@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
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  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
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  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
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  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
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
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  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
  1076. package/esm/util/temporaryAssembly.d.ts +21 -0
  1077. package/esm/util/temporaryAssembly.js +29 -0
  1078. package/esm/util/thresholdScale.d.ts +91 -0
  1079. package/esm/util/thresholdScale.js +166 -0
  1080. package/esm/util/tickLabels.d.ts +36 -0
  1081. package/esm/util/tickLabels.js +45 -0
  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  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
  1121. package/esm/util/unzip.d.ts +1 -0
  1122. package/esm/util/unzip.js +6 -0
  1123. package/esm/util/useEventCallback.d.ts +1 -0
  1124. package/esm/util/useEventCallback.js +16 -0
  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
  1126. package/esm/util/useFeatureSequence.js +55 -77
  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
  1130. package/esm/util/useFetchPlugins.js +18 -0
  1131. package/esm/util/useMeasure.d.ts +11 -1
  1132. package/esm/util/useMeasure.js +20 -6
  1133. package/esm/util/usePanZoom.d.ts +75 -0
  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
  1136. package/esm/util/usePanelVirtualScroll.js +15 -0
  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  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
  1144. package/esm/util/useRowVirtualScroll.js +22 -0
  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
  1149. package/esm/util/viewStatus.d.ts +90 -0
  1150. package/esm/util/viewStatus.js +54 -0
  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
  1160. package/esm/util/withFeatureDetails.js +59 -0
  1161. package/esm/util/withLaunchInput.d.ts +174 -0
  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  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
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
  1172. package/esm/ReExports/BaseFeatureDetails.js +0 -9
  1173. package/esm/ReExports/DataGrid.d.ts +0 -1
  1174. package/esm/ReExports/DataGrid.js +0 -1
  1175. package/esm/ReExports/index.d.ts +0 -1
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  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
  1181. package/esm/data_adapters/util.js +0 -6
  1182. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1183. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1184. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1185. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1186. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1187. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1188. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1189. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1190. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1191. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1192. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1193. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1195. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1196. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
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  1198. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1199. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1200. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1201. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1202. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1203. package/esm/rpc/baseRpcConfig.js +0 -10
  1204. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1205. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1206. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
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  1208. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
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  1218. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
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  1220. package/esm/ui/MenuButton.d.ts +0 -1
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  1222. package/esm/ui/MenuItems.d.ts +0 -15
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  1224. package/esm/ui/useEvent.d.ts +0 -1
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  1234. package/esm/util/layouts/MultiLayout.js +0 -40
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  1243. package/esm/util/map-obj/index.d.ts +0 -13
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  1245. package/esm/util/nextTick.d.ts +0 -1
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  1247. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
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  1249. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1250. package/esm/util/offscreenCanvasUtils.js +0 -19
  1251. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
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  1253. package/esm/util/stopToken.d.ts +0 -19
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  1255. package/esm/util/transferables.d.ts +0 -2
  1256. package/esm/util/transferables.js +0 -35
  1257. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1258. package/esm/util/tss-react/mui/index.js +0 -1
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  1260. package/esm/util/tss-react/mui/mui.js +0 -5
  1261. package/esm/util/when.d.ts +0 -1
  1262. package/esm/util/when.js +0 -1
  1263. /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,57 +1,89 @@
1
- const COORD_REGEX = /^(-?\d+)(?:(?:\.\.|[-–])(-?\d+))?(\.\.|[-–])?$/;
1
+ import { BP_QUANTITY_SOURCE, parseBpString } from './bpUtils.js';
2
+ import { toLocale } from './numericUtils.js';
3
+ import { shorten } from './stringUtils.js';
4
+ // Thrown when the input doesn't resolve to any known refName. Callers
5
+ // (e.g. the LGV locstring path) catch this to fall back to alternative
6
+ // interpretations like "refname start end" triplets — string-matching
7
+ // the error message would be brittle.
8
+ export class UnknownRefNameError extends Error {
9
+ name = 'UnknownRefNameError';
10
+ }
11
+ // matches coordinate strings: "100", "100-200", "100..200", "100.." (open-ended).
12
+ // Each coordinate may carry a metric unit suffix, so "34M-35M" and "1.5kb..2kb"
13
+ // parse too; the numbers are converted eagerly here and nothing downstream ever
14
+ // sees the shorthand. Assembled locStrings are always plain digits, so this is
15
+ // a spelling the parser accepts and the formatter never emits.
16
+ // groups: [1]=start [2]=end (if range) [3]=trailing separator (if open-ended)
17
+ const COORD_REGEX = new RegExp(String.raw `^(${BP_QUANTITY_SOURCE})(?:(?:\.\.|[-–])(${BP_QUANTITY_SOURCE}))?(\.\.|[-–])?$`, 'i');
18
+ // matches optional "{assemblyName}" prefix followed by the rest of the location
19
+ // groups: [1]=assemblyName (without braces) [2]=remainder
2
20
  const ASSEMBLY_REGEX = /^(?:\{([^}]+)\})?(.+)/;
3
21
  function parseCoords(suffix, locString) {
22
+ // strip commas before matching so regex only needs to handle plain digits
4
23
  const match = COORD_REGEX.exec(suffix.replaceAll(',', ''));
5
- if (!match) {
24
+ const [, startStr, endStr, trailing] = match ?? [];
25
+ const start = startStr === undefined ? undefined : parseBpString(startStr);
26
+ if (start === undefined) {
6
27
  throw new Error(`could not parse range "${suffix}" on location "${locString}"`);
7
28
  }
8
- const [, startStr, endStr, trailing] = match;
9
- const start = +startStr;
10
- return { start, end: endStr ? +endStr : trailing ? undefined : start };
29
+ return {
30
+ start,
31
+ end: endStr ? parseBpString(endStr) : trailing ? undefined : start,
32
+ };
11
33
  }
12
34
  export function parseLocStringOneBased(locString, isValidRefName) {
13
35
  if (!locString) {
14
36
  throw new Error('no location string provided, could not parse');
15
37
  }
38
+ // handle reverse strand notation e.g. "chr1:1-100[rev]"
16
39
  let reversed = false;
17
40
  if (locString.endsWith('[rev]')) {
18
41
  reversed = true;
19
42
  locString = locString.slice(0, -5);
20
43
  }
21
44
  locString = locString.replaceAll(/\s/g, '');
45
+ // extract optional assembly name in braces e.g. "{hg19}chr1:1-100"
22
46
  const assemblyMatch = ASSEMBLY_REGEX.exec(locString);
23
47
  if (!assemblyMatch) {
24
48
  throw new Error(`invalid location string: "${locString}"`);
25
49
  }
26
50
  const [, assemblyName, location] = assemblyMatch;
51
+ // reject empty braces e.g. "{}chr1:1-100"
27
52
  if (!assemblyName && location.startsWith('{}')) {
28
53
  throw new Error(`no assembly name was provided in location "${location}"`);
29
54
  }
55
+ // refNames can contain colons (see SAM spec), so find the last colon to split
30
56
  const lastColonIdx = location.lastIndexOf(':');
57
+ // no colon means just a refName with no coordinates e.g. "chr1"
31
58
  if (lastColonIdx === -1) {
32
59
  if (isValidRefName(location, assemblyName)) {
33
60
  return { assemblyName, refName: location, reversed };
34
61
  }
35
- throw new Error(`Unknown feature or sequence "${location}"`);
62
+ throw new UnknownRefNameError(`Unknown feature or sequence "${location}"`);
36
63
  }
64
+ // split into refName (prefix) and coordinate part (suffix) at the last colon
37
65
  const prefix = location.slice(0, lastColonIdx);
38
66
  const suffix = location.slice(lastColonIdx + 1);
39
67
  const prefixValid = isValidRefName(prefix, assemblyName);
40
68
  const locationValid = isValidRefName(location, assemblyName);
69
+ // both interpretations valid is ambiguous e.g. refName "chr1:1" and "chr1" both exist
41
70
  if (prefixValid && locationValid) {
42
71
  throw new Error(`ambiguous location string: "${locString}"`);
43
72
  }
73
+ // the colon is part of the refName, not a coordinate separator
44
74
  if (locationValid) {
45
75
  return { assemblyName, refName: location, reversed };
46
76
  }
77
+ // standard case: prefix is refName, suffix is coordinates
47
78
  if (prefixValid) {
79
+ // colon with no suffix means just refName e.g. "chr1:"
48
80
  if (!suffix) {
49
81
  return { assemblyName, refName: prefix, reversed };
50
82
  }
51
83
  const coords = parseCoords(suffix, locString);
52
84
  return { assemblyName, refName: prefix, reversed, ...coords };
53
85
  }
54
- throw new Error(`unknown reference sequence name in location "${locString}"`);
86
+ throw new UnknownRefNameError(`unknown reference sequence name in location "${locString}"`);
55
87
  }
56
88
  export function parseLocString(locString, isValidRefName) {
57
89
  const parsed = parseLocStringOneBased(locString, isValidRefName);
@@ -60,3 +92,142 @@ export function parseLocString(locString, isValidRefName) {
60
92
  }
61
93
  return parsed;
62
94
  }
95
+ /**
96
+ * Assemble a 1-based "locString" from an interbase genomic location
97
+ * @param region - Region
98
+ * @example
99
+ * ```ts
100
+ * assembleLocString({ refName: 'chr1', start: 0, end: 100 })
101
+ * // ↳ 'chr1:1..100'
102
+ * ```
103
+ * @example
104
+ * ```ts
105
+ * assembleLocString({ assemblyName: 'hg19', refName: 'chr1', start: 0, end: 100 })
106
+ * // ↳ '{hg19}chr1:1..100'
107
+ * ```
108
+ * @example
109
+ * ```ts
110
+ * assembleLocString({ refName: 'chr1' })
111
+ * // ↳ 'chr1'
112
+ * ```
113
+ * @example
114
+ * ```ts
115
+ * assembleLocString({ refName: 'chr1', start: 0 })
116
+ * // ↳ 'chr1:1..'
117
+ * ```
118
+ * @example
119
+ * ```ts
120
+ * assembleLocString({ refName: 'chr1', end: 100 })
121
+ * // ↳ 'chr1:1..100'
122
+ * ```
123
+ * @example
124
+ * ```ts
125
+ * assembleLocString({ refName: 'chr1', start: 0, end: 1 })
126
+ * // ↳ 'chr1:1'
127
+ * ```
128
+ */
129
+ export function assembleLocString(region) {
130
+ return assembleLocStringWith(region, toLocale);
131
+ }
132
+ /**
133
+ * Same as {@link assembleLocString}, but with the coordinates left unformatted:
134
+ * no thousand separators, and never affected by the `numberGrouping` display
135
+ * preference. Use this wherever the result is compared, keyed on, or parsed
136
+ * rather than read — block keys, dedup buckets, locStrings handed back to
137
+ * `parseLocString` — both because it is faster (block calculations assemble a
138
+ * great many of these) and because a display convention shifting under an
139
+ * identity string is a correctness bug, not a cosmetic one.
140
+ */
141
+ export function assembleLocStringRaw(region) {
142
+ return assembleLocStringWith(region);
143
+ }
144
+ /**
145
+ * One space-separated string for a set of regions — what the header of a
146
+ * multi-region view says it is showing, and what an export of those regions
147
+ * labels itself with.
148
+ *
149
+ * The assembly name appears only when the regions disagree about it: naming it
150
+ * on every one of a dozen same-assembly blocks is noise, and dropping it where
151
+ * they differ loses the only thing telling them apart.
152
+ */
153
+ export function assembleLocStrings(regions) {
154
+ const sameAssembly = regions.every(r => r.assemblyName === regions[0].assemblyName);
155
+ return regions
156
+ .map(r => assembleLocString({
157
+ ...r,
158
+ assemblyName: sameAssembly ? undefined : r.assemblyName,
159
+ }))
160
+ .join(' ');
161
+ }
162
+ function assembleLocStringWith(region, cb = (n) => n) {
163
+ const { assemblyName, refName, start, end, reversed } = region;
164
+ const assemblyNameString = assemblyName ? `{${assemblyName}}` : '';
165
+ let startString;
166
+ if (start !== undefined) {
167
+ startString = `:${cb(start + 1)}`;
168
+ }
169
+ else if (end !== undefined) {
170
+ startString = ':1';
171
+ }
172
+ else {
173
+ startString = '';
174
+ }
175
+ let endString;
176
+ if (end !== undefined) {
177
+ endString = start !== undefined && start + 1 === end ? '' : `..${cb(end)}`;
178
+ }
179
+ else {
180
+ endString = start !== undefined ? '..' : '';
181
+ }
182
+ let rev = '';
183
+ if (reversed) {
184
+ rev = '[rev]';
185
+ }
186
+ return `${assemblyNameString}${refName}${startString}${endString}${rev}`;
187
+ }
188
+ export function compareLocs(locA, locB) {
189
+ const assemblyComp = locA.assemblyName || locB.assemblyName
190
+ ? (locA.assemblyName || '').localeCompare(locB.assemblyName || '')
191
+ : 0;
192
+ if (assemblyComp) {
193
+ return assemblyComp;
194
+ }
195
+ const refComp = locA.refName || locB.refName
196
+ ? (locA.refName || '').localeCompare(locB.refName || '')
197
+ : 0;
198
+ if (refComp) {
199
+ return refComp;
200
+ }
201
+ if (locA.start !== undefined && locB.start !== undefined) {
202
+ const startComp = locA.start - locB.start;
203
+ if (startComp) {
204
+ return startComp;
205
+ }
206
+ }
207
+ if (locA.end !== undefined && locB.end !== undefined) {
208
+ const endComp = locA.end - locB.end;
209
+ if (endComp) {
210
+ return endComp;
211
+ }
212
+ }
213
+ return 0;
214
+ }
215
+ export function compareLocStrings(a, b, isValidRefName) {
216
+ const locA = parseLocString(a, isValidRefName);
217
+ const locB = parseLocString(b, isValidRefName);
218
+ return compareLocs(locA, locB);
219
+ }
220
+ /**
221
+ * A cursor/coordinate readout: `{assembly}chr1:1,234`, with the refName
222
+ * shortened and the coordinate locale-grouped. The *display* counterpart to
223
+ * {@link assembleLocString} — this one is for showing a single position to a
224
+ * user, never for a location string that will be parsed back.
225
+ */
226
+ export function stringify({ refName, coord, assemblyName, oob, }, useAssemblyName) {
227
+ return [
228
+ assemblyName && useAssemblyName ? `{${assemblyName}}` : '',
229
+ refName
230
+ ? `${shorten(refName)}:${toLocale(coord)}${oob ? ' (out of bounds)' : ''}`
231
+ : '',
232
+ ].join('');
233
+ }
@@ -0,0 +1,10 @@
1
+ import type { Region } from './types/data.ts';
2
+ export interface RefNameSource {
3
+ isValidRefName: (refName: string) => boolean;
4
+ getCanonicalRefName2: (refName: string) => string;
5
+ regions?: readonly {
6
+ refName: string;
7
+ end: number;
8
+ }[];
9
+ }
10
+ export declare function locStringsToRegions(locStrings: string, assembly: RefNameSource, assemblyName: string): Region[];
@@ -0,0 +1,35 @@
1
+ import { parseLocString } from './locString.js';
2
+ // Parses locstrings a user wrote -- into a dialog's region field, or into a
3
+ // display's `clusterRegion` in a session -- to the regions a fetch runs over.
4
+ // Throws on an unparsable ref name or an empty range, so a caller surfaces the
5
+ // typo rather than quietly running over something else. Whitespace separates
6
+ // regions, so a multi-region rubberband selection round-trips through a field,
7
+ // and a setting can name more than one locus.
8
+ //
9
+ // A bare refName means the whole contig, so its length is required, not a
10
+ // fallback: defaulting a missing length to 0 turned "this contig has no length
11
+ // on record" into "empty region", which reads as the user having typed a bad
12
+ // range.
13
+ export function locStringsToRegions(locStrings, assembly, assemblyName) {
14
+ return locStrings
15
+ .trim()
16
+ .split(/\s+/)
17
+ .map(locString => {
18
+ const parsed = parseLocString(locString, refName => assembly.isValidRefName(refName));
19
+ const refName = assembly.getCanonicalRefName2(parsed.refName);
20
+ // scans rather than calling the assembly's getRegionForRefName, because
21
+ // `RefNameSource` is a narrow duck type several fakes satisfy — growing it
22
+ // a method to save a scan over a list this reads once per typed locstring
23
+ // is the wrong trade
24
+ const refLength = assembly.regions?.find(r => r.refName === refName)?.end;
25
+ if (refLength === undefined) {
26
+ throw new Error(`no length on record for "${refName}"`);
27
+ }
28
+ const start = Math.max(parsed.start ?? 0, 0);
29
+ const end = Math.min(parsed.end ?? refLength, refLength);
30
+ if (end <= start) {
31
+ throw new Error(`empty region: "${locString}"`);
32
+ }
33
+ return { assemblyName, refName, start, end };
34
+ });
35
+ }
@@ -0,0 +1,36 @@
1
+ export declare const localStorageAvailable: () => boolean, localStorageGetItem: (key: string) => string | undefined, localStorageSetItem: (key: string, value: string) => boolean, localStorageRemoveItem: (key: string) => boolean;
2
+ /**
3
+ * Call `fn` whenever `key` changes — in another tab, or here via
4
+ * {@link notifyLocalStorageKey}. Returns the unsubscribe.
5
+ *
6
+ * `fn` takes no argument on purpose: it is told that the key changed, and reads
7
+ * the store itself. A payload would be a second copy of the value, and a
8
+ * `clear()` has none to hand over.
9
+ */
10
+ export declare function subscribeToLocalStorageKey(key: string, fn: () => void): () => void;
11
+ /** Announce a write made in this tab, which `storage` never reports back. */
12
+ export declare function notifyLocalStorageKey(key: string): void;
13
+ export declare function localStorageGetNumber(key: string, defaultVal: number): number;
14
+ export declare function localStorageGetJSON<T>(key: string, defaultVal: T): T;
15
+ /**
16
+ * The list of strings at `key` — absent, unreadable, malformed, or holding
17
+ * anything else all read as empty.
18
+ *
19
+ * The element filter is the part {@link localStorageGetJSON} cannot do: a
20
+ * stored array of the wrong element type parses fine and then behaves as a list
21
+ * of values that match nothing, which looks the same as an empty list except
22
+ * that it is never noticed. Three keys wanted exactly this and each spelled it
23
+ * out — hidden facet columns, trusted plugin URLs, and the desktop safe-mode
24
+ * marker, which additionally has to survive the bare `1` older builds wrote
25
+ * there.
26
+ */
27
+ export declare function localStorageGetStringArray(key: string): string[];
28
+ /**
29
+ * Writes `val` as JSON, except when it is null/undefined — those are skipped
30
+ * rather than stored, so a tri-state setting whose "unset" value means "follow
31
+ * the config" leaves whatever was there instead of pinning `null` over it.
32
+ */
33
+ export declare function localStorageSetJSON(key: string, val: unknown): void;
34
+ export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
35
+ export declare function localStorageSetBoolean(key: string, value: boolean): void;
36
+ export declare function localStorageSetNumber(key: string, value: number): void;
@@ -0,0 +1,137 @@
1
+ // localStorage: the guarded primitives from webStorage.ts (read that file for
2
+ // the three ways a Web Storage store fails and why every accessor here is
3
+ // total), plus the typed reads and the key subscription, which only this store
4
+ // has callers for.
5
+ import { guardedLocalStorage } from './webStorage.js';
6
+ export const { available: localStorageAvailable, getItem: localStorageGetItem, setItem: localStorageSetItem, removeItem: localStorageRemoveItem, } = guardedLocalStorage;
7
+ // Watchers of a key, and the one `storage` listener they share.
8
+ //
9
+ // Two different events reach them, which is why this is not simply a `storage`
10
+ // listener at each call site. Another TAB writing the key raises `storage` —
11
+ // but never in the tab that wrote it, so a write from THIS tab reaches nobody
12
+ // and has to be announced by hand. Missing that half is what let two components
13
+ // on one key show different values until one of them remounted.
14
+ //
15
+ // Announcing is deliberately not folded into localStorageSetItem. A writer
16
+ // that persists from an autorun over its own state would, if its write called
17
+ // its own subscriber back, re-enter that autorun and write again, forever. A
18
+ // writer says when its write is news.
19
+ const listeners = new Map();
20
+ // Installed on the first subscription rather than at module scope, so importing
21
+ // this file from a worker or a test never touches `window`.
22
+ let storageListenerInstalled = false;
23
+ function installStorageListener() {
24
+ if (storageListenerInstalled || typeof window === 'undefined') {
25
+ return;
26
+ }
27
+ storageListenerInstalled = true;
28
+ window.addEventListener('storage', e => {
29
+ // sessionStorage raises the same event on the same window, and jbrowse-web
30
+ // mirrors whole sessions into it
31
+ if (e.storageArea !== window.localStorage) {
32
+ return;
33
+ }
34
+ if (e.key === null) {
35
+ // a clear(): a factory reset, a test's teardown. Every key at once
36
+ for (const k of [...listeners.keys()]) {
37
+ notifyLocalStorageKey(k);
38
+ }
39
+ }
40
+ else if (listeners.has(e.key)) {
41
+ notifyLocalStorageKey(e.key);
42
+ }
43
+ });
44
+ }
45
+ /**
46
+ * Call `fn` whenever `key` changes — in another tab, or here via
47
+ * {@link notifyLocalStorageKey}. Returns the unsubscribe.
48
+ *
49
+ * `fn` takes no argument on purpose: it is told that the key changed, and reads
50
+ * the store itself. A payload would be a second copy of the value, and a
51
+ * `clear()` has none to hand over.
52
+ */
53
+ export function subscribeToLocalStorageKey(key, fn) {
54
+ installStorageListener();
55
+ let set = listeners.get(key);
56
+ if (!set) {
57
+ set = new Set();
58
+ listeners.set(key, set);
59
+ }
60
+ set.add(fn);
61
+ return () => {
62
+ set.delete(fn);
63
+ if (!set.size) {
64
+ listeners.delete(key);
65
+ }
66
+ };
67
+ }
68
+ /** Announce a write made in this tab, which `storage` never reports back. */
69
+ export function notifyLocalStorageKey(key) {
70
+ for (const fn of listeners.get(key) ?? []) {
71
+ fn();
72
+ }
73
+ }
74
+ export function localStorageGetNumber(key, defaultVal) {
75
+ const stored = localStorageGetItem(key);
76
+ // rejected before the coercion rather than after it: `+''` is 0, so an entry
77
+ // written as the empty string would otherwise read back as a real 0 instead
78
+ // of falling back. isFinite rather than !isNaN so 'Infinity' falls back too —
79
+ // every one of these is a pixel width or a base-pair count.
80
+ if (!stored) {
81
+ return defaultVal;
82
+ }
83
+ const parsed = +stored;
84
+ return Number.isFinite(parsed) ? parsed : defaultVal;
85
+ }
86
+ export function localStorageGetJSON(key, defaultVal) {
87
+ const stored = localStorageGetItem(key);
88
+ if (stored) {
89
+ try {
90
+ return JSON.parse(stored);
91
+ }
92
+ catch (e) {
93
+ console.warn(`Invalid localStorage value for ${key}:`, stored, e);
94
+ }
95
+ }
96
+ return defaultVal;
97
+ }
98
+ /**
99
+ * The list of strings at `key` — absent, unreadable, malformed, or holding
100
+ * anything else all read as empty.
101
+ *
102
+ * The element filter is the part {@link localStorageGetJSON} cannot do: a
103
+ * stored array of the wrong element type parses fine and then behaves as a list
104
+ * of values that match nothing, which looks the same as an empty list except
105
+ * that it is never noticed. Three keys wanted exactly this and each spelled it
106
+ * out — hidden facet columns, trusted plugin URLs, and the desktop safe-mode
107
+ * marker, which additionally has to survive the bare `1` older builds wrote
108
+ * there.
109
+ */
110
+ export function localStorageGetStringArray(key) {
111
+ const parsed = localStorageGetJSON(key, []);
112
+ return Array.isArray(parsed) ? parsed.filter(x => typeof x === 'string') : [];
113
+ }
114
+ /**
115
+ * Writes `val` as JSON, except when it is null/undefined — those are skipped
116
+ * rather than stored, so a tri-state setting whose "unset" value means "follow
117
+ * the config" leaves whatever was there instead of pinning `null` over it.
118
+ */
119
+ export function localStorageSetJSON(key, val) {
120
+ if (val !== undefined && val !== null) {
121
+ localStorageSetItem(key, JSON.stringify(val));
122
+ }
123
+ }
124
+ export function localStorageGetBoolean(key, defaultVal) {
125
+ const stored = localStorageGetJSON(key, defaultVal);
126
+ // falls back rather than coercing when the key holds something that is not a
127
+ // boolean (an older build's format, a hand-edited value). `Boolean(null)` is
128
+ // false, which would silently override a `true` default — which is what most
129
+ // of these are.
130
+ return typeof stored === 'boolean' ? stored : defaultVal;
131
+ }
132
+ export function localStorageSetBoolean(key, value) {
133
+ localStorageSetItem(key, JSON.stringify(value));
134
+ }
135
+ export function localStorageSetNumber(key, value) {
136
+ localStorageSetItem(key, JSON.stringify(value));
137
+ }
@@ -0,0 +1,54 @@
1
+ export interface MakeAssemblyOptions {
2
+ /** URL to a FASTA (`.fa`/`.fasta`, optionally bgzipped) or a `.2bit` file */
3
+ fastaUri: string;
4
+ /** defaults to the file's base name, e.g. `hg38.fa.gz` -> `hg38` */
5
+ name?: string;
6
+ faiUri?: string;
7
+ gziUri?: string;
8
+ aliases?: string[];
9
+ refNameAliasesUri?: string;
10
+ }
11
+ /** true when a string names a sequence file (vs. a hub name like `hg38`) */
12
+ export declare function isSequenceUri(uri: string): boolean;
13
+ /** strip path and sequence extension: `.../hg19.fa.gz` -> `hg19` */
14
+ export declare function assemblyNameFromUri(uri: string): string;
15
+ /**
16
+ * Build an assembly config for a sequence file (indexed FASTA, bgzipped FASTA,
17
+ * or `.2bit`) — the boilerplate you'd otherwise write by hand. In the common
18
+ * case it is the flat `{ name, uri }` shorthand: jbrowse-core's assembly config
19
+ * picks the concrete adapter type (`IndexedFastaAdapter`/`BgzipFastaAdapter`/
20
+ * `TwoBitAdapter`) from the extension, derives the `.fai`/`.gzi` siblings, and
21
+ * fills in the `ReferenceSequenceTrack` at load time, so no adapter-type
22
+ * knowledge lives here. A non-sibling index (`faiUri`/`gziUri`) widens `sequence`
23
+ * to its adapter form, the only shape with a slot for the override.
24
+ * `refNameAliasesUri` points at a tab-separated aliases file (as UCSC publishes)
25
+ * so a track whose reference names differ from the sequence (e.g. a BAM using
26
+ * `chr1` against a `1`-named reference) still lines up.
27
+ */
28
+ export declare function makeAssembly(opts: MakeAssemblyOptions): {
29
+ name: string;
30
+ aliases: string[];
31
+ sequence: {
32
+ type: string;
33
+ trackId: string;
34
+ adapter: {
35
+ uri: string;
36
+ faiLocation?: {
37
+ uri: string;
38
+ } | undefined;
39
+ gziLocation?: {
40
+ uri: string;
41
+ } | undefined;
42
+ };
43
+ };
44
+ refNameAliases?: {
45
+ uri: string;
46
+ } | undefined;
47
+ } | {
48
+ name: string;
49
+ aliases: string[];
50
+ uri: string;
51
+ refNameAliases?: {
52
+ uri: string;
53
+ } | undefined;
54
+ };
@@ -0,0 +1,52 @@
1
+ // sequence extensions core's own guesser recognizes (plugins/sequence)
2
+ const SEQUENCE_EXT_RE = /\.(fa|fasta|fas|fna|mfa|2bit)(\.b?gz)?$/i;
3
+ function cleanUri(uri) {
4
+ return uri.split(/[?#]/)[0] ?? uri;
5
+ }
6
+ /** true when a string names a sequence file (vs. a hub name like `hg38`) */
7
+ export function isSequenceUri(uri) {
8
+ return SEQUENCE_EXT_RE.test(cleanUri(uri));
9
+ }
10
+ /** strip path and sequence extension: `.../hg19.fa.gz` -> `hg19` */
11
+ export function assemblyNameFromUri(uri) {
12
+ const file = cleanUri(uri).split('/').at(-1) ?? uri;
13
+ return file.replace(SEQUENCE_EXT_RE, '');
14
+ }
15
+ /**
16
+ * Build an assembly config for a sequence file (indexed FASTA, bgzipped FASTA,
17
+ * or `.2bit`) — the boilerplate you'd otherwise write by hand. In the common
18
+ * case it is the flat `{ name, uri }` shorthand: jbrowse-core's assembly config
19
+ * picks the concrete adapter type (`IndexedFastaAdapter`/`BgzipFastaAdapter`/
20
+ * `TwoBitAdapter`) from the extension, derives the `.fai`/`.gzi` siblings, and
21
+ * fills in the `ReferenceSequenceTrack` at load time, so no adapter-type
22
+ * knowledge lives here. A non-sibling index (`faiUri`/`gziUri`) widens `sequence`
23
+ * to its adapter form, the only shape with a slot for the override.
24
+ * `refNameAliasesUri` points at a tab-separated aliases file (as UCSC publishes)
25
+ * so a track whose reference names differ from the sequence (e.g. a BAM using
26
+ * `chr1` against a `1`-named reference) still lines up.
27
+ */
28
+ export function makeAssembly(opts) {
29
+ const { fastaUri, name = assemblyNameFromUri(fastaUri), faiUri, gziUri, aliases = [], refNameAliasesUri, } = opts;
30
+ return {
31
+ name,
32
+ aliases,
33
+ // flat { name, uri } shorthand; a non-sibling index has no home there, so it
34
+ // widens to the sequence.adapter form (the bare uri still infers the type)
35
+ ...(faiUri || gziUri
36
+ ? {
37
+ sequence: {
38
+ type: 'ReferenceSequenceTrack',
39
+ trackId: `${name}-ReferenceSequenceTrack`,
40
+ adapter: {
41
+ uri: fastaUri,
42
+ ...(faiUri ? { faiLocation: { uri: faiUri } } : {}),
43
+ ...(gziUri ? { gziLocation: { uri: gziUri } } : {}),
44
+ },
45
+ },
46
+ }
47
+ : { uri: fastaUri }),
48
+ ...(refNameAliasesUri
49
+ ? { refNameAliases: { uri: refNameAliasesUri } }
50
+ : {}),
51
+ };
52
+ }
@@ -0,0 +1,14 @@
1
+ /**
2
+ * Build a track id from a track name, shared by the add-track workflows so the
3
+ * slug rule lives in one place. `timestamp` defaults to now but can be pinned so
4
+ * a batch of tracks shares it; `index` then disambiguates ids within that batch
5
+ * when several files share a name. Admin-vs-session is not encoded in the id —
6
+ * it follows from where the session stores the track (`sessionTracks` vs the
7
+ * base config), which is also what drives the selector's "Session tracks" group
8
+ * (see generateHierarchy).
9
+ */
10
+ export declare function makeTrackId({ name, timestamp, index, }: {
11
+ name: string;
12
+ timestamp?: number;
13
+ index?: number;
14
+ }): string;
@@ -0,0 +1,14 @@
1
+ /**
2
+ * Build a track id from a track name, shared by the add-track workflows so the
3
+ * slug rule lives in one place. `timestamp` defaults to now but can be pinned so
4
+ * a batch of tracks shares it; `index` then disambiguates ids within that batch
5
+ * when several files share a name. Admin-vs-session is not encoded in the id —
6
+ * it follows from where the session stores the track (`sessionTracks` vs the
7
+ * base config), which is also what drives the selector's "Session tracks" group
8
+ * (see generateHierarchy).
9
+ */
10
+ export function makeTrackId({ name, timestamp = Date.now(), index, }) {
11
+ const slug = name.trim().toLowerCase().replaceAll(' ', '_');
12
+ const suffix = index === undefined ? '' : `-${index}`;
13
+ return `${slug}-${timestamp}${suffix}`;
14
+ }