@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
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  1024. package/esm/util/rpc.d.ts +16 -1
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  1099. package/esm/util/tss-react/types.d.ts +1 -1
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  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
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@@ -0,0 +1,11 @@
1
+ // Shared clickable color-swatch button style, used by ColorPicker's preset grid
2
+ // and PopoverPicker's trigger swatch.
3
+ export const swatchStyle = {
4
+ width: 24,
5
+ height: 24,
6
+ margin: 4,
7
+ border: 'none',
8
+ padding: 0,
9
+ cursor: 'pointer',
10
+ outline: 'none',
11
+ };
@@ -1,10 +1,127 @@
1
1
  declare const category10: string[];
2
- declare const dark2: string[];
3
2
  declare const set1: string[];
4
- declare const set2: string[];
5
- declare const tableau10: string[];
6
- declare const ggplot2Colors6: string[];
7
- declare const ggplot2Colors5: string[];
8
- declare const ggplot2Colors4: string[];
9
- declare const ggplot2Colors3: string[];
10
- export { category10, dark2, ggplot2Colors3, ggplot2Colors4, ggplot2Colors5, ggplot2Colors6, set1, set2, tableau10, };
3
+ export declare const paletteColors: {
4
+ category10: string[];
5
+ dark2: string[];
6
+ ggplot2Colors3: string[];
7
+ ggplot2Colors4: string[];
8
+ ggplot2Colors5: string[];
9
+ ggplot2Colors6: string[];
10
+ set1: string[];
11
+ set2: string[];
12
+ tableau10: string[];
13
+ };
14
+ /**
15
+ * The wide qualitative palette: every scheme above, in order, deduped and with
16
+ * the neutrals dropped. ~40 entries.
17
+ *
18
+ * One list, because "give each row a distinct color" is one question this repo
19
+ * answers in two places — the multi-row painter handing colors out by row
20
+ * index, and the arrangement dialog's palette-by-attribute — and two lists
21
+ * would mean a track's automatic colors and the colors it takes when a user
22
+ * palettes it by hand were different palettes for no reason a reader could see.
23
+ *
24
+ * `tableau10` leads because its hues are the most evenly separated, so a track
25
+ * with a handful of rows spends only that. The tail is what makes the 26
26
+ * 1000-Genomes population codes, or a repeat painting's classes, all get a
27
+ * curated color instead of falling out to `randomColor`.
28
+ *
29
+ * Past the end is the caller's problem, and the two callers answer differently
30
+ * on purpose: an attribute palette-by hashes the VALUE (stable across
31
+ * re-palettes), while a by-position painter has no value to hash and wraps.
32
+ *
33
+ * **It holds 14 pairs `similarColors` calls the same** — five schemes' blues,
34
+ * oranges, greens, reds and pinks — and deduping it at construction is the
35
+ * wrong reading of that, measured on the 38 GENCODE gene biotypes. Hashed,
36
+ * which is what a track with no `colorDomain` does, 30 of them land on 22
37
+ * colors and 38 on 26; the loss is the birthday collision on 40 slots, not the
38
+ * near-twins, and only 3 of the pairs they land on read alike. Pruning to the
39
+ * 30 distinct entries makes that 23 and 24, so it costs ten colors and buys
40
+ * nothing.
41
+ *
42
+ * The near-twins bite the PINNED case instead, where a `domain` spends the
43
+ * list in order: 30 listed values take 30 colors today and 7 of those pairs
44
+ * read alike. Ordering the distinct 30 first and the twins behind them fixes
45
+ * that outright (0 pairs at 30 listed values, 11 at 38 where the twins are
46
+ * reached anyway) and costs no colors — but it moves every hashed color in
47
+ * marks, GWAS, canvas, multi-row and the arrangement dialog, so it is a pass
48
+ * with a figure refresh in it.
49
+ */
50
+ export declare const categoricalPalette: string[];
51
+ /**
52
+ * The palette color a categorical value paints, derived from the value rather
53
+ * than from the order it was met: values stream in as regions load, and a
54
+ * discovery-order slot would let one region paint `chr2` blue and the next
55
+ * paint it pink. A non-negative integer takes the slot it names, anchored at
56
+ * 1, so `1`, `2`, `3` walk the palette in order and stay distinct; anything
57
+ * else hashes in, stable for the same reason at the cost of an occasional
58
+ * collision. `categoricalScale` is the same rule with a domain.
59
+ */
60
+ export declare function categoricalValueColor(value: string): string;
61
+ export declare function categoricalValueColor<T>(value: string, palette: readonly T[]): T;
62
+ /**
63
+ * The categorical rule every scaled channel resolves through. With no
64
+ * `domain` a value takes `categoricalValueColor`'s slot in `range`. With one,
65
+ * the listed values take `range` in order, continuing into the `fallback`
66
+ * entries `range` lacks past its end, and any other value takes a slot of the
67
+ * whole list derived from itself that no listed value holds, nor one
68
+ * `isNear` calls the same. A value's entry depends only on the value and the
69
+ * declaration, so every region agrees on it, and adding a listed value moves
70
+ * only the unlisted values on the slots it takes.
71
+ */
72
+ export declare function categoricalScale<T>(domain: readonly (string | number)[] | undefined, range: readonly T[], { fallback, isNear, }?: {
73
+ fallback?: readonly T[];
74
+ isNear?: (a: T, b: T) => boolean;
75
+ }): (value: string) => T;
76
+ /**
77
+ * Whether two CSS colors read as one: under 0.05 apart in OKLab, where the
78
+ * wide palette's tableau and category10 oranges sit 0.003 apart.
79
+ */
80
+ export declare function similarColors(a: string, b: string): boolean;
81
+ /**
82
+ * `categoricalScale` for a color channel: `palette` (the wide palette when
83
+ * empty) spent in `domain` order and continued into the wide palette, and an
84
+ * unlisted value never on a listed value's color or one that reads the same.
85
+ */
86
+ export declare function categoricalColorScale(domain: readonly (string | number)[] | undefined, palette?: readonly string[]): (value: string) => string;
87
+ /**
88
+ * The color one value of a categorical color channel paints, by
89
+ * `categoricalColorScale`. A value-less feature is neutral grey, and an array
90
+ * value joins the way a group key does.
91
+ */
92
+ export declare function categoricalColor(value: unknown, domain?: readonly string[], palette?: readonly string[]): string;
93
+ /**
94
+ * Deterministic non-negative 32-bit hash of a string.
95
+ */
96
+ export declare function hashString(str: string): number;
97
+ /**
98
+ * Stable category10 color for a sequence name, via `hashString`.
99
+ *
100
+ * Kept as a published export; in-tree, prefer {@link refNameColor}, which hands
101
+ * the palette out by position where the caller knows the assembly's chromosome
102
+ * order and only hashes where it does not.
103
+ */
104
+ export declare function getQueryColor(queryName: string): string;
105
+ /** The palette color for a chromosome at `position` in its assembly. */
106
+ export declare function refNamePaletteColorAt(position: number): string;
107
+ /**
108
+ * The color a refName paints, BY POSITION IN THE ASSEMBLY where the caller
109
+ * knows its chromosome order.
110
+ *
111
+ * Handing the palette out rather than hashing into it is what stops a genome
112
+ * painting two of its own chromosomes the same color: nine slots means ten or
113
+ * more chromosomes re-use one, and by the birthday bound long before that. On
114
+ * hg38 the hash puts chr1, chr12, chr21 and chrY on one color.
115
+ *
116
+ * `position` is undefined for the case the order genuinely is not available —
117
+ * an assembly still loading, or a refName the assembly does not list (a
118
+ * scaffold under an alias). There a stable arbitrary color beats no color, so
119
+ * it falls back to the hash.
120
+ */
121
+ export declare function refNameColor(name: string, position: number | undefined): string;
122
+ /**
123
+ * A palette named in `namedPalettes`, or a comma-separated list of CSS
124
+ * colours; undefined, with a warning, for anything else.
125
+ */
126
+ export declare function paletteFromSpec(spec: unknown): readonly string[] | undefined;
127
+ export { category10, set1 };
package/esm/ui/colors.js CHANGED
@@ -1,3 +1,8 @@
1
+ import * as convert from '../util/color-bits/convert.js';
2
+ import { NO_CATEGORY_COLOR, relight } from '../util/color/index.js';
3
+ import { cssColorToNormalizedRgb } from '../util/colorBits.js';
4
+ import { isCssColor } from '../util/cssColorParse.js';
5
+ import { valueText } from '../util/groupKeys.js';
1
6
  const category10 = [
2
7
  '#1f77b4',
3
8
  '#ff7f0e',
@@ -64,4 +69,362 @@ const ggplot2Colors6 = [
64
69
  const ggplot2Colors5 = ['#F8766D', '#A3A500', '#00BF7D', '#00B0F6', '#E76BF3'];
65
70
  const ggplot2Colors4 = ['#F8766D', '#7CAE00', '#00BFC4', '#C77CFF'];
66
71
  const ggplot2Colors3 = ['#F8766D', '#00BA38', '#619CFF'];
67
- export { category10, dark2, ggplot2Colors3, ggplot2Colors4, ggplot2Colors5, ggplot2Colors6, set1, set2, tableau10, };
72
+ // A neutral has no place in a categorical palette that paints FILLS. Grey reads
73
+ // as "uncolored / no value" — it is what `randomColor` hands a value-less
74
+ // feature, what a synteny ribbon defaults to, what alignments paint a read with
75
+ // no tag — so a category landing on one says the opposite of what the palette
76
+ // is for. `refNameColorHexes` below drops category10's grey for this reason and
77
+ // has since it was written; this is the same rule applied to every scheme at
78
+ // once.
79
+ const NEUTRALS = new Set([
80
+ '#bab0ab',
81
+ '#999999',
82
+ '#666666',
83
+ '#b3b3b3',
84
+ '#7f7f7f',
85
+ ]);
86
+ export const paletteColors = {
87
+ category10,
88
+ dark2,
89
+ ggplot2Colors3,
90
+ ggplot2Colors4,
91
+ ggplot2Colors5,
92
+ ggplot2Colors6,
93
+ set1,
94
+ set2,
95
+ tableau10,
96
+ };
97
+ /**
98
+ * The wide qualitative palette: every scheme above, in order, deduped and with
99
+ * the neutrals dropped. ~40 entries.
100
+ *
101
+ * One list, because "give each row a distinct color" is one question this repo
102
+ * answers in two places — the multi-row painter handing colors out by row
103
+ * index, and the arrangement dialog's palette-by-attribute — and two lists
104
+ * would mean a track's automatic colors and the colors it takes when a user
105
+ * palettes it by hand were different palettes for no reason a reader could see.
106
+ *
107
+ * `tableau10` leads because its hues are the most evenly separated, so a track
108
+ * with a handful of rows spends only that. The tail is what makes the 26
109
+ * 1000-Genomes population codes, or a repeat painting's classes, all get a
110
+ * curated color instead of falling out to `randomColor`.
111
+ *
112
+ * Past the end is the caller's problem, and the two callers answer differently
113
+ * on purpose: an attribute palette-by hashes the VALUE (stable across
114
+ * re-palettes), while a by-position painter has no value to hash and wraps.
115
+ *
116
+ * **It holds 14 pairs `similarColors` calls the same** — five schemes' blues,
117
+ * oranges, greens, reds and pinks — and deduping it at construction is the
118
+ * wrong reading of that, measured on the 38 GENCODE gene biotypes. Hashed,
119
+ * which is what a track with no `colorDomain` does, 30 of them land on 22
120
+ * colors and 38 on 26; the loss is the birthday collision on 40 slots, not the
121
+ * near-twins, and only 3 of the pairs they land on read alike. Pruning to the
122
+ * 30 distinct entries makes that 23 and 24, so it costs ten colors and buys
123
+ * nothing.
124
+ *
125
+ * The near-twins bite the PINNED case instead, where a `domain` spends the
126
+ * list in order: 30 listed values take 30 colors today and 7 of those pairs
127
+ * read alike. Ordering the distinct 30 first and the twins behind them fixes
128
+ * that outright (0 pairs at 30 listed values, 11 at 38 where the twins are
129
+ * reached anyway) and costs no colors — but it moves every hashed color in
130
+ * marks, GWAS, canvas, multi-row and the arrangement dialog, so it is a pass
131
+ * with a figure refresh in it.
132
+ */
133
+ export const categoricalPalette = [
134
+ ...new Set([...tableau10, ...set1, ...dark2, ...set2, ...category10].filter(hex => !NEUTRALS.has(hex.toLowerCase()))),
135
+ ];
136
+ export function categoricalValueColor(value, palette = categoricalPalette) {
137
+ return palette[valueSlot(value, palette.length)];
138
+ }
139
+ function valueSlot(value, n) {
140
+ const num = Number(value);
141
+ return value !== '' && Number.isInteger(num) && num >= 0
142
+ ? (num + n - 1) % n
143
+ : hashString(value) % n;
144
+ }
145
+ function entryKey(entry) {
146
+ return typeof entry === 'string' ? entry.toLowerCase() : entry;
147
+ }
148
+ // The first slot derived from the value that `taken` does not hold, trying
149
+ // rehashes before walking, so the values landing on a taken slot spread over
150
+ // the free ones instead of piling onto the next.
151
+ function freeSlot(value, size, taken) {
152
+ let slot = valueSlot(value, size);
153
+ for (let salt = 1; taken.has(slot) && salt <= size; salt++) {
154
+ slot = hashString(`${salt}:${value}`) % size;
155
+ }
156
+ for (let step = 0; taken.has(slot) && step < size; step++) {
157
+ slot = (slot + 1) % size;
158
+ }
159
+ return slot;
160
+ }
161
+ /**
162
+ * The categorical rule every scaled channel resolves through. With no
163
+ * `domain` a value takes `categoricalValueColor`'s slot in `range`. With one,
164
+ * the listed values take `range` in order, continuing into the `fallback`
165
+ * entries `range` lacks past its end, and any other value takes a slot of the
166
+ * whole list derived from itself that no listed value holds, nor one
167
+ * `isNear` calls the same. A value's entry depends only on the value and the
168
+ * declaration, so every region agrees on it, and adding a listed value moves
169
+ * only the unlisted values on the slots it takes.
170
+ */
171
+ export function categoricalScale(domain, range, { fallback = [], isNear, } = {}) {
172
+ const base = range.length ? range : fallback;
173
+ const listed = [...new Set((domain ?? []).map(String))].filter(v => v !== '');
174
+ if (listed.length === 0) {
175
+ return value => base[valueSlot(value, base.length)];
176
+ }
177
+ const seen = new Set(base.map(entryKey));
178
+ const entries = [
179
+ ...base,
180
+ ...fallback.filter(entry => {
181
+ const key = entryKey(entry);
182
+ return seen.has(key) ? false : (seen.add(key), true);
183
+ }),
184
+ ];
185
+ const size = entries.length;
186
+ const rank = new Map(listed.map((value, i) => [value, i]));
187
+ const listedSlots = new Set(listed.map((_, i) => i % size));
188
+ const taken = new Set(entries.flatMap((entry, i) => listedSlots.has(i) ||
189
+ (isNear && [...listedSlots].some(j => isNear(entries[j], entry)))
190
+ ? [i]
191
+ : []));
192
+ return value => {
193
+ const i = rank.get(value);
194
+ return entries[i !== undefined
195
+ ? i % size
196
+ : taken.size < size
197
+ ? freeSlot(value, size, taken)
198
+ : valueSlot(value, size)];
199
+ };
200
+ }
201
+ const oklabByColor = new Map();
202
+ function oklabOf(color) {
203
+ let lab = oklabByColor.get(color);
204
+ if (lab === undefined) {
205
+ lab = convert.xyzd65ToOklab(...convert.xyzd50ToD65(...convert.srgbToXyzd50(...cssColorToNormalizedRgb(color))));
206
+ oklabByColor.set(color, lab);
207
+ }
208
+ return lab;
209
+ }
210
+ /**
211
+ * Whether two CSS colors read as one: under 0.05 apart in OKLab, where the
212
+ * wide palette's tableau and category10 oranges sit 0.003 apart.
213
+ */
214
+ export function similarColors(a, b) {
215
+ const [l1, a1, b1] = oklabOf(a);
216
+ const [l2, a2, b2] = oklabOf(b);
217
+ return Math.hypot(l1 - l2, a1 - a2, b1 - b2) < 0.05;
218
+ }
219
+ /**
220
+ * `categoricalScale` for a color channel: `palette` (the wide palette when
221
+ * empty) spent in `domain` order and continued into the wide palette, and an
222
+ * unlisted value never on a listed value's color or one that reads the same.
223
+ */
224
+ export function categoricalColorScale(domain, palette = []) {
225
+ return categoricalScale(domain, palette, {
226
+ fallback: categoricalPalette,
227
+ isNear: similarColors,
228
+ });
229
+ }
230
+ const MAX_CACHED_SCALES = 16;
231
+ const scaleCache = new Map();
232
+ function cachedColorScale(domain, palette) {
233
+ const key = `${domain.join('\u001F')}\u001E${palette.join('\u001F')}`;
234
+ let scale = scaleCache.get(key);
235
+ if (scale === undefined) {
236
+ if (scaleCache.size >= MAX_CACHED_SCALES) {
237
+ scaleCache.delete(scaleCache.keys().next().value);
238
+ }
239
+ scale = categoricalColorScale(domain, palette);
240
+ scaleCache.set(key, scale);
241
+ }
242
+ return scale;
243
+ }
244
+ /**
245
+ * The color one value of a categorical color channel paints, by
246
+ * `categoricalColorScale`. A value-less feature is neutral grey, and an array
247
+ * value joins the way a group key does.
248
+ */
249
+ export function categoricalColor(value, domain = [], palette = []) {
250
+ const label = valueText(value);
251
+ if (label === '') {
252
+ return NO_CATEGORY_COLOR;
253
+ }
254
+ return domain.length === 0 && palette.length === 0
255
+ ? categoricalValueColor(label)
256
+ : cachedColorScale(domain, palette)(label);
257
+ }
258
+ // only category10 and set1 are imported by name; the rest are reached through
259
+ // paletteColors above
260
+ /**
261
+ * Deterministic non-negative 32-bit hash of a string.
262
+ */
263
+ export function hashString(str) {
264
+ let hash = 0;
265
+ for (let i = 0; i < str.length; i++) {
266
+ const char = str.charCodeAt(i);
267
+ hash = (hash << 5) - hash + char;
268
+ hash |= 0;
269
+ }
270
+ return Math.abs(hash);
271
+ }
272
+ /**
273
+ * Stable category10 color for a sequence name, via `hashString`.
274
+ *
275
+ * Kept as a published export; in-tree, prefer {@link refNameColor}, which hands
276
+ * the palette out by position where the caller knows the assembly's chromosome
277
+ * order and only hashes where it does not.
278
+ */
279
+ export function getQueryColor(queryName) {
280
+ return category10[hashString(queryName) % category10.length];
281
+ }
282
+ // The by-refName painting palette: category10 with its grey dropped, since a
283
+ // grey chromosome reads as "uncolored/broken" (see NEUTRALS).
284
+ //
285
+ // category10 rather than the wide `categoricalPalette` — a karyotype wants nine
286
+ // hues it can re-light into tones a reader can compare, not forty unrelated
287
+ // ones, and `PALETTE_LAP_TONES` below is what that costs.
288
+ const refNameColorHexes = category10.filter(hex => !NEUTRALS.has(hex));
289
+ // Nine do not cover a karyotype, so each LAP around the list re-lights the same
290
+ // hues: chromosome 10 is a deep version of chromosome 1's blue, chromosome 19 a
291
+ // pale one. Three laps is 27 colors, past every karyotype these figures anchor
292
+ // on (human 24, rice 12, bread wheat 21), and a fourth lap starts the tones
293
+ // again rather than fading to nothing — a repeat 27 positions away is one no
294
+ // reader is comparing.
295
+ //
296
+ // THE COLORS ARE THE PALETTE'S, not a ramp's. This spent a round as the next hue
297
+ // on the golden angle at a fixed HSL 70%/50%, which is collision-free for any
298
+ // karyotype and was rejected on sight by figure review ("the previous palette is
299
+ // better"): an even hue circle at one saturation is a rainbow, and a five-genome
300
+ // synteny figure drawn in one is a hundred thousand ribbons of pure red, green,
301
+ // blue and magenta. category10's nine are uneven on purpose — that is what makes
302
+ // them read as a set.
303
+ //
304
+ // It is not the weaker option for distinguishability either, which is what the
305
+ // ramp was reached for. Closest pair in OKLab over 24 positions: 0.077 for these
306
+ // laps, 0.019 for the golden angle at HSL 70%/50% — an even hue circle is even
307
+ // in HSL's hue, and HSL's hue is not perceptually even.
308
+ const PALETTE_LAP_TONES = [
309
+ // lap 0 is the palette color itself, untouched
310
+ undefined,
311
+ // deep before pale, because these are drawn at a low alpha over white (the
312
+ // OrthoFinder figures run at 0.06) and a pale color at 0.06 is a color a
313
+ // reader cannot see. Chroma held, and the gamut takes what it must down here.
314
+ { lightnessShift: -0.17, chromaScale: 1 },
315
+ // pale. Chroma comes down with lightness: held at full, the light lap's reds
316
+ // and pinks all pin against the top of the sRGB gamut and converge there.
317
+ { lightnessShift: 0.18, chromaScale: 0.8 },
318
+ ];
319
+ /** The palette color for a chromosome at `position` in its assembly. */
320
+ export function refNamePaletteColorAt(position) {
321
+ const hex = refNameColorHexes[position % refNameColorHexes.length];
322
+ const lap = PALETTE_LAP_TONES[Math.floor(position / refNameColorHexes.length) % PALETTE_LAP_TONES.length];
323
+ return lap ? relight(hex, lap.lightnessShift, lap.chromaScale) : hex;
324
+ }
325
+ /**
326
+ * The color a refName paints, BY POSITION IN THE ASSEMBLY where the caller
327
+ * knows its chromosome order.
328
+ *
329
+ * Handing the palette out rather than hashing into it is what stops a genome
330
+ * painting two of its own chromosomes the same color: nine slots means ten or
331
+ * more chromosomes re-use one, and by the birthday bound long before that. On
332
+ * hg38 the hash puts chr1, chr12, chr21 and chrY on one color.
333
+ *
334
+ * `position` is undefined for the case the order genuinely is not available —
335
+ * an assembly still loading, or a refName the assembly does not list (a
336
+ * scaffold under an alias). There a stable arbitrary color beats no color, so
337
+ * it falls back to the hash.
338
+ */
339
+ export function refNameColor(name, position) {
340
+ return position === undefined
341
+ ? refNameColorHexes[hashString(name) % refNameColorHexes.length]
342
+ : refNamePaletteColorAt(position);
343
+ }
344
+ // The four below are as their sources publish them less the black or grey,
345
+ // which reads as "no value" on a fill (see NEUTRALS).
346
+ // Okabe & Ito, "Color Universal Design" (2008), jfly.uni-koeln.de/color
347
+ const okabeIto = [
348
+ '#e69f00',
349
+ '#56b4e9',
350
+ '#009e73',
351
+ '#f0e442',
352
+ '#0072b2',
353
+ '#d55e00',
354
+ '#cc79a7',
355
+ ];
356
+ // Paul Tol, "Colour Schemes", SRON/EPS/TN/09-002 (2021), the bright scheme
357
+ const tolBright = [
358
+ '#4477aa',
359
+ '#ee6677',
360
+ '#228833',
361
+ '#ccbb44',
362
+ '#66ccee',
363
+ '#aa3377',
364
+ ];
365
+ // Paul Tol, "Colour Schemes", SRON/EPS/TN/09-002 (2021), the muted scheme
366
+ const tolMuted = [
367
+ '#cc6677',
368
+ '#332288',
369
+ '#ddcc77',
370
+ '#117733',
371
+ '#88ccee',
372
+ '#882255',
373
+ '#44aa99',
374
+ '#999933',
375
+ '#aa4499',
376
+ ];
377
+ // Tableau 20, Tableau 10.0's paired palette (Maureen Stone, 2016)
378
+ const tableau20 = [
379
+ '#4e79a7',
380
+ '#a0cbe8',
381
+ '#f28e2b',
382
+ '#ffbe7d',
383
+ '#59a14f',
384
+ '#8cd17d',
385
+ '#b6992d',
386
+ '#f1ce63',
387
+ '#499894',
388
+ '#86bcb6',
389
+ '#e15759',
390
+ '#ff9d9a',
391
+ '#d37295',
392
+ '#fabfd2',
393
+ '#b07aa1',
394
+ '#d4a6c8',
395
+ '#9d7660',
396
+ '#d7b5a6',
397
+ ];
398
+ /** The palettes a capture run can deal the rows from by name (`paletteFromSpec`). */
399
+ const namedPalettes = {
400
+ set1: () => set1,
401
+ categoricalPalette: () => categoricalPalette,
402
+ tableau10: () => tableau10,
403
+ // ColorBrewer Set2, which d3-scale-chromatic publishes as schemeSet2
404
+ schemeSet2: () => set2,
405
+ okabeIto: () => okabeIto,
406
+ tolBright: () => tolBright,
407
+ tolMuted: () => tolMuted,
408
+ tableau20: () => tableau20,
409
+ // every lap `refNamePaletteColorAt` re-lights category10 through
410
+ relit: () => Array.from({ length: refNameColorHexes.length * PALETTE_LAP_TONES.length }, (_, i) => refNamePaletteColorAt(i)),
411
+ };
412
+ /**
413
+ * A palette named in `namedPalettes`, or a comma-separated list of CSS
414
+ * colours; undefined, with a warning, for anything else.
415
+ */
416
+ export function paletteFromSpec(spec) {
417
+ if (typeof spec !== 'string' || spec === '') {
418
+ return undefined;
419
+ }
420
+ if (Object.hasOwn(namedPalettes, spec)) {
421
+ return namedPalettes[spec]();
422
+ }
423
+ const colors = spec.split(/,(?![^(]*\))/).map(c => c.trim());
424
+ if (colors.every(isCssColor)) {
425
+ return colors;
426
+ }
427
+ console.warn(`palette "${spec}" is neither one of ${Object.keys(namedPalettes).join(', ')} nor a comma-separated list of CSS colours`);
428
+ return undefined;
429
+ }
430
+ export { category10, set1 };
@@ -0,0 +1,38 @@
1
+ /**
2
+ * Which tracks a contribution is for. Every track-scoped extension point fires
3
+ * for every track, so a contribution with no selector applies to all of them.
4
+ * {@link matchesTrackSelector} is what applies one.
5
+ */
6
+ export interface TrackSelector {
7
+ /** track type, e.g. `'VariantTrack'`, usually what "for my tracks" means */
8
+ trackType?: string | string[];
9
+ /** track id; a plain string also matches the user's copies of that track */
10
+ trackId?: string | RegExp | (string | RegExp)[];
11
+ /** widget model type, e.g. `'AlignmentsFeatureWidget'`, for the slot points */
12
+ widgetType?: string | string[];
13
+ }
14
+ /** the model fields a declarative selector can match on */
15
+ export interface SelectableModel {
16
+ type?: string;
17
+ trackId?: string;
18
+ trackType?: string;
19
+ }
20
+ /**
21
+ * What a track-scoped extension point contribution is for: whether the widget
22
+ * model or track config in `subject` satisfies every field of `select`. Every
23
+ * field given must match, and an empty selector matches everything.
24
+ *
25
+ * Every one of those points fires for every track, so a contribution that does
26
+ * not call this applies to all of them. Hand-writing `config.trackId === 'x'`
27
+ * instead is what silently stops applying the first time a user copies the
28
+ * track: `copyTrackSnapshot` suffixes the id, and this knows that.
29
+ *
30
+ * Not to be confused with {@link matchTrackId}, which tests an id against
31
+ * patterns you supply and so leaves that normalization to you.
32
+ */
33
+ export declare function matchesTrackSelector(select: TrackSelector | undefined, subject: {
34
+ /** a widget model, if the point's props carry one */
35
+ model?: SelectableModel;
36
+ /** a track config, if they carry that instead — `type` is the track type */
37
+ config?: Record<string, unknown>;
38
+ }): boolean;
@@ -0,0 +1,49 @@
1
+ import { matchTrackId } from '../util/matchTrackId.js';
2
+ // "Copy track" appends `-${Date.now()}` to the trackId (copyTrackSnapshot), and
3
+ // copying a copy appends again, so a bare id in a selector means "this track,
4
+ // including the user's copies of it". Doing this in the framework is the point:
5
+ // scoping by `trackId ===` is what people write by hand, and it silently stops
6
+ // applying the moment a user copies the track.
7
+ function matchesTrackId(trackId, pattern) {
8
+ return typeof pattern === 'string'
9
+ ? trackId === pattern ||
10
+ (trackId?.startsWith(`${pattern}-`) === true &&
11
+ trackId
12
+ .slice(pattern.length + 1)
13
+ .split('-')
14
+ .every(part => /^\d+$/.test(part)))
15
+ : matchTrackId(trackId, [pattern]);
16
+ }
17
+ function matchesOneOf(value, expected) {
18
+ return typeof expected === 'string'
19
+ ? value === expected
20
+ : expected.includes(value ?? '');
21
+ }
22
+ /** Whether `model` satisfies every declarative field of `select`. */
23
+ function selectorMatchesModel(select, model) {
24
+ const { widgetType, trackType, trackId } = select ?? {};
25
+ return ((widgetType === undefined || matchesOneOf(model.type, widgetType)) &&
26
+ (trackType === undefined || matchesOneOf(model.trackType, trackType)) &&
27
+ (trackId === undefined ||
28
+ (Array.isArray(trackId) ? trackId : [trackId]).some(pattern => matchesTrackId(model.trackId, pattern))));
29
+ }
30
+ /**
31
+ * What a track-scoped extension point contribution is for: whether the widget
32
+ * model or track config in `subject` satisfies every field of `select`. Every
33
+ * field given must match, and an empty selector matches everything.
34
+ *
35
+ * Every one of those points fires for every track, so a contribution that does
36
+ * not call this applies to all of them. Hand-writing `config.trackId === 'x'`
37
+ * instead is what silently stops applying the first time a user copies the
38
+ * track: `copyTrackSnapshot` suffixes the id, and this knows that.
39
+ *
40
+ * Not to be confused with {@link matchTrackId}, which tests an id against
41
+ * patterns you supply and so leaves that normalization to you.
42
+ */
43
+ export function matchesTrackSelector(select, subject) {
44
+ const { model, config } = subject;
45
+ return selectorMatchesModel(select, model ?? {
46
+ trackId: config?.trackId,
47
+ trackType: config?.type,
48
+ });
49
+ }