — the
6
+ * span lies wholly off the end of the contig.
7
+ *
8
+ * **The undefined is the point.** A one-sided clamp is the shape this keeps
9
+ * getting written as, and it inverts: a span past the contig end comes back with
10
+ * its end below its start, which every consumer that SUMS region lengths then
11
+ * subtracts. That is silent, and it happens for real, on a GFF3 or a BAM
12
+ * annotated against a longer assembly than the FASTA in use — which JBrowse
13
+ * otherwise just draws past the end of. Two callers wrote the one-sided version
14
+ * and only one of them ever guarded it.
15
+ *
16
+ * `start` is floored at 0 even when the contig extents are unknown (`regions`
17
+ * still loading, or a refName this assembly doesn't have), because interbase has
18
+ * no coordinate below 0 whatever the contig turns out to be. Only the high end
19
+ * needs a length to clamp against, so without one it is left alone — and with no
20
+ * high bound there is nothing to invert, so such a span always comes back.
21
+ */
22
+ export declare function clampToContig(assembly: Assembly, region: {
23
+ refName: string;
24
+ start: number;
25
+ end: number;
26
+ }): Region | undefined;
27
+ /**
28
+ * `clampToContig` for a refName that may not be on the assembly at all, which
29
+ * is the shape a location nobody requested arrives in — a BAM's `nextRef`, an
30
+ * SA record's contig (REFNAME_NAMESPACES.md). `clampToContig` alone passes an
31
+ * unknown name through with nothing to clamp against, so it cannot tell "past
32
+ * the end of a contig we have" from "a contig we do not have", and both callers
33
+ * need that apart to say which happened.
34
+ */
35
+ export declare function clampToListedContig(assembly: Assembly, region: {
36
+ refName: string;
37
+ start: number;
38
+ end: number;
39
+ }): {
40
+ refName: string;
41
+ onAssembly: boolean;
42
+ region: Region | undefined;
43
+ };
@@ -0,0 +1,47 @@
1
+ /**
2
+ * Clamp a span to the extents of the contig it names, resolving the refName to
3
+ * canonical on the way. Returns undefined when the clamp leaves nothing — the
4
+ * span lies wholly off the end of the contig.
5
+ *
6
+ * **The undefined is the point.** A one-sided clamp is the shape this keeps
7
+ * getting written as, and it inverts: a span past the contig end comes back with
8
+ * its end below its start, which every consumer that SUMS region lengths then
9
+ * subtracts. That is silent, and it happens for real, on a GFF3 or a BAM
10
+ * annotated against a longer assembly than the FASTA in use — which JBrowse
11
+ * otherwise just draws past the end of. Two callers wrote the one-sided version
12
+ * and only one of them ever guarded it.
13
+ *
14
+ * `start` is floored at 0 even when the contig extents are unknown (`regions`
15
+ * still loading, or a refName this assembly doesn't have), because interbase has
16
+ * no coordinate below 0 whatever the contig turns out to be. Only the high end
17
+ * needs a length to clamp against, so without one it is left alone — and with no
18
+ * high bound there is nothing to invert, so such a span always comes back.
19
+ */
20
+ export function clampToContig(assembly, region) {
21
+ const refName = assembly.getCanonicalRefName2(region.refName);
22
+ const bounds = assembly.getRegionForRefName(refName);
23
+ const start = Math.max(bounds?.start ?? 0, region.start);
24
+ const end = bounds ? Math.min(bounds.end, region.end) : region.end;
25
+ return end > start
26
+ ? { ...region, assemblyName: assembly.name, refName, start, end }
27
+ : undefined;
28
+ }
29
+ /**
30
+ * `clampToContig` for a refName that may not be on the assembly at all, which
31
+ * is the shape a location nobody requested arrives in — a BAM's `nextRef`, an
32
+ * SA record's contig (REFNAME_NAMESPACES.md). `clampToContig` alone passes an
33
+ * unknown name through with nothing to clamp against, so it cannot tell "past
34
+ * the end of a contig we have" from "a contig we do not have", and both callers
35
+ * need that apart to say which happened.
36
+ */
37
+ export function clampToListedContig(assembly, region) {
38
+ const refName = assembly.getCanonicalRefName2(region.refName);
39
+ const onAssembly = assembly.getRegionForRefName(refName) !== undefined;
40
+ return {
41
+ refName,
42
+ onAssembly,
43
+ region: onAssembly
44
+ ? clampToContig(assembly, { ...region, refName })
45
+ : undefined,
46
+ };
47
+ }
@@ -0,0 +1 @@
1
+ export declare function cmpStr(a: string, b: string): number;
@@ -0,0 +1,7 @@
1
+ // Deterministic, locale-independent string ordering. Returns 0 when equal so
2
+ // it chains with `||` in multi-key comparators. Prefer this over
3
+ // `localeCompare` wherever the order must be reproducible across environments
4
+ // (e.g. sort keys feeding deterministic worker output or screenshot renders).
5
+ export function cmpStr(a, b) {
6
+ return a < b ? -1 : a > b ? 1 : 0;
7
+ }
@@ -1,17 +1,4 @@
1
+ // not a sanitizer, this just removes html tags where only the text is shown
1
2
  export function coarseStripHTML(s) {
2
- let result = '';
3
- let inTag = false;
4
- for (let i = 0, l = s.length; i < l; i++) {
5
- const char = s[i];
6
- if (char === '<') {
7
- inTag = true;
8
- }
9
- else if (char === '>') {
10
- inTag = false;
11
- }
12
- else if (!inTag) {
13
- result += char;
14
- }
15
- }
16
- return result;
3
+ return s.replaceAll(/<[^<>]*>/g, '');
17
4
  }
@@ -1,2 +1,3 @@
1
1
  export declare function namedColorToHex(name: string): string | undefined;
2
2
  export declare function isNamedColor(name: string): boolean;
3
+ export declare const CSS_COLOR_NAMES: readonly string[];
@@ -1,3 +1,4 @@
1
+ // from https://www.w3.org/TR/css-color-4/#named-colors
1
2
  const colors = {
2
3
  aliceblue: '#F0F8FF',
3
4
  antiquewhite: '#FAEBD7',
@@ -148,9 +149,13 @@ const colors = {
148
149
  yellow: '#FFFF00',
149
150
  yellowgreen: '#9ACD32',
150
151
  };
152
+ // Object.hasOwn rather than a bare index: the table is a plain object, so
153
+ // `colors.constructor` and `colors.toString` come back as functions typed
154
+ // `string`, and isNamedColor('toString') was true.
151
155
  export function namedColorToHex(name) {
152
- return colors[name];
156
+ return Object.hasOwn(colors, name) ? colors[name] : undefined;
153
157
  }
154
158
  export function isNamedColor(name) {
155
- return !!colors[name];
159
+ return Object.hasOwn(colors, name);
156
160
  }
161
+ export const CSS_COLOR_NAMES = Object.keys(colors);
@@ -1,5 +1,86 @@
1
- export declare function contrastingTextColor(color: string): string;
1
+ /**
2
+ * Darken or lighten a color, depending on its luminance.
3
+ * Light colors are darkened, dark colors are lightened.
4
+ *
5
+ * @param color - CSS color, i.e. one of: #nnn, #nnnnnn, rgb(), rgba(),
6
+ * hsl(), hsla(), or named color
7
+ * @param coefficient - multiplier in the range 0 - 1, defaults to 0.15
8
+ * @returns A CSS color string. Hex input values are returned as rgb
9
+ */
2
10
  export declare function emphasize(color: string, coefficient?: number): string;
11
+ /**
12
+ * Push `foreground` away from `background` until it clears `minContrastRatio`,
13
+ * returning the closest it got when that ratio is unreachable.
14
+ *
15
+ * `minContrastRatio` genuinely cannot be met against a mid-luminance
16
+ * background: lighten/darken clamp their coefficient at 1, so the candidate
17
+ * pins at white/black, and against a `#b0b0b0` paper the best ratio any color
18
+ * reaches is about 2.2. This used to be a `while (ratio < min)` loop with an
19
+ * unbounded coefficient, which froze the render thread outright for 38 of the 40
20
+ * default refName colors.
21
+ */
3
22
  export declare function makeContrasting(foreground: string, background?: string, minContrastRatio?: number): string;
4
- export { isNamedColor, namedColorToHex } from './cssColorsLevel4.ts';
5
- export declare function randomColor(str: string): string;
23
+ export { CSS_COLOR_NAMES, isNamedColor, namedColorToHex, } from './cssColorsLevel4.ts';
24
+ export declare const NO_CATEGORY_COLOR = "#afafaf";
25
+ export declare const MISCONFIGURED_COLOR = "#808080";
26
+ /**
27
+ * #api
28
+ * Move a color's OKLCH lightness by `lightnessShift` and scale its chroma,
29
+ * holding its hue.
30
+ *
31
+ * For extending a categorical palette past its length. Cycling a nine-color
32
+ * list over a 24-chromosome karyotype repeats the color outright; cycling it
33
+ * with a lightness shift per lap gives the hue back as a variant still told
34
+ * apart from the original — tab20's construction, which pairs a light and a
35
+ * dark of each hue.
36
+ *
37
+ * SHIFT rather than a fixed lightness, and SCALE rather than a fixed chroma,
38
+ * because a categorical palette is uneven on purpose: category10's brown and
39
+ * its red are 5 degrees apart in hue and are told apart by chroma alone, so
40
+ * re-lighting both to one (lightness, chroma) makes them the same color.
41
+ * Keeping each color's own relative chroma keeps brown reading as brown.
42
+ *
43
+ * In OKLCH rather than through `lighten`/`darken`, which work in sRGB, where
44
+ * the same coefficient moves a yellow and a blue by visibly different amounts:
45
+ * a lap has to read as one tone across the whole palette or it reads as noise.
46
+ *
47
+ * @param color - CSS color to transform
48
+ * @param lightnessShift - added to its OKLCH lightness (which is 0 - 1)
49
+ * @param chromaScale - multiplies its OKLCH chroma; the result is reduced at
50
+ * constant hue if that lands out of gamut
51
+ * @returns A CSS hex color string
52
+ */
53
+ export declare function relight(color: string, lightnessShift: number, chromaScale?: number): string;
54
+ /**
55
+ * Generate a consistent random color for a given string.
56
+ * The same string will always generate the same color, with no shared palette
57
+ * state — so the same value (e.g. a gene symbol used as an ortholog id) gets the
58
+ * same color across independent tracks/panels.
59
+ *
60
+ * Statelessness is why this hashes into a color space rather than indexing a
61
+ * fixed palette of N: with no allocator there is no "next unused color", so an
62
+ * N-color palette collides by the birthday problem — six values into a
63
+ * twenty-color palette collide more often than not — while a hue circle does
64
+ * not repeat until 360 values. What a curated palette actually buys is
65
+ * perceptual evenness, and that comes from the space, not the list: hues are
66
+ * placed in OKLCH at a fixed lightness and chroma, so every value is equally
67
+ * light and equally colorful. HSL, which this used to use, is neither — its
68
+ * hue wheel spends a quarter of itself on greens that look identical and a
69
+ * sliver on yellow, and at one lightness its yellows glare while its blues go
70
+ * murky. That unevenness is what reads as "random RGB".
71
+ *
72
+ * A value that is absent gets NO_CATEGORY_COLOR rather than a hue, and that is
73
+ * the difference between this being usable on real data and not. The everyday
74
+ * caller is a `jexl:randomColor(get(feature,'<attr>'))` color slot over a
75
+ * whole track — and most files
76
+ * have the attribute on some features and not others, so most of the time this
77
+ * is handed `undefined`. It used to throw on that (`str.length` of undefined),
78
+ * once per feature, and what a reader saw was every unlabelled feature in one
79
+ * strong color: a large fake category, drawn over the real ones. Grey says the
80
+ * only true thing about a feature with no value for the attribute you asked to
81
+ * colour by.
82
+ *
83
+ * @param str - The string to generate a color from
84
+ * @returns A CSS hex color string
85
+ */
86
+ export declare function randomColor(str: string | undefined | null): string;