@jbrowse/core 4.3.0 → 5.0.0-beta.2

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 (1140) hide show
  1. package/README.md +822 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +62 -93
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  311. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  312. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  313. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  314. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  315. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  316. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
  317. package/esm/pluggableElementTypes/models/uriMatchesDomains.js +62 -0
  318. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts +5 -4
  319. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +20 -10
  320. package/esm/pluginDefinitions.d.ts +198 -0
  321. package/esm/pluginDefinitions.js +220 -0
  322. package/esm/rpc/BaseRpcDriver.d.ts +27 -35
  323. package/esm/rpc/BaseRpcDriver.js +74 -107
  324. package/esm/rpc/MainThreadRpcDriver.d.ts +9 -10
  325. package/esm/rpc/MainThreadRpcDriver.js +18 -29
  326. package/esm/rpc/RpcClient.d.ts +38 -0
  327. package/esm/rpc/RpcClient.js +154 -0
  328. package/esm/rpc/RpcManager.d.ts +116 -27
  329. package/esm/rpc/RpcManager.js +177 -50
  330. package/esm/rpc/RpcRegistry.d.ts +275 -0
  331. package/esm/rpc/RpcRegistry.js +1 -0
  332. package/esm/rpc/RpcServer.d.ts +41 -0
  333. package/esm/rpc/RpcServer.js +235 -0
  334. package/esm/rpc/WebWorkerRpcDriver.d.ts +71 -24
  335. package/esm/rpc/WebWorkerRpcDriver.js +312 -27
  336. package/esm/rpc/byteBudget.d.ts +58 -0
  337. package/esm/rpc/byteBudget.js +50 -0
  338. package/esm/rpc/configSchema.d.ts +27 -5
  339. package/esm/rpc/configSchema.js +40 -16
  340. package/esm/rpc/coreRpcMethods.d.ts +3 -5
  341. package/esm/rpc/coreRpcMethods.js +10 -12
  342. package/esm/rpc/explainTransferError.d.ts +35 -0
  343. package/esm/rpc/explainTransferError.js +158 -0
  344. package/esm/rpc/methods/CoreFreeResources.d.ts +19 -4
  345. package/esm/rpc/methods/CoreFreeResources.js +17 -6
  346. package/esm/rpc/methods/CoreGetExportData.d.ts +5 -18
  347. package/esm/rpc/methods/CoreGetExportData.js +26 -15
  348. package/esm/rpc/methods/CoreGetFeatureDensity.d.ts +11 -0
  349. package/esm/rpc/methods/CoreGetFeatureDensity.js +22 -0
  350. package/esm/rpc/methods/CoreGetFeatures.d.ts +6 -15
  351. package/esm/rpc/methods/CoreGetFeatures.js +15 -17
  352. package/esm/rpc/methods/CoreGetInfo.d.ts +6 -0
  353. package/esm/rpc/methods/CoreGetInfo.js +12 -0
  354. package/esm/rpc/methods/CoreGetMetadata.d.ts +4 -7
  355. package/esm/rpc/methods/CoreGetMetadata.js +6 -9
  356. package/esm/rpc/methods/CoreGetRefNames.d.ts +4 -8
  357. package/esm/rpc/methods/CoreGetRefNames.js +24 -13
  358. package/esm/rpc/methods/CoreGetRegionByteEstimate.d.ts +6 -0
  359. package/esm/rpc/methods/CoreGetRegionByteEstimate.js +19 -0
  360. package/esm/rpc/methods/CoreGetRegions.d.ts +4 -6
  361. package/esm/rpc/methods/CoreGetRegions.js +6 -9
  362. package/esm/rpc/methods/CoreGetSequence.d.ts +4 -11
  363. package/esm/rpc/methods/CoreGetSequence.js +12 -13
  364. package/esm/rpc/serializeError/index.d.ts +9 -0
  365. package/esm/rpc/serializeError/index.js +86 -0
  366. package/esm/svg/SvgExport.d.ts +30 -0
  367. package/esm/svg/SvgExport.js +53 -0
  368. package/esm/svg/constants.d.ts +1 -0
  369. package/esm/svg/constants.js +5 -0
  370. package/esm/svg/saveSvgAsImage.d.ts +6 -0
  371. package/esm/svg/saveSvgAsImage.js +90 -0
  372. package/esm/svg/svgId.d.ts +42 -0
  373. package/esm/svg/svgId.js +84 -0
  374. package/esm/svg/svgReady.d.ts +137 -0
  375. package/esm/svg/svgReady.js +164 -0
  376. package/esm/svg/trackNames.d.ts +27 -0
  377. package/esm/svg/trackNames.js +31 -0
  378. package/esm/svg/wrapSvgExport.d.ts +12 -0
  379. package/esm/svg/wrapSvgExport.js +78 -0
  380. package/esm/ui/ActionLink.d.ts +7 -0
  381. package/esm/ui/ActionLink.js +9 -0
  382. package/esm/ui/AddCustomPluginDialog.d.ts +14 -0
  383. package/esm/ui/AddCustomPluginDialog.js +61 -0
  384. package/esm/ui/AddGenomePane.d.ts +8 -0
  385. package/esm/ui/AddGenomePane.js +228 -0
  386. package/esm/ui/AdvancedOptions.d.ts +6 -0
  387. package/esm/ui/AdvancedOptions.js +17 -0
  388. package/esm/ui/AppLogo.d.ts +1 -1
  389. package/esm/ui/AppLogo.js +2 -2
  390. package/esm/ui/AssemblySelector.d.ts +5 -8
  391. package/esm/ui/AssemblySelector.js +8 -26
  392. package/esm/ui/BaseExportSvgDialog.d.ts +16 -0
  393. package/esm/ui/BaseExportSvgDialog.js +84 -0
  394. package/esm/ui/BaseTooltip.d.ts +14 -3
  395. package/esm/ui/BaseTooltip.js +151 -34
  396. package/esm/ui/CascadingMenu.d.ts +9 -18
  397. package/esm/ui/CascadingMenu.js +390 -41
  398. package/esm/ui/CascadingMenuButton.d.ts +9 -11
  399. package/esm/ui/CascadingMenuButton.js +36 -18
  400. package/esm/ui/CascadingMenuHelpDialog.d.ts +2 -2
  401. package/esm/ui/CascadingMenuHelpDialog.js +4 -5
  402. package/esm/ui/CascadingMenuHelpIconButton.d.ts +2 -1
  403. package/esm/ui/CascadingMenuHelpIconButton.js +18 -9
  404. package/esm/ui/ColorPicker.d.ts +6 -9
  405. package/esm/ui/ColorPicker.js +36 -39
  406. package/esm/ui/ConfirmDialog.d.ts +2 -9
  407. package/esm/ui/ConfirmDialog.js +6 -9
  408. package/esm/ui/ContextMenu.d.ts +50 -0
  409. package/esm/ui/ContextMenu.js +55 -0
  410. package/esm/ui/CopyToClipboardButton.d.ts +10 -0
  411. package/esm/ui/CopyToClipboardButton.js +14 -0
  412. package/esm/ui/Crosshairs.d.ts +10 -0
  413. package/esm/ui/Crosshairs.js +15 -0
  414. package/esm/ui/DOMPurifySanitizedHTML.d.ts +1 -1
  415. package/esm/ui/DOMPurifySanitizedHTML.js +5 -5
  416. package/esm/ui/DataGridFlexContainer.d.ts +9 -2
  417. package/esm/ui/DataGridFlexContainer.js +4 -3
  418. package/esm/ui/Dialog.d.ts +5 -2
  419. package/esm/ui/Dialog.js +35 -27
  420. package/esm/ui/DraggableDialog.d.ts +3 -3
  421. package/esm/ui/DraggableDialog.js +50 -12
  422. package/esm/ui/DropDownMenu.d.ts +4 -2
  423. package/esm/ui/DropDownMenu.js +4 -4
  424. package/esm/ui/EditableTypography.d.ts +3 -1
  425. package/esm/ui/EditableTypography.js +34 -26
  426. package/esm/ui/ErrorActions.d.ts +24 -0
  427. package/esm/ui/ErrorActions.js +20 -0
  428. package/esm/ui/ErrorBanner.d.ts +7 -0
  429. package/esm/ui/ErrorBanner.js +35 -0
  430. package/esm/ui/ErrorBar.d.ts +6 -0
  431. package/esm/ui/ErrorBar.js +35 -0
  432. package/esm/ui/ErrorBoundary.d.ts +29 -5
  433. package/esm/ui/ErrorBoundary.js +32 -2
  434. package/esm/ui/ErrorMessage.d.ts +2 -4
  435. package/esm/ui/ErrorMessage.js +17 -52
  436. package/esm/ui/ErrorMessageStackTraceContents.d.ts +1 -1
  437. package/esm/ui/ErrorMessageStackTraceContents.js +3 -3
  438. package/esm/ui/ErrorMessageStackTraceDialog.d.ts +1 -1
  439. package/esm/ui/ErrorMessageStackTraceDialog.js +57 -96
  440. package/esm/ui/ErrorOverlay.d.ts +8 -0
  441. package/esm/ui/ErrorOverlay.js +5 -0
  442. package/esm/ui/ExportSvgDialog.d.ts +7 -0
  443. package/esm/ui/ExportSvgDialog.js +9 -0
  444. package/esm/ui/ExternalLink.d.ts +1 -1
  445. package/esm/ui/FactoryResetDialog.d.ts +1 -1
  446. package/esm/ui/FactoryResetDialog.js +6 -15
  447. package/esm/ui/FatalErrorDialog.d.ts +3 -2
  448. package/esm/ui/FatalErrorDialog.js +6 -5
  449. package/esm/ui/FileDropZone.d.ts +25 -0
  450. package/esm/ui/FileDropZone.js +128 -0
  451. package/esm/ui/FileSelector/FileSelector.d.ts +1 -1
  452. package/esm/ui/FileSelector/FileSelector.js +59 -30
  453. package/esm/ui/FileSelector/LocalFileChooser.d.ts +7 -2
  454. package/esm/ui/FileSelector/LocalFileChooser.js +61 -47
  455. package/esm/ui/FileSelector/LocationInput.d.ts +1 -1
  456. package/esm/ui/FileSelector/LocationInput.js +8 -12
  457. package/esm/ui/FileSelector/SourceTypeSelector.d.ts +5 -5
  458. package/esm/ui/FileSelector/SourceTypeSelector.js +9 -7
  459. package/esm/ui/FileSelector/UrlChooser.d.ts +1 -1
  460. package/esm/ui/FileSelector/UrlChooser.js +26 -2
  461. package/esm/ui/FileSelector/emptySourceType.d.ts +2 -0
  462. package/esm/ui/FileSelector/emptySourceType.js +14 -0
  463. package/esm/ui/FileSelector/useInternetAccounts.d.ts +383 -71
  464. package/esm/ui/FileSelector/useInternetAccounts.js +13 -6
  465. package/esm/ui/FileSelector/util.d.ts +58 -3
  466. package/esm/ui/FileSelector/util.js +128 -11
  467. package/esm/ui/GpuFallbackButton.d.ts +12 -0
  468. package/esm/ui/GpuFallbackButton.js +20 -0
  469. package/esm/ui/HoverMenu.d.ts +12 -3
  470. package/esm/ui/HoverMenu.js +31 -9
  471. package/esm/ui/HoverTooltip.d.ts +27 -0
  472. package/esm/ui/HoverTooltip.js +24 -0
  473. package/esm/ui/Icons.d.ts +6 -4
  474. package/esm/ui/Icons.js +9 -0
  475. package/esm/ui/InfoDialog.d.ts +7 -0
  476. package/esm/ui/InfoDialog.js +16 -0
  477. package/esm/ui/InlineMenuControls.d.ts +6 -0
  478. package/esm/ui/InlineMenuControls.js +17 -0
  479. package/esm/ui/JexlFilterDialog.d.ts +23 -0
  480. package/esm/ui/JexlFilterDialog.js +94 -0
  481. package/esm/ui/LabeledCheckbox.d.ts +9 -0
  482. package/esm/ui/LabeledCheckbox.js +7 -0
  483. package/esm/ui/LegendSwatchGlyph.d.ts +7 -0
  484. package/esm/ui/LegendSwatchGlyph.js +25 -0
  485. package/esm/ui/LoadingDots.d.ts +1 -0
  486. package/esm/ui/LoadingDots.js +30 -0
  487. package/esm/ui/LoadingEllipses.d.ts +17 -1
  488. package/esm/ui/LoadingEllipses.js +20 -29
  489. package/esm/ui/LoadingOverlay.d.ts +23 -0
  490. package/esm/ui/LoadingOverlay.js +137 -0
  491. package/esm/ui/LoadingProgress.d.ts +16 -0
  492. package/esm/ui/LoadingProgress.js +16 -0
  493. package/esm/ui/Logo.d.ts +2 -2
  494. package/esm/ui/Logo.js +23 -24
  495. package/esm/ui/Menu.js +1 -1
  496. package/esm/ui/MenuItemChevron.d.ts +3 -0
  497. package/esm/ui/MenuItemChevron.js +19 -0
  498. package/esm/ui/MenuItemEndDecoration.d.ts +4 -0
  499. package/esm/ui/MenuItemEndDecoration.js +28 -0
  500. package/esm/ui/MenuItemTrailing.d.ts +12 -0
  501. package/esm/ui/MenuItemTrailing.js +42 -0
  502. package/esm/ui/MenuTypes.d.ts +134 -5
  503. package/esm/ui/MenuTypes.js +16 -1
  504. package/esm/ui/MonospaceTextField.d.ts +9 -0
  505. package/esm/ui/MonospaceTextField.js +37 -0
  506. package/esm/ui/NumberTextField.d.ts +31 -0
  507. package/esm/ui/NumberTextField.js +33 -0
  508. package/esm/ui/PaletteContext.d.ts +92 -0
  509. package/esm/ui/PaletteContext.js +133 -0
  510. package/esm/ui/PinAdornment.d.ts +5 -0
  511. package/esm/ui/PinAdornment.js +85 -0
  512. package/esm/ui/PluggableComponent.d.ts +10 -0
  513. package/esm/ui/PluggableComponent.js +19 -0
  514. package/esm/ui/PluggableComponents.d.ts +29 -0
  515. package/esm/ui/PluggableComponents.js +28 -0
  516. package/esm/ui/PluggableElements.d.ts +23 -0
  517. package/esm/ui/PluggableElements.js +24 -0
  518. package/esm/ui/PluginStoreCard.d.ts +17 -0
  519. package/esm/ui/PluginStoreCard.js +45 -0
  520. package/esm/ui/PopoverPicker.d.ts +6 -0
  521. package/esm/ui/PopoverPicker.js +25 -0
  522. package/esm/ui/PrerenderedCanvas.d.ts +1 -1
  523. package/esm/ui/PrerenderedCanvas.js +5 -4
  524. package/esm/ui/ProgressChip.d.ts +37 -0
  525. package/esm/ui/ProgressChip.js +66 -0
  526. package/esm/ui/RedErrorMessageBox.d.ts +1 -1
  527. package/esm/ui/RedErrorMessageBox.js +9 -3
  528. package/esm/ui/RefNameAutocomplete/EndAdornment.d.ts +5 -0
  529. package/esm/ui/RefNameAutocomplete/EndAdornment.js +31 -0
  530. package/esm/ui/RefNameAutocomplete/HelpDialog.d.ts +3 -0
  531. package/esm/ui/RefNameAutocomplete/HelpDialog.js +7 -0
  532. package/esm/ui/RefNameAutocomplete/index.d.ts +22 -0
  533. package/esm/ui/RefNameAutocomplete/index.js +78 -0
  534. package/esm/ui/RefNameAutocomplete/util.d.ts +49 -0
  535. package/esm/ui/RefNameAutocomplete/util.js +168 -0
  536. package/esm/ui/ReplaceCurrentViewButton.d.ts +19 -0
  537. package/esm/ui/ReplaceCurrentViewButton.js +22 -0
  538. package/esm/ui/ResizeHandle.d.ts +13 -7
  539. package/esm/ui/ResizeHandle.js +42 -55
  540. package/esm/ui/ReturnToImportFormDialog.d.ts +1 -1
  541. package/esm/ui/ReturnToImportFormDialog.js +7 -9
  542. package/esm/ui/SanitizedHTML.d.ts +6 -1
  543. package/esm/ui/SanitizedHTML.js +7 -47
  544. package/esm/ui/ScrollEdgeShadow.d.ts +44 -0
  545. package/esm/ui/ScrollEdgeShadow.js +98 -0
  546. package/esm/ui/ScrollZoomToggle.d.ts +38 -0
  547. package/esm/ui/ScrollZoomToggle.js +92 -0
  548. package/esm/ui/SequenceAdapterInputs.d.ts +9 -0
  549. package/esm/ui/SequenceAdapterInputs.js +30 -0
  550. package/esm/ui/SettingsChangesTable.d.ts +14 -0
  551. package/esm/ui/SettingsChangesTable.js +49 -0
  552. package/esm/ui/ShareLinkField.d.ts +6 -0
  553. package/esm/ui/ShareLinkField.js +42 -0
  554. package/esm/ui/SingleSlider.d.ts +8 -0
  555. package/esm/ui/SingleSlider.js +11 -0
  556. package/esm/ui/SizeSliderRow.d.ts +16 -0
  557. package/esm/ui/SizeSliderRow.js +50 -0
  558. package/esm/ui/SliderTooltip.d.ts +2 -0
  559. package/esm/ui/SliderTooltip.js +17 -0
  560. package/esm/ui/Snackbar.d.ts +4 -2
  561. package/esm/ui/Snackbar.js +11 -8
  562. package/esm/ui/SnackbarContents.d.ts +1 -1
  563. package/esm/ui/SnackbarContents.js +21 -3
  564. package/esm/ui/SnackbarModel.d.ts +40 -0
  565. package/esm/ui/SnackbarModel.js +43 -11
  566. package/esm/ui/StackTraceButton.d.ts +5 -0
  567. package/esm/ui/StackTraceButton.js +16 -0
  568. package/esm/ui/StatusProgressBar.d.ts +37 -0
  569. package/esm/ui/StatusProgressBar.js +76 -0
  570. package/esm/ui/SubmitDialog.d.ts +6 -0
  571. package/esm/ui/SubmitDialog.js +9 -0
  572. package/esm/ui/SubmitForm.d.ts +23 -0
  573. package/esm/ui/SubmitForm.js +23 -0
  574. package/esm/ui/SvgColorLegend.d.ts +13 -0
  575. package/esm/ui/SvgColorLegend.js +65 -0
  576. package/esm/ui/SvgGradientLegend.d.ts +26 -0
  577. package/esm/ui/SvgGradientLegend.js +26 -0
  578. package/esm/ui/TagTextField.d.ts +40 -0
  579. package/esm/ui/TagTextField.js +32 -0
  580. package/esm/ui/VerticalScrollbar.d.ts +45 -0
  581. package/esm/ui/VerticalScrollbar.js +158 -0
  582. package/esm/ui/ViewLoadingScreen.d.ts +24 -0
  583. package/esm/ui/ViewLoadingScreen.js +76 -0
  584. package/esm/ui/addExtensionElement.d.ts +18 -0
  585. package/esm/ui/addExtensionElement.js +23 -0
  586. package/esm/ui/buildExtraTrackMenuItems.d.ts +22 -0
  587. package/esm/ui/buildExtraTrackMenuItems.js +14 -0
  588. package/esm/ui/colorSwatchStyle.d.ts +9 -0
  589. package/esm/ui/colorSwatchStyle.js +11 -0
  590. package/esm/ui/colors.d.ts +61 -8
  591. package/esm/ui/colors.js +135 -1
  592. package/esm/ui/extensionSelectors.d.ts +38 -0
  593. package/esm/ui/extensionSelectors.js +49 -0
  594. package/esm/ui/filterMenuItems.d.ts +112 -0
  595. package/esm/ui/filterMenuItems.js +86 -0
  596. package/esm/ui/formatErrorStack.d.ts +1 -0
  597. package/esm/ui/formatErrorStack.js +56 -0
  598. package/esm/ui/gpuFallback.d.ts +33 -0
  599. package/esm/ui/gpuFallback.js +39 -0
  600. package/esm/ui/highlightChipReveal.d.ts +32 -0
  601. package/esm/ui/highlightChipReveal.js +39 -0
  602. package/esm/ui/hoverBoxStyle.d.ts +11 -0
  603. package/esm/ui/hoverBoxStyle.js +13 -0
  604. package/esm/ui/index.d.ts +76 -4
  605. package/esm/ui/index.js +90 -19
  606. package/esm/ui/inlineMenuRowWidth.d.ts +1 -0
  607. package/esm/ui/inlineMenuRowWidth.js +8 -0
  608. package/esm/ui/launchTargetsMenuItem.d.ts +18 -0
  609. package/esm/ui/launchTargetsMenuItem.js +24 -0
  610. package/esm/ui/launchViewMenu.d.ts +4 -0
  611. package/esm/ui/launchViewMenu.js +42 -0
  612. package/esm/ui/legendMenuItem.d.ts +38 -0
  613. package/esm/ui/legendMenuItem.js +44 -0
  614. package/esm/ui/legendSpec.d.ts +62 -0
  615. package/esm/ui/legendSpec.js +78 -0
  616. package/esm/ui/loadingDotKeyframes.d.ts +18 -0
  617. package/esm/ui/loadingDotKeyframes.js +17 -0
  618. package/esm/ui/makeSizeMenu.d.ts +30 -0
  619. package/esm/ui/makeSizeMenu.js +82 -0
  620. package/esm/ui/mapStackTrace.d.ts +8 -0
  621. package/esm/ui/mapStackTrace.js +108 -0
  622. package/esm/ui/measureLegendText.d.ts +1 -0
  623. package/esm/ui/measureLegendText.js +8 -0
  624. package/esm/ui/menuItemAdornment.d.ts +33 -0
  625. package/esm/ui/menuItemAdornment.js +50 -0
  626. package/esm/ui/menuItems.d.ts +28 -0
  627. package/esm/ui/menuItems.js +26 -0
  628. package/esm/ui/menuLabels.d.ts +41 -0
  629. package/esm/ui/menuLabels.js +43 -0
  630. package/esm/ui/multiTrackMenuItems.d.ts +19 -0
  631. package/esm/ui/multiTrackMenuItems.js +15 -0
  632. package/esm/ui/palette.d.ts +559 -0
  633. package/esm/ui/palette.js +746 -0
  634. package/esm/ui/parseError.d.ts +4 -0
  635. package/esm/ui/parseError.js +18 -0
  636. package/esm/ui/persistentScrollbarStyle.d.ts +49 -0
  637. package/esm/ui/persistentScrollbarStyle.js +53 -0
  638. package/esm/ui/promotableMenuItems.d.ts +19 -0
  639. package/esm/ui/promotableMenuItems.js +91 -0
  640. package/esm/ui/promotablePinCoverage.d.ts +44 -0
  641. package/esm/ui/promotablePinCoverage.js +88 -0
  642. package/esm/ui/radioSubMenu.d.ts +33 -0
  643. package/esm/ui/radioSubMenu.js +32 -0
  644. package/esm/ui/react-colorful.js +5 -1
  645. package/esm/ui/replaceViewAction.d.ts +31 -0
  646. package/esm/ui/replaceViewAction.js +39 -0
  647. package/esm/ui/rewriteExternalAnchors.d.ts +1 -0
  648. package/esm/ui/rewriteExternalAnchors.js +8 -0
  649. package/esm/ui/scrollZoomLabels.d.ts +17 -0
  650. package/esm/ui/scrollZoomLabels.js +22 -0
  651. package/esm/ui/showSubMenu.d.ts +19 -0
  652. package/esm/ui/showSubMenu.js +30 -0
  653. package/esm/ui/sliderScale.d.ts +6 -0
  654. package/esm/ui/sliderScale.js +30 -0
  655. package/esm/ui/statusProgressKeyframes.d.ts +6 -0
  656. package/esm/ui/statusProgressKeyframes.js +14 -0
  657. package/esm/ui/stripStackTraceMessage.d.ts +1 -0
  658. package/esm/ui/stripStackTraceMessage.js +9 -0
  659. package/esm/ui/styleTheme.d.ts +158 -0
  660. package/esm/ui/styleTheme.js +115 -0
  661. package/esm/ui/submenuAim.d.ts +30 -0
  662. package/esm/ui/submenuAim.js +37 -0
  663. package/esm/ui/theme.d.ts +343 -29
  664. package/esm/ui/theme.js +258 -342
  665. package/esm/ui/toggleMenuItems.d.ts +42 -0
  666. package/esm/ui/toggleMenuItems.js +60 -0
  667. package/esm/ui/useAssemblySelection.d.ts +153 -0
  668. package/esm/ui/useAssemblySelection.js +54 -0
  669. package/esm/ui/useCoalescedPointer.d.ts +36 -0
  670. package/esm/ui/useCoalescedPointer.js +60 -0
  671. package/esm/ui/useCopyToClipboard.d.ts +15 -0
  672. package/esm/ui/useCopyToClipboard.js +41 -0
  673. package/esm/ui/useExportSvgPreference.d.ts +1 -0
  674. package/esm/ui/useExportSvgPreference.js +4 -0
  675. package/esm/ui/useMouseTracking.d.ts +71 -0
  676. package/esm/ui/useMouseTracking.js +179 -0
  677. package/esm/ui/useRecentLocations.d.ts +28 -0
  678. package/esm/ui/useRecentLocations.js +31 -0
  679. package/esm/ui/wrapComponent.d.ts +47 -0
  680. package/esm/ui/wrapComponent.js +58 -0
  681. package/esm/ui/zIndexes.d.ts +28 -0
  682. package/esm/ui/zIndexes.js +38 -0
  683. package/esm/util/Base1DUtils.d.ts +204 -16
  684. package/esm/util/Base1DUtils.js +310 -175
  685. package/esm/util/Base1DViewModel.d.ts +97 -20
  686. package/esm/util/Base1DViewModel.js +148 -39
  687. package/esm/util/FileSaver/index.d.ts +1 -0
  688. package/esm/util/FileSaver/index.js +27 -0
  689. package/esm/util/IntervalTree.d.ts +18 -39
  690. package/esm/util/IntervalTree.js +63 -244
  691. package/esm/util/SvgCanvas.d.ts +81 -0
  692. package/esm/util/SvgCanvas.js +500 -0
  693. package/esm/util/TimeTraveller.d.ts +12 -0
  694. package/esm/util/TimeTraveller.js +130 -27
  695. package/esm/util/aborting.d.ts +17 -4
  696. package/esm/util/aborting.js +30 -25
  697. package/esm/util/adapterMetadata.d.ts +20 -0
  698. package/esm/util/adapterMetadata.js +39 -0
  699. package/esm/util/addAndShowTrack.d.ts +22 -0
  700. package/esm/util/addAndShowTrack.js +27 -0
  701. package/esm/util/addRelativeUris.d.ts +17 -0
  702. package/esm/util/addRelativeUris.js +42 -0
  703. package/esm/util/addTrackComponent.d.ts +72 -0
  704. package/esm/util/addTrackComponent.js +53 -0
  705. package/esm/util/addTrackFromWidget.d.ts +94 -0
  706. package/esm/util/addTrackFromWidget.js +90 -0
  707. package/esm/util/analytics.d.ts +32 -3
  708. package/esm/util/analytics.js +102 -49
  709. package/esm/util/animationAllowed.d.ts +17 -0
  710. package/esm/util/animationAllowed.js +22 -0
  711. package/esm/util/applyRowResizeWheel.d.ts +10 -0
  712. package/esm/util/applyRowResizeWheel.js +34 -0
  713. package/esm/util/assemblyConfigUtils.d.ts +144 -0
  714. package/esm/util/assemblyConfigUtils.js +498 -0
  715. package/esm/util/bandHeight.d.ts +53 -0
  716. package/esm/util/bandHeight.js +56 -0
  717. package/esm/util/bandLayout.d.ts +51 -0
  718. package/esm/util/bandLayout.js +36 -0
  719. package/esm/util/bezierConnector.d.ts +14 -0
  720. package/esm/util/bezierConnector.js +108 -0
  721. package/esm/util/bgzfWorkerPool.d.ts +78 -0
  722. package/esm/util/bgzfWorkerPool.js +81 -0
  723. package/esm/util/blockTypes.d.ts +64 -45
  724. package/esm/util/blockTypes.js +67 -74
  725. package/esm/util/bpUtils.d.ts +81 -0
  726. package/esm/util/bpUtils.js +103 -0
  727. package/esm/util/cacheBudgets.d.ts +55 -0
  728. package/esm/util/cacheBudgets.js +55 -0
  729. package/esm/util/cachedSetup.d.ts +51 -0
  730. package/esm/util/cachedSetup.js +87 -0
  731. package/esm/util/calculateDynamicBlocks.d.ts +5 -0
  732. package/esm/util/calculateDynamicBlocks.js +85 -82
  733. package/esm/util/calculateStaticBlocks.d.ts +2 -3
  734. package/esm/util/calculateStaticBlocks.js +48 -71
  735. package/esm/util/chooseGridPitch.d.ts +9 -0
  736. package/esm/util/chooseGridPitch.js +31 -0
  737. package/esm/util/clampToContig.d.ts +26 -0
  738. package/esm/util/clampToContig.js +28 -0
  739. package/esm/util/cmpStr.d.ts +1 -0
  740. package/esm/util/cmpStr.js +7 -0
  741. package/esm/util/coarseStripHTML.js +3 -15
  742. package/esm/util/color/cssColorsLevel4.js +6 -2
  743. package/esm/util/color/index.d.ts +81 -2
  744. package/esm/util/color/index.js +194 -25
  745. package/esm/util/color-bits/bit.d.ts +4 -0
  746. package/esm/util/color-bits/bit.js +37 -0
  747. package/esm/util/color-bits/convert.d.ts +23 -0
  748. package/esm/util/color-bits/convert.js +294 -0
  749. package/esm/util/color-bits/core.d.ts +34 -0
  750. package/esm/util/color-bits/core.js +67 -0
  751. package/esm/util/color-bits/format.d.ts +24 -0
  752. package/esm/util/color-bits/format.js +82 -0
  753. package/esm/util/color-bits/functions.d.ts +33 -0
  754. package/esm/util/color-bits/functions.js +70 -0
  755. package/esm/util/color-bits/index.d.ts +5 -0
  756. package/esm/util/color-bits/index.js +4 -0
  757. package/esm/util/color-bits/parse.d.ts +17 -0
  758. package/esm/util/color-bits/parse.js +382 -0
  759. package/esm/util/colorBits.d.ts +39 -0
  760. package/esm/util/colorBits.js +180 -0
  761. package/esm/util/colorRamp.d.ts +37 -0
  762. package/esm/util/colorRamp.js +93 -0
  763. package/esm/util/colord.d.ts +8 -0
  764. package/esm/util/colord.js +43 -191
  765. package/esm/util/convertCodingSequenceToPeptides.d.ts +17 -3
  766. package/esm/util/convertCodingSequenceToPeptides.js +51 -4
  767. package/esm/util/copyText.d.ts +18 -0
  768. package/esm/util/copyText.js +30 -0
  769. package/esm/util/copyToClipboard.d.ts +4 -0
  770. package/esm/util/copyToClipboard.js +58 -0
  771. package/esm/util/createStopTokenRotation.d.ts +118 -0
  772. package/esm/util/createStopTokenRotation.js +127 -0
  773. package/esm/util/createSvgRasterCanvas.d.ts +7 -0
  774. package/esm/util/createSvgRasterCanvas.js +22 -0
  775. package/esm/util/crypto.d.ts +24 -0
  776. package/esm/util/crypto.js +85 -2
  777. package/esm/util/dataGridUtils.d.ts +9 -0
  778. package/esm/util/dataGridUtils.js +36 -0
  779. package/esm/util/dedupe.js +1 -0
  780. package/esm/util/deepEqual.d.ts +8 -0
  781. package/esm/util/deepEqual.js +22 -0
  782. package/esm/util/deepMerge.d.ts +20 -0
  783. package/esm/util/deepMerge.js +44 -0
  784. package/esm/util/diagonalizeRegions.d.ts +23 -0
  785. package/esm/util/diagonalizeRegions.js +192 -0
  786. package/esm/util/environment.d.ts +4 -0
  787. package/esm/util/environment.js +43 -0
  788. package/esm/util/eventPoint.d.ts +32 -0
  789. package/esm/util/eventPoint.js +28 -0
  790. package/esm/util/fetchAndMaybeUnzip.d.ts +6 -0
  791. package/esm/util/fetchAndMaybeUnzip.js +64 -0
  792. package/esm/util/fetchContext.d.ts +82 -0
  793. package/esm/util/fetchContext.js +59 -0
  794. package/esm/util/fetchHub.d.ts +15 -0
  795. package/esm/util/fetchHub.js +31 -0
  796. package/esm/util/fetchJson.d.ts +1 -0
  797. package/esm/util/fetchJson.js +7 -0
  798. package/esm/util/fetchPhases.d.ts +77 -0
  799. package/esm/util/fetchPhases.js +1 -0
  800. package/esm/util/fetchSeq.d.ts +5 -1
  801. package/esm/util/fetchSeq.js +18 -6
  802. package/esm/util/fileHandleStore.d.ts +19 -2
  803. package/esm/util/fileHandleStore.js +95 -35
  804. package/esm/util/flatbush/index.d.ts +27 -6
  805. package/esm/util/flatbush/index.js +194 -218
  806. package/esm/util/formatBytes.d.ts +9 -0
  807. package/esm/util/formatBytes.js +18 -0
  808. package/esm/util/formatFastaStrings.d.ts +13 -0
  809. package/esm/util/formatFastaStrings.js +13 -0
  810. package/esm/util/formatGuessers.d.ts +30 -0
  811. package/esm/util/formatGuessers.js +69 -0
  812. package/esm/util/formatRelativeTime.d.ts +1 -0
  813. package/esm/util/formatRelativeTime.js +25 -0
  814. package/esm/util/frameCoalescer.d.ts +30 -0
  815. package/esm/util/frameCoalescer.js +22 -0
  816. package/esm/util/freezeDeep.d.ts +28 -0
  817. package/esm/util/freezeDeep.js +41 -0
  818. package/esm/util/geneticCodes.d.ts +56 -0
  819. package/esm/util/geneticCodes.js +371 -0
  820. package/esm/util/getFileName.d.ts +11 -0
  821. package/esm/util/getFileName.js +34 -0
  822. package/esm/util/getLocationUri.d.ts +49 -0
  823. package/esm/util/getLocationUri.js +63 -0
  824. package/esm/util/getRelativeX.d.ts +4 -0
  825. package/esm/util/getRelativeX.js +7 -0
  826. package/esm/util/getStr.d.ts +6 -0
  827. package/esm/util/getStr.js +15 -0
  828. package/esm/util/highlights.d.ts +21 -0
  829. package/esm/util/highlights.js +100 -0
  830. package/esm/util/hooks.d.ts +168 -0
  831. package/esm/util/hooks.js +443 -0
  832. package/esm/util/htmlText.d.ts +13 -0
  833. package/esm/util/htmlText.js +66 -0
  834. package/esm/util/idMaker.d.ts +1 -1
  835. package/esm/util/idMaker.js +31 -18
  836. package/esm/util/index.d.ts +81 -268
  837. package/esm/util/index.js +135 -853
  838. package/esm/util/indexCandidates.d.ts +50 -0
  839. package/esm/util/indexCandidates.js +101 -0
  840. package/esm/util/installClearHoverOnSurfaceMove.d.ts +40 -0
  841. package/esm/util/installClearHoverOnSurfaceMove.js +41 -0
  842. package/esm/util/installFetch.d.ts +220 -0
  843. package/esm/util/installFetch.js +206 -0
  844. package/esm/util/installInitAutorun.d.ts +62 -0
  845. package/esm/util/installInitAutorun.js +107 -0
  846. package/esm/util/intervals.d.ts +20 -0
  847. package/esm/util/intervals.js +37 -0
  848. package/esm/util/io/RemoteFileWithRangeCache.d.ts +10 -11
  849. package/esm/util/io/RemoteFileWithRangeCache.js +10 -148
  850. package/esm/util/io/index.d.ts +39 -2
  851. package/esm/util/io/index.js +115 -12
  852. package/esm/util/isDataCurrent.d.ts +7 -0
  853. package/esm/util/isDataCurrent.js +9 -0
  854. package/esm/util/isWebWorker.js +1 -2
  855. package/esm/util/iupac.d.ts +4 -0
  856. package/esm/util/iupac.js +59 -0
  857. package/esm/util/jexl.js +141 -17
  858. package/esm/util/jexlFilters.d.ts +75 -0
  859. package/esm/util/jexlFilters.js +49 -0
  860. package/esm/util/jexlStrings.d.ts +22 -1
  861. package/esm/util/jexlStrings.js +21 -14
  862. package/esm/util/layouts/GranularRectLayout.d.ts +13 -25
  863. package/esm/util/layouts/GranularRectLayout.js +99 -356
  864. package/esm/util/layouts/index.d.ts +1 -7
  865. package/esm/util/layouts/index.js +2 -6
  866. package/esm/util/layouts/intervalUtils.d.ts +12 -1
  867. package/esm/util/layouts/intervalUtils.js +13 -31
  868. package/esm/util/layouts/placeRect.d.ts +50 -0
  869. package/esm/util/layouts/placeRect.js +97 -0
  870. package/esm/util/lazyAfterAttach.d.ts +13 -0
  871. package/esm/util/lazyAfterAttach.js +31 -0
  872. package/esm/util/leadingEdgeAutorun.d.ts +40 -0
  873. package/esm/util/leadingEdgeAutorun.js +51 -0
  874. package/esm/util/legendCandidates.d.ts +50 -0
  875. package/esm/util/legendCandidates.js +87 -0
  876. package/esm/util/librpc.d.ts +5 -2
  877. package/esm/util/librpc.js +6 -1
  878. package/esm/util/linkify.js +2 -0
  879. package/esm/util/locString.d.ts +72 -0
  880. package/esm/util/locString.js +178 -7
  881. package/esm/util/locStringsToRegions.d.ts +10 -0
  882. package/esm/util/locStringsToRegions.js +35 -0
  883. package/esm/util/localStorage.d.ts +36 -0
  884. package/esm/util/localStorage.js +137 -0
  885. package/esm/util/makeAssembly.d.ts +54 -0
  886. package/esm/util/makeAssembly.js +52 -0
  887. package/esm/util/makeTrackId.d.ts +14 -0
  888. package/esm/util/makeTrackId.js +14 -0
  889. package/esm/util/matchTrackId.d.ts +11 -0
  890. package/esm/util/matchTrackId.js +14 -0
  891. package/esm/util/measureText.d.ts +24 -0
  892. package/esm/util/measureText.js +51 -0
  893. package/esm/util/mst-reflection.d.ts +14 -4
  894. package/esm/util/mst-reflection.js +33 -32
  895. package/esm/util/mstUtils.d.ts +100 -0
  896. package/esm/util/mstUtils.js +140 -0
  897. package/esm/util/nanoid.d.ts +0 -4
  898. package/esm/util/nanoid.js +10 -20
  899. package/esm/util/numericUtils.d.ts +20 -0
  900. package/esm/util/numericUtils.js +127 -0
  901. package/esm/util/objectUtils.d.ts +2 -0
  902. package/esm/util/objectUtils.js +9 -0
  903. package/esm/util/offscreenCanvasPonyfill.d.ts +5 -4
  904. package/esm/util/offscreenCanvasPonyfill.js +5 -47
  905. package/esm/util/openDisplays.d.ts +23 -0
  906. package/esm/util/openDisplays.js +79 -0
  907. package/esm/util/openFeatureWidget.d.ts +33 -0
  908. package/esm/util/openFeatureWidget.js +64 -0
  909. package/esm/util/paintLayer.d.ts +32 -0
  910. package/esm/util/paintLayer.js +33 -0
  911. package/esm/util/parentWalk.d.ts +32 -0
  912. package/esm/util/parentWalk.js +84 -0
  913. package/esm/util/parseLineByLine.d.ts +45 -2
  914. package/esm/util/parseLineByLine.js +156 -15
  915. package/esm/util/parseMotifList.d.ts +17 -0
  916. package/esm/util/parseMotifList.js +69 -0
  917. package/esm/util/pluginStore.d.ts +114 -0
  918. package/esm/util/pluginStore.js +260 -0
  919. package/esm/util/pointerPresence.d.ts +5 -0
  920. package/esm/util/pointerPresence.js +21 -0
  921. package/esm/util/progress.d.ts +459 -0
  922. package/esm/util/progress.js +820 -0
  923. package/esm/util/range.d.ts +46 -1
  924. package/esm/util/range.js +68 -2
  925. package/esm/util/renameRegions.d.ts +21 -0
  926. package/esm/util/renameRegions.js +129 -0
  927. package/esm/util/renderToStaticMarkup.d.ts +2 -0
  928. package/esm/util/renderToStaticMarkup.js +50 -0
  929. package/esm/util/reorder.d.ts +35 -0
  930. package/esm/util/reorder.js +83 -0
  931. package/esm/util/resolveRowHeight.d.ts +27 -0
  932. package/esm/util/resolveRowHeight.js +30 -0
  933. package/esm/util/revlist.d.ts +13 -0
  934. package/esm/util/revlist.js +14 -0
  935. package/esm/util/rowStackGeometry.d.ts +66 -0
  936. package/esm/util/rowStackGeometry.js +70 -0
  937. package/esm/util/rpc.d.ts +16 -1
  938. package/esm/util/rpc.js +12 -1
  939. package/esm/util/rxjs.d.ts +30 -1
  940. package/esm/util/rxjs.js +88 -10
  941. package/esm/util/sameStrings.d.ts +16 -0
  942. package/esm/util/sameStrings.js +20 -0
  943. package/esm/util/scrollLatch.d.ts +4 -0
  944. package/esm/util/scrollLatch.js +59 -0
  945. package/esm/util/selectNamedRegions.d.ts +136 -0
  946. package/esm/util/selectNamedRegions.js +222 -0
  947. package/esm/util/seqUtils.d.ts +17 -0
  948. package/esm/util/seqUtils.js +80 -0
  949. package/esm/util/sessionServices.d.ts +29 -0
  950. package/esm/util/sessionServices.js +46 -0
  951. package/esm/util/sessionSharing.d.ts +38 -0
  952. package/esm/util/sessionSharing.js +154 -0
  953. package/esm/util/sessionStorage.d.ts +1 -0
  954. package/esm/util/sessionStorage.js +15 -0
  955. package/esm/util/setStackTraceLimit.d.ts +6 -0
  956. package/esm/util/setStackTraceLimit.js +20 -0
  957. package/esm/util/simpleFeature.d.ts +112 -4
  958. package/esm/util/simpleFeature.js +181 -29
  959. package/esm/util/springAnimate.d.ts +20 -0
  960. package/esm/util/springAnimate.js +80 -0
  961. package/esm/util/stats.d.ts +25 -2
  962. package/esm/util/stats.js +39 -8
  963. package/esm/util/stopToken.d.ts +207 -15
  964. package/esm/util/stopToken.js +403 -55
  965. package/esm/util/stringUtils.d.ts +5 -0
  966. package/esm/util/stringUtils.js +34 -0
  967. package/esm/util/svgColorProps.d.ts +7 -0
  968. package/esm/util/svgColorProps.js +28 -0
  969. package/esm/util/tabix.d.ts +126 -0
  970. package/esm/util/tabix.js +149 -0
  971. package/esm/util/tags.d.ts +2 -0
  972. package/esm/util/tags.js +5 -0
  973. package/esm/util/temporaryAssembly.d.ts +21 -0
  974. package/esm/util/temporaryAssembly.js +29 -0
  975. package/esm/util/tickLabels.d.ts +36 -0
  976. package/esm/util/tickLabels.js +45 -0
  977. package/esm/util/timeGate.d.ts +26 -0
  978. package/esm/util/timeGate.js +79 -0
  979. package/esm/util/trackConfigDelta.d.ts +84 -0
  980. package/esm/util/trackConfigDelta.js +190 -0
  981. package/esm/util/tracks.d.ts +398 -30
  982. package/esm/util/tracks.js +699 -191
  983. package/esm/util/tss-react/cssAndCx.js +11 -66
  984. package/esm/util/tss-react/index.d.ts +11 -2
  985. package/esm/util/tss-react/index.js +9 -2
  986. package/esm/util/tss-react/makeStyles.js +7 -4
  987. package/esm/util/tss-react/mergeClasses.js +1 -0
  988. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  989. package/esm/util/tss-react/tools/classnames.js +3 -0
  990. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  991. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  992. package/esm/util/tss-react/types.d.ts +1 -1
  993. package/esm/util/tss-react/types.js +1 -6
  994. package/esm/util/types/ElementId.js +1 -1
  995. package/esm/util/types/data.d.ts +75 -0
  996. package/esm/util/types/data.js +41 -0
  997. package/esm/util/types/index.d.ts +402 -120
  998. package/esm/util/types/index.js +90 -64
  999. package/esm/util/types/isAny.d.ts +11 -0
  1000. package/esm/util/types/isAny.js +1 -0
  1001. package/esm/util/types/mst.d.ts +71 -47
  1002. package/esm/util/types/mst.js +27 -22
  1003. package/esm/util/types/predicate.d.ts +9 -0
  1004. package/esm/util/types/predicate.js +1 -0
  1005. package/esm/util/types/renderingServices.d.ts +16 -0
  1006. package/esm/util/types/renderingServices.js +1 -0
  1007. package/esm/util/types/services.d.ts +55 -0
  1008. package/esm/util/types/services.js +10 -0
  1009. package/esm/util/types/util.d.ts +8 -2
  1010. package/esm/util/unknownSnapshotKeys.d.ts +36 -0
  1011. package/esm/util/unknownSnapshotKeys.js +69 -0
  1012. package/esm/util/unzip.d.ts +1 -0
  1013. package/esm/util/unzip.js +6 -0
  1014. package/esm/util/useEventCallback.d.ts +1 -0
  1015. package/esm/util/useEventCallback.js +16 -0
  1016. package/esm/util/useFeatureSequence.d.ts +13 -7
  1017. package/esm/util/useFeatureSequence.js +56 -78
  1018. package/esm/util/useFetch.d.ts +56 -0
  1019. package/esm/util/useFetch.js +188 -0
  1020. package/esm/util/useFetchPlugins.d.ts +12 -0
  1021. package/esm/util/useFetchPlugins.js +14 -0
  1022. package/esm/util/useMeasure.d.ts +11 -1
  1023. package/esm/util/useMeasure.js +20 -6
  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,51 @@
1
+ // prettier-ignore
2
+ const widths = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.2796875, 0.2765625, 0.3546875, 0.5546875, 0.5546875, 0.8890625, 0.665625, 0.190625, 0.3328125, 0.3328125, 0.3890625, 0.5828125, 0.2765625, 0.3328125, 0.2765625, 0.3015625, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.2765625, 0.2765625, 0.584375, 0.5828125, 0.584375, 0.5546875, 1.0140625, 0.665625, 0.665625, 0.721875, 0.721875, 0.665625, 0.609375, 0.7765625, 0.721875, 0.2765625, 0.5, 0.665625, 0.5546875, 0.8328125, 0.721875, 0.7765625, 0.665625, 0.7765625, 0.721875, 0.665625, 0.609375, 0.721875, 0.665625, 0.94375, 0.665625, 0.665625, 0.609375, 0.2765625, 0.3546875, 0.2765625, 0.4765625, 0.5546875, 0.3328125, 0.5546875, 0.5546875, 0.5, 0.5546875, 0.5546875, 0.2765625, 0.5546875, 0.5546875, 0.221875, 0.240625, 0.5, 0.221875, 0.8328125, 0.5546875, 0.5546875, 0.5546875, 0.5546875, 0.3328125, 0.5, 0.2765625, 0.5546875, 0.5, 0.721875, 0.5, 0.5, 0.5, 0.3546875, 0.259375, 0.353125, 0.5890625];
3
+ const avgWidth = 0.5279276315789471;
4
+ // Advance width of one monospace glyph, in em — the same for every character,
5
+ // which is what makes the table above unusable for one: it is Helvetica, where
6
+ // `i` is 0.22em and `m` is 0.94em, so a monospace string of narrow letters
7
+ // measures far too small and one of wide letters far too large. The mainstream
8
+ // faces cluster tightly here (Courier and DejaVu Sans Mono 0.600, Menlo 0.602,
9
+ // Liberation Mono 0.600, Consolas 0.550), and rounding *up* is the safe
10
+ // direction for every caller: all of them measure to reserve room.
11
+ const MONOSPACE_EM = 0.61;
12
+ // xref https://gist.github.com/tophtucker/62f93a4658387bb61e4510c37e2e97cf
13
+ //
14
+ // `fontFamily` is only consulted to pick monospace, which is a different metric
15
+ // rather than a different table. Proportional families are all measured against
16
+ // the Helvetica table: it is what the app renders in, and for the two other
17
+ // families the SVG export can be asked for it is close (system-ui) or narrower
18
+ // (serif, which over-reserves — the harmless direction).
19
+ export function measureText(str, fontSize = 10, fontFamily) {
20
+ const s = String(str);
21
+ if (fontFamily?.includes('monospace')) {
22
+ return s.length * MONOSPACE_EM * fontSize;
23
+ }
24
+ let total = 0;
25
+ for (let i = 0, l = s.length; i < l; i++) {
26
+ total += widths[s.charCodeAt(i)] ?? avgWidth;
27
+ }
28
+ return total * fontSize;
29
+ }
30
+ /**
31
+ * A CSS font string and its own measurement, built from one set of inputs so a
32
+ * caller cannot paint in one font and reserve room in another.
33
+ *
34
+ * Two files describing one font is the normal shape — something measures to
35
+ * decide whether a label fits, something else sets `ctx.font` and draws it — and
36
+ * the two drift silently, because a label that overflows its box by a pixel
37
+ * looks like a label. plugin-maf drew its deletion count in `bold 10px Courier
38
+ * New,monospace` and measured it here without naming the family, so a monospace
39
+ * label was answered from the Helvetica table above: 0.55px short per digit,
40
+ * which its 2px of padding covered for exactly three digits and no more.
41
+ *
42
+ * `weight` reaches the CSS and not the measurement, which is right for the
43
+ * digits these callers measure — monospace bold and regular share an advance,
44
+ * and Helvetica's ten digits are one width in either.
45
+ */
46
+ export function measuredFont(fontSize, fontFamily, weight) {
47
+ return {
48
+ css: `${weight ? `${weight} ` : ''}${fontSize}px ${fontFamily}`,
49
+ measure: text => measureText(text, fontSize, fontFamily),
50
+ };
51
+ }
@@ -1,11 +1,21 @@
1
- import type { IAnyComplexType, IAnyType, IModelReflectionPropertiesData, ISimpleType, UnionStringArray } from '@jbrowse/mobx-state-tree';
1
+ import type { IAnyType, IModelReflectionPropertiesData, ISimpleType, UnionStringArray } from '@jbrowse/mobx-state-tree';
2
2
  export interface ILiteralType<T> extends ISimpleType<T> {
3
3
  value: T;
4
4
  }
5
+ /**
6
+ * get the inner type of an MST optional, refinement, array, map, or late type
7
+ */
5
8
  export declare function getSubType(type: IAnyType): IAnyType;
6
- export declare function getUnionSubTypes(unionType: IAnyType): IAnyType[];
9
+ /**
10
+ * get the type of one of the properties of the given MST model type
11
+ */
7
12
  export declare function getPropertyType(type: IModelReflectionPropertiesData, propertyName: string): IAnyType;
13
+ /**
14
+ * get the default value out of an MST optional type
15
+ */
8
16
  export declare function getDefaultValue(type: IAnyType): any;
9
17
  export type IEnumerationType<T extends string> = ISimpleType<UnionStringArray<T[]>>;
10
- export declare function getEnumerationValues(type: IAnyComplexType): string[];
11
- export declare function resolveLateType(maybeLate: IAnyType): any;
18
+ /** get the string values of an MST enumeration type */
19
+ export declare function getEnumerationValues(type: IAnyType): string[];
20
+ export declare function resolveLateType(maybeLate: IAnyType): IAnyType;
21
+ export { getUnionSubtypes as getUnionSubTypes } from '@jbrowse/mobx-state-tree';
@@ -1,54 +1,55 @@
1
- import { isArrayType, isLateType, isMapType, isOptionalType, isUnionType, } from '@jbrowse/mobx-state-tree';
2
- export function getSubType(type) {
3
- let t;
4
- if (isOptionalType(type)) {
5
- t = type._subtype || type.type;
6
- }
7
- else if (isArrayType(type) || isMapType(type)) {
8
- t = type._subtype || type._subType || type.subType;
9
- }
10
- else if (typeof type.getSubType === 'function') {
11
- return type.getSubType();
12
- }
13
- else {
14
- throw new TypeError('unsupported mst type');
15
- }
16
- if (!t) {
17
- throw new Error('failed to get subtype');
18
- }
19
- return t;
1
+ import { getUnionSubtypes, isArrayType, isLateType, isMapType, isOptionalType, isUnionType, } from '@jbrowse/mobx-state-tree';
2
+ // MST's getSubTypes() returns this sentinel string when a type can't report a
3
+ // single subtype. It isn't exported by name, so we detect it structurally: a
4
+ // real subtype is an IAnyType object, never a string or null.
5
+ function isSubtype(t) {
6
+ return typeof t === 'object' && t !== null;
20
7
  }
21
- export function getUnionSubTypes(unionType) {
22
- if (!isUnionType(unionType)) {
23
- throw new TypeError('not an MST union type');
8
+ /**
9
+ * get the inner type of an MST optional, refinement, array, map, or late type
10
+ */
11
+ export function getSubType(type) {
12
+ // optional/refinement/late report their wrapped type here; union returns an
13
+ // array (handled by getUnionSubTypes) and array/map return null
14
+ const sub = type.getSubTypes();
15
+ if (isSubtype(sub)) {
16
+ return sub;
24
17
  }
25
- const t = unionType._types ||
26
- unionType.types ||
27
- getSubType(unionType)._types ||
28
- getSubType(unionType).types;
29
- if (!t) {
30
- throw new Error('failed to extract subtypes from mst union');
18
+ if (isArrayType(type) || isMapType(type)) {
19
+ return type.getChildType();
31
20
  }
32
- return t;
21
+ throw new TypeError('unsupported mst type');
33
22
  }
23
+ /**
24
+ * get the type of one of the properties of the given MST model type
25
+ */
34
26
  export function getPropertyType(type, propertyName) {
35
27
  return type.properties[propertyName];
36
28
  }
29
+ /**
30
+ * get the default value out of an MST optional type
31
+ */
37
32
  export function getDefaultValue(type) {
38
33
  if (!isOptionalType(type)) {
39
34
  throw new TypeError('type must be an optional type');
40
35
  }
41
- return type._defaultValue || type.defaultValue;
36
+ // isOptionalType is a same-type guard, so narrow to the optional interface
37
+ // that publishes getDefaultInstanceOrSnapshot
38
+ return type.getDefaultInstanceOrSnapshot();
42
39
  }
40
+ /** get the string values of an MST enumeration type */
43
41
  export function getEnumerationValues(type) {
44
- const subtypes = getUnionSubTypes(type);
42
+ const subtypes = getUnionSubtypes(type);
43
+ // the subtypes should all be literals with a value member
45
44
  return subtypes.map(t => t.value);
46
45
  }
47
46
  export function resolveLateType(maybeLate) {
48
47
  if (!isUnionType(maybeLate) &&
49
48
  !isArrayType(maybeLate) &&
50
49
  isLateType(maybeLate)) {
51
- return maybeLate.getSubType();
50
+ const sub = maybeLate.getSubTypes();
51
+ return isSubtype(sub) ? sub : maybeLate;
52
52
  }
53
53
  return maybeLate;
54
54
  }
55
+ export { getUnionSubtypes as getUnionSubTypes } from '@jbrowse/mobx-state-tree';
@@ -0,0 +1,100 @@
1
+ import type PluginManager from '../PluginManager.ts';
2
+ import type { AbstractDisplayModel, AbstractSessionModel, AbstractViewContainer, AbstractTrackModel, AbstractViewModel } from './types/index.ts';
3
+ import type { AssemblyHost, RenderingServices } from './types/renderingServices.ts';
4
+ import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
5
+ export { findParentThat, findParentThatIs, getRpcSessionId, } from './parentWalk.ts';
6
+ /**
7
+ * #api core/util
8
+ * Returns the JBrowse session model for any node in the state tree. Throws if
9
+ * the node has no session ancestor.
10
+ */
11
+ export declare function getSession(node: IAnyStateTreeNode): AbstractSessionModel;
12
+ /**
13
+ * #api core/util
14
+ * Returns the view model that contains the given node. Throws if the node has no
15
+ * containing view.
16
+ */
17
+ export declare function getContainingView(node: IAnyStateTreeNode): AbstractViewModel;
18
+ /**
19
+ * #api core/util
20
+ * Returns the track model that contains the given node. Throws if the node has
21
+ * no containing track.
22
+ */
23
+ export declare function getContainingTrack(node: IAnyStateTreeNode): AbstractTrackModel;
24
+ /**
25
+ * #api core/util
26
+ * Returns the display model that contains the given node. Throws if the node has
27
+ * no containing display.
28
+ */
29
+ export declare function getContainingDisplay(node: IAnyStateTreeNode): AbstractDisplayModel;
30
+ /**
31
+ * #api core/util
32
+ * The host's assembly manager, for a module that resolves names and nothing
33
+ * else.
34
+ *
35
+ * Unlike the accessors in `sessionServices.ts` this one buys the caller no
36
+ * smaller type graph — an `AssemblyManager` is an MST model a `PluginManager`
37
+ * built, so naming it costs what naming a session costs. It is here to say
38
+ * which service is wanted, and because that cost is the finding: the assembly
39
+ * manager is the one thing on `AbstractSessionModel` a third-party host cannot
40
+ * simply implement.
41
+ */
42
+ export declare function getAssemblyHost(node: IAnyStateTreeNode): AssemblyHost;
43
+ /**
44
+ * #api core/util
45
+ * Everything a display needs of its host in order to draw a region: the
46
+ * assemblies, the RPC entry point and the colors.
47
+ */
48
+ export declare function getRenderingServices(node: IAnyStateTreeNode): RenderingServices;
49
+ /**
50
+ * #api core/util
51
+ * Resolve user-authored refName text against the assembly of the view
52
+ * containing `node` — the one normalization layer, which resolves aliases and
53
+ * casing together. Falls back to the input when the assembly is absent or its
54
+ * aliases have not loaded.
55
+ *
56
+ * Keyed off the VIEW's assembly rather than the track's, because the view is
57
+ * what the comparison is against: displayed regions, loaded regions and blocks
58
+ * all carry the refNames the view laid out.
59
+ *
60
+ * Reach for this wherever a refName a *person* wrote is about to be compared
61
+ * against regions, features or blocks, which carry the assembly's canonical
62
+ * name. A refName a display copied off a region is canonical already and needs
63
+ * nothing; one that arrived in a session spec, a config slot or a URL is
64
+ * whatever the author read out of the location box.
65
+ *
66
+ * Skipping it fails silently and, worse, assembly-dependently: `chr12` matches
67
+ * on an assembly canonicalized `chr12` and matches nothing on one canonicalized
68
+ * `12`, so the same spec key works on one config and quietly does nothing on
69
+ * the next, with no error for anyone to act on.
70
+ *
71
+ * Resolves through `getCanonicalRefName2`, whose fallback is what keeps a spec
72
+ * read before the alias file has loaded from throwing — and the getters that
73
+ * read user specs do run from the first render.
74
+ *
75
+ * Takes a refName, not a spec that might hold one: the resolver reads
76
+ * `refName.toLowerCase()`, so anything else throws once the aliases are there,
77
+ * and a caller reading an untyped `frozen` slot has to establish that it names
78
+ * a refName at all before this is the right question to ask of it.
79
+ */
80
+ export declare function canonicalizeViewRefName(node: IAnyStateTreeNode, refName: string): string;
81
+ /**
82
+ * #api core/util
83
+ * Returns the MST environment for a node, which carries the `pluginManager`.
84
+ */
85
+ export declare function getEnv(obj: IAnyStateTreeNode): {
86
+ pluginManager: PluginManager;
87
+ };
88
+ /**
89
+ * #api core/util
90
+ * `addOrReplaceView` for view types whose state model may be lazily loaded;
91
+ * the synchronous `addOrReplaceView` requires it loaded already.
92
+ */
93
+ export declare function launchOrReplaceView(args: {
94
+ session: AbstractViewContainer;
95
+ typeName: string;
96
+ initialState?: Record<string, unknown>;
97
+ replacing?: AbstractViewModel;
98
+ }): Promise<AbstractViewModel>;
99
+ export declare function hashCode(str: string): number;
100
+ export declare function objectHash(obj: object): string;
@@ -0,0 +1,140 @@
1
+ import { getEnv as getEnvMST, isStateTreeNode } from '@jbrowse/mobx-state-tree';
2
+ import { cachedParent, findParentThatIs } from './parentWalk.js';
3
+ import { addOrReplaceView, isDisplayModel, isSessionModel, isTrackModel, isViewModel, } from './types/index.js';
4
+ export { findParentThat, findParentThatIs, getRpcSessionId, } from './parentWalk.js';
5
+ const containingDisplayCache = new WeakMap();
6
+ const containingTrackCache = new WeakMap();
7
+ const containingViewCache = new WeakMap();
8
+ const sessionCache = new WeakMap();
9
+ /**
10
+ * #api core/util
11
+ * Returns the JBrowse session model for any node in the state tree. Throws if
12
+ * the node has no session ancestor.
13
+ */
14
+ export function getSession(node) {
15
+ return cachedParent(sessionCache, node, () => findParentThatIs(node, isSessionModel), 'no session model found!');
16
+ }
17
+ /**
18
+ * #api core/util
19
+ * Returns the view model that contains the given node. Throws if the node has no
20
+ * containing view.
21
+ */
22
+ export function getContainingView(node) {
23
+ return cachedParent(containingViewCache, node, () => findParentThatIs(node, isViewModel), 'no containing view found');
24
+ }
25
+ /**
26
+ * #api core/util
27
+ * Returns the track model that contains the given node. Throws if the node has
28
+ * no containing track.
29
+ */
30
+ export function getContainingTrack(node) {
31
+ return cachedParent(containingTrackCache, node, () => findParentThatIs(node, isTrackModel), 'no containing track found');
32
+ }
33
+ /**
34
+ * #api core/util
35
+ * Returns the display model that contains the given node. Throws if the node has
36
+ * no containing display.
37
+ */
38
+ export function getContainingDisplay(node) {
39
+ return cachedParent(containingDisplayCache, node, () => findParentThatIs(node, isDisplayModel), 'no containing display found');
40
+ }
41
+ /**
42
+ * #api core/util
43
+ * The host's assembly manager, for a module that resolves names and nothing
44
+ * else.
45
+ *
46
+ * Unlike the accessors in `sessionServices.ts` this one buys the caller no
47
+ * smaller type graph — an `AssemblyManager` is an MST model a `PluginManager`
48
+ * built, so naming it costs what naming a session costs. It is here to say
49
+ * which service is wanted, and because that cost is the finding: the assembly
50
+ * manager is the one thing on `AbstractSessionModel` a third-party host cannot
51
+ * simply implement.
52
+ */
53
+ export function getAssemblyHost(node) {
54
+ return getSession(node);
55
+ }
56
+ /**
57
+ * #api core/util
58
+ * Everything a display needs of its host in order to draw a region: the
59
+ * assemblies, the RPC entry point and the colors.
60
+ */
61
+ export function getRenderingServices(node) {
62
+ return getSession(node);
63
+ }
64
+ /**
65
+ * #api core/util
66
+ * Resolve user-authored refName text against the assembly of the view
67
+ * containing `node` — the one normalization layer, which resolves aliases and
68
+ * casing together. Falls back to the input when the assembly is absent or its
69
+ * aliases have not loaded.
70
+ *
71
+ * Keyed off the VIEW's assembly rather than the track's, because the view is
72
+ * what the comparison is against: displayed regions, loaded regions and blocks
73
+ * all carry the refNames the view laid out.
74
+ *
75
+ * Reach for this wherever a refName a *person* wrote is about to be compared
76
+ * against regions, features or blocks, which carry the assembly's canonical
77
+ * name. A refName a display copied off a region is canonical already and needs
78
+ * nothing; one that arrived in a session spec, a config slot or a URL is
79
+ * whatever the author read out of the location box.
80
+ *
81
+ * Skipping it fails silently and, worse, assembly-dependently: `chr12` matches
82
+ * on an assembly canonicalized `chr12` and matches nothing on one canonicalized
83
+ * `12`, so the same spec key works on one config and quietly does nothing on
84
+ * the next, with no error for anyone to act on.
85
+ *
86
+ * Resolves through `getCanonicalRefName2`, whose fallback is what keeps a spec
87
+ * read before the alias file has loaded from throwing — and the getters that
88
+ * read user specs do run from the first render.
89
+ *
90
+ * Takes a refName, not a spec that might hold one: the resolver reads
91
+ * `refName.toLowerCase()`, so anything else throws once the aliases are there,
92
+ * and a caller reading an untyped `frozen` slot has to establish that it names
93
+ * a refName at all before this is the right question to ask of it.
94
+ */
95
+ export function canonicalizeViewRefName(node, refName) {
96
+ const { assemblyManager } = getSession(node);
97
+ const name = getContainingView(node).assemblyNames?.[0];
98
+ const assembly = name ? assemblyManager.get(name) : undefined;
99
+ return assembly?.getCanonicalRefName2(refName) ?? refName;
100
+ }
101
+ /**
102
+ * #api core/util
103
+ * Returns the MST environment for a node, which carries the `pluginManager`.
104
+ */
105
+ export function getEnv(obj) {
106
+ return getEnvMST(obj);
107
+ }
108
+ /**
109
+ * #api core/util
110
+ * `addOrReplaceView` for view types whose state model may be lazily loaded;
111
+ * the synchronous `addOrReplaceView` requires it loaded already.
112
+ */
113
+ export async function launchOrReplaceView(args) {
114
+ // a test's fake session is not an MST node; addView's own guard is the
115
+ // error path there
116
+ if (isStateTreeNode(args.session)) {
117
+ const { pluginManager } = getEnvMST(args.session);
118
+ await pluginManager?.getViewType(args.typeName).loadStateModel();
119
+ // the displays of the tracks a launch opens with are dynamic imports too
120
+ await pluginManager?.preloadSessionTypes({
121
+ views: [{ type: args.typeName, ...args.initialState }],
122
+ });
123
+ }
124
+ return addOrReplaceView(args);
125
+ }
126
+ export function hashCode(str) {
127
+ let hash = 0;
128
+ if (str.length === 0) {
129
+ return hash;
130
+ }
131
+ for (let i = 0; i < str.length; i++) {
132
+ const chr = str.charCodeAt(i);
133
+ hash = (hash << 5) - hash + chr;
134
+ hash |= 0;
135
+ }
136
+ return hash;
137
+ }
138
+ export function objectHash(obj) {
139
+ return `${hashCode(JSON.stringify(obj))}`;
140
+ }
@@ -1,5 +1 @@
1
- export declare const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
2
- export declare const random: (bytes: number) => Uint8Array<ArrayBuffer>;
3
- export declare const customRandom: (alphabet: string, defaultSize: number, getRandom: (bytes: number) => Uint8Array) => (size?: number) => string;
4
- export declare const customAlphabet: (alphabet: string, size?: number) => (size?: number) => string;
5
1
  export declare const nanoid: (size?: number) => string;
@@ -1,29 +1,19 @@
1
- export const urlAlphabet = 'useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict';
2
- export const random = (bytes) => crypto.getRandomValues(new Uint8Array(bytes));
3
- export const customRandom = (alphabet, defaultSize, getRandom) => {
4
- const mask = (2 << (Math.log(alphabet.length - 1) / Math.LN2)) - 1;
5
- const step = -~((1.6 * mask * defaultSize) / alphabet.length);
6
- return (size = defaultSize) => {
7
- let id = '';
8
- while (true) {
9
- const bytes = getRandom(step);
10
- let j = step;
11
- while (j--) {
12
- id += alphabet[bytes[j] & mask] || '';
13
- if (id.length === size) {
14
- return id;
15
- }
16
- }
17
- }
18
- };
19
- };
20
- export const customAlphabet = (alphabet, size = 21) => customRandom(alphabet, size, random);
1
+ // The web-crypto branch of nanoid (https://github.com/ai/nanoid, MIT), reduced
2
+ // to the one generator we call. The custom-alphabet machinery was carried along
3
+ // unused; restore it from upstream if a non-default alphabet is ever needed.
21
4
  export const nanoid = (size = 21) => crypto.getRandomValues(new Uint8Array(size)).reduce((id, byte) => {
5
+ // It is incorrect to use bytes exceeding the alphabet size.
6
+ // The following mask reduces the random byte in the 0-255 value
7
+ // range to the 0-63 value range. Therefore, adding hacks, such
8
+ // as empty string fallback or magic numbers, is unnecessary because
9
+ // the bitmask trims bytes down to the alphabet size.
22
10
  byte &= 63;
23
11
  if (byte < 36) {
12
+ // `0-9a-z`
24
13
  id += byte.toString(36);
25
14
  }
26
15
  else if (byte < 62) {
16
+ // `A-Z`
27
17
  id += (byte - 26).toString(36).toUpperCase();
28
18
  }
29
19
  else if (byte > 62) {
@@ -0,0 +1,20 @@
1
+ export declare function clamp(num: number, min: number, max: number): number;
2
+ export declare function minmax(a: number, b: number): readonly [number, number];
3
+ export declare function max(arr: ArrayLike<number>, init?: number): number;
4
+ export declare function maxFinite(arr: ArrayLike<number>, init?: number): number;
5
+ export declare function min(arr: ArrayLike<number>, init?: number): number;
6
+ export declare function sum(arr: ArrayLike<number>): number;
7
+ export declare function avg(arr: ArrayLike<number>): number;
8
+ export declare function setNumberGrouping(enabled: boolean): void;
9
+ export declare function getNumberGrouping(): boolean;
10
+ export declare function toLocale(n: number): string;
11
+ export declare function toPrecision(s: number, n?: number): number;
12
+ export declare function reducePrecision(s: number, n?: number): string;
13
+ /**
14
+ * A byte count as a person reads it. Shared by the region-too-large banner and
15
+ * the save-track-data dialog, which quote the same index estimate and would
16
+ * otherwise word the same number two ways.
17
+ */
18
+ export declare function getDisplayStr(totalBytes: number): string;
19
+ export declare function radToDeg(radians: number): number;
20
+ export declare function polarToCartesian(rho: number, theta: number): [number, number];
@@ -0,0 +1,127 @@
1
+ export function clamp(num, min, max) {
2
+ if (num < min) {
3
+ return min;
4
+ }
5
+ if (num > max) {
6
+ return max;
7
+ }
8
+ return num;
9
+ }
10
+ export function minmax(a, b) {
11
+ return [Math.min(a, b), Math.max(a, b)];
12
+ }
13
+ // Index iteration so these accept both arrays and typed arrays (e.g.
14
+ // Float32Array) without requiring Iterable.
15
+ export function max(arr, init = Number.NEGATIVE_INFINITY) {
16
+ let max = init;
17
+ for (let i = 0; i < arr.length; i++) {
18
+ max = Math.max(arr[i], max);
19
+ }
20
+ return max;
21
+ }
22
+ // Like max() but skips NaN/Infinity entries rather than propagating them (a
23
+ // single NaN poisons Math.max). Used where an array can legitimately carry
24
+ // gaps, e.g. a score series with unmeasured bins in it.
25
+ export function maxFinite(arr, init = Number.NEGATIVE_INFINITY) {
26
+ let max = init;
27
+ for (let i = 0; i < arr.length; i++) {
28
+ const v = arr[i];
29
+ if (Number.isFinite(v) && v > max) {
30
+ max = v;
31
+ }
32
+ }
33
+ return max;
34
+ }
35
+ export function min(arr, init = Number.POSITIVE_INFINITY) {
36
+ let min = init;
37
+ for (let i = 0; i < arr.length; i++) {
38
+ min = Math.min(arr[i], min);
39
+ }
40
+ return min;
41
+ }
42
+ export function sum(arr) {
43
+ let sum = 0;
44
+ for (let i = 0; i < arr.length; i++) {
45
+ sum += arr[i];
46
+ }
47
+ return sum;
48
+ }
49
+ export function avg(arr) {
50
+ return sum(arr) / arr.length;
51
+ }
52
+ // Thousand separators are a display convention, not part of the number. They
53
+ // make a coordinate readable, but they survive a copy-paste into tools that
54
+ // then choke on them, so users who copy coordinates out of the app more than
55
+ // they read them can turn them off (the `numberGrouping` preference).
56
+ //
57
+ // A plain variable rather than an observable, because every number the app
58
+ // displays funnels through here — including strings built worker-side, where a
59
+ // jexl `mouseover` slot formats a tooltip against the full feature. A
60
+ // main-thread-only reactive value would leave those stale, so the app would sit
61
+ // half-formatted until every track refetched. Instead each realm sets this once
62
+ // at startup (the worker gets it in its boot configuration, see RpcManager) and
63
+ // the preference asks for a reload, which buys uniformity for one page load.
64
+ let numberGrouping = true;
65
+ export function setNumberGrouping(enabled) {
66
+ numberGrouping = enabled;
67
+ }
68
+ // read when handing the setting to another realm; not a display path
69
+ export function getNumberGrouping() {
70
+ return numberGrouping;
71
+ }
72
+ // Fast number formatter with thousand separators.
73
+ // Benchmarked at 5-67x faster than toLocaleString('en-US')
74
+ export function toLocale(n) {
75
+ const abs = Math.abs(n);
76
+ // `!(abs >= 1000)` also covers NaN, which has no digits to group, and
77
+ // String() switches to exponential form at 1e21 and for Infinity, where a
78
+ // thousands separator is meaningless
79
+ if (!numberGrouping || !(abs >= 1000) || abs >= 1e21) {
80
+ return String(n);
81
+ }
82
+ const str = String(abs);
83
+ // separators count from the decimal point, not the end of the string
84
+ const intLen = Number.isInteger(abs) ? str.length : str.indexOf('.');
85
+ let result = n < 0 ? '-' : '';
86
+ for (let i = 0; i < intLen; i++) {
87
+ if (i > 0 && (intLen - i) % 3 === 0) {
88
+ result += ',';
89
+ }
90
+ result += str[i];
91
+ }
92
+ return intLen === str.length ? result : result + str.slice(intLen);
93
+ }
94
+ // numeric significant-figure rounding; reducePrecision is the formatted form
95
+ export function toPrecision(s, n = 3) {
96
+ return Number.parseFloat(s.toPrecision(n));
97
+ }
98
+ export function reducePrecision(s, n = 3) {
99
+ return toLocale(toPrecision(s, n));
100
+ }
101
+ /**
102
+ * A byte count as a person reads it. Shared by the region-too-large banner and
103
+ * the save-track-data dialog, which quote the same index estimate and would
104
+ * otherwise word the same number two ways.
105
+ */
106
+ export function getDisplayStr(totalBytes) {
107
+ // pick the unit from the rounded value so e.g. 999,999 bytes reads "1 Mb"
108
+ // rather than "1000 Kb"
109
+ const mb = toPrecision(totalBytes / 1_000_000);
110
+ const kb = toPrecision(totalBytes / 1000);
111
+ if (mb >= 1) {
112
+ return `${mb} Mb`;
113
+ }
114
+ else if (kb >= 1) {
115
+ return `${kb} Kb`;
116
+ }
117
+ else {
118
+ return `${Math.floor(totalBytes)} bytes`;
119
+ }
120
+ }
121
+ const oneEightyOverPi = 180 / Math.PI;
122
+ export function radToDeg(radians) {
123
+ return (radians * oneEightyOverPi) % 360;
124
+ }
125
+ export function polarToCartesian(rho, theta) {
126
+ return [rho * Math.cos(theta), rho * Math.sin(theta)];
127
+ }
@@ -0,0 +1,2 @@
1
+ export declare function isObject(x: unknown): x is Record<string | symbol | number, unknown>;
2
+ export declare function isPlainObject(x: unknown): x is Record<string, unknown>;
@@ -0,0 +1,9 @@
1
+ // MIT https://github.com/inspect-js/is-object
2
+ export function isObject(x) {
3
+ return typeof x === 'object' && x !== null;
4
+ }
5
+ // `isObject` minus arrays: the branch `deepEqual` and `deepMerge` recurse into
6
+ // key by key, as opposed to the one they walk by index.
7
+ export function isPlainObject(x) {
8
+ return isObject(x) && !Array.isArray(x);
9
+ }
@@ -1,5 +1,6 @@
1
- export { collectTransferables, isDetachedBuffer } from './transferables.ts';
2
- export declare function isImageBitmap(value: unknown): value is ImageBitmap;
1
+ /**
2
+ * Paint a worker-produced image onto a 2d context: either a real
3
+ * ImageBitmap/canvas, or the serialized canvas-sequencer command list a worker
4
+ * without OffscreenCanvas sends instead.
5
+ */
3
6
  export declare function drawImageOntoCanvasContext(imageData: any, context: CanvasRenderingContext2D): void;
4
- export declare function createCanvas(width: number, height: number): any;
5
- export declare function createImageBitmap(canvas: any): Promise<unknown>;