@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  315. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +26 -8
  316. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  317. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +31 -17
  318. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  319. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +142 -65
  320. package/esm/pluggableElementTypes/models/baseTrackConfig.js +215 -90
  321. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  322. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +111 -139
  323. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +54 -0
  324. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  325. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +50 -0
  326. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +147 -0
  327. package/esm/pluggableElementTypes/models/index.d.ts +5 -3
  328. package/esm/pluggableElementTypes/models/index.js +9 -8
  329. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +48 -0
  330. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +114 -0
  331. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  332. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +10 -3
  333. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +272 -100
  334. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  335. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  336. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  337. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  338. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  339. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
  340. package/esm/pluggableElementTypes/models/uriMatchesDomains.js +62 -0
  341. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts +5 -4
  342. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +20 -10
  343. package/esm/pluginDefinitions.d.ts +225 -0
  344. package/esm/pluginDefinitions.js +254 -0
  345. package/esm/rpc/BaseRpcDriver.d.ts +27 -35
  346. package/esm/rpc/BaseRpcDriver.js +68 -106
  347. package/esm/rpc/MainThreadRpcDriver.d.ts +9 -10
  348. package/esm/rpc/MainThreadRpcDriver.js +23 -29
  349. package/esm/rpc/RpcClient.d.ts +50 -0
  350. package/esm/rpc/RpcClient.js +189 -0
  351. package/esm/rpc/RpcManager.d.ts +120 -27
  352. package/esm/rpc/RpcManager.js +187 -50
  353. package/esm/rpc/RpcRegistry.d.ts +298 -0
  354. package/esm/rpc/RpcServer.d.ts +43 -0
  355. package/esm/rpc/RpcServer.js +242 -0
  356. package/esm/rpc/WebWorkerRpcDriver.d.ts +78 -24
  357. package/esm/rpc/WebWorkerRpcDriver.js +311 -30
  358. package/esm/rpc/byteBudget.d.ts +64 -0
  359. package/esm/rpc/byteBudget.js +61 -0
  360. package/esm/rpc/configSchema.d.ts +13 -5
  361. package/esm/rpc/configSchema.js +40 -16
  362. package/esm/rpc/coreRpcMethods.d.ts +6 -5
  363. package/esm/rpc/coreRpcMethods.js +13 -12
  364. package/esm/rpc/explainTransferError.d.ts +35 -0
  365. package/esm/rpc/explainTransferError.js +158 -0
  366. package/esm/rpc/methods/CoreFreeResources.d.ts +19 -4
  367. package/esm/rpc/methods/CoreFreeResources.js +17 -6
  368. package/esm/rpc/methods/CoreGetEncodedFeature.d.ts +13 -0
  369. package/esm/rpc/methods/CoreGetEncodedFeature.js +32 -0
  370. package/esm/rpc/methods/CoreGetEncodedLayers.d.ts +16 -0
  371. package/esm/rpc/methods/CoreGetEncodedLayers.js +59 -0
  372. package/esm/rpc/methods/CoreGetExportData.d.ts +5 -18
  373. package/esm/rpc/methods/CoreGetExportData.js +25 -15
  374. package/esm/rpc/methods/CoreGetFeatureDensity.d.ts +11 -0
  375. package/esm/rpc/methods/CoreGetFeatureDensity.js +22 -0
  376. package/esm/rpc/methods/CoreGetFeatures.d.ts +6 -15
  377. package/esm/rpc/methods/CoreGetFeatures.js +14 -18
  378. package/esm/rpc/methods/CoreGetInfo.d.ts +6 -0
  379. package/esm/rpc/methods/CoreGetInfo.js +12 -0
  380. package/esm/rpc/methods/CoreGetMetadata.d.ts +4 -7
  381. package/esm/rpc/methods/CoreGetMetadata.js +6 -9
  382. package/esm/rpc/methods/CoreGetRefNames.d.ts +4 -8
  383. package/esm/rpc/methods/CoreGetRefNames.js +16 -15
  384. package/esm/rpc/methods/CoreGetRegionByteEstimate.d.ts +6 -0
  385. package/esm/rpc/methods/CoreGetRegionByteEstimate.js +19 -0
  386. package/esm/rpc/methods/CoreGetRegions.d.ts +4 -6
  387. package/esm/rpc/methods/CoreGetRegions.js +6 -9
  388. package/esm/rpc/methods/CoreGetSequence.d.ts +4 -11
  389. package/esm/rpc/methods/CoreGetSequence.js +12 -13
  390. package/esm/rpc/methods/CoreLoadAdapterCode.d.ts +13 -0
  391. package/esm/rpc/methods/CoreLoadAdapterCode.js +16 -0
  392. package/esm/rpc/methods/layerFeatures.d.ts +33 -0
  393. package/esm/rpc/methods/layerFeatures.js +29 -0
  394. package/esm/rpc/serializeError/index.d.ts +9 -0
  395. package/esm/rpc/serializeError/index.js +86 -0
  396. package/esm/svg/SvgExport.d.ts +30 -0
  397. package/esm/svg/SvgExport.js +52 -0
  398. package/esm/svg/SvgThemeProviders.d.ts +12 -0
  399. package/esm/svg/SvgThemeProviders.js +15 -0
  400. package/esm/svg/constants.d.ts +1 -0
  401. package/esm/svg/constants.js +5 -0
  402. package/esm/svg/exportViewSvg.d.ts +28 -0
  403. package/esm/svg/exportViewSvg.js +13 -0
  404. package/esm/svg/normalizeSvgMarkup.d.ts +7 -0
  405. package/esm/svg/normalizeSvgMarkup.js +99 -0
  406. package/esm/svg/saveSvgAsImage.d.ts +6 -0
  407. package/esm/svg/saveSvgAsImage.js +90 -0
  408. package/esm/svg/serializeSvg.d.ts +7 -0
  409. package/esm/svg/serializeSvg.js +11 -0
  410. package/esm/svg/svgId.d.ts +42 -0
  411. package/esm/svg/svgId.js +84 -0
  412. package/esm/svg/svgReady.d.ts +138 -0
  413. package/esm/svg/svgReady.js +165 -0
  414. package/esm/svg/trackNames.d.ts +29 -0
  415. package/esm/svg/trackNames.js +34 -0
  416. package/esm/svg/wrapSvgExport.d.ts +12 -0
  417. package/esm/svg/wrapSvgExport.js +10 -0
  418. package/esm/ui/ActionLink.d.ts +7 -0
  419. package/esm/ui/ActionLink.js +9 -0
  420. package/esm/ui/AddCustomPluginDialog.d.ts +14 -0
  421. package/esm/ui/AddCustomPluginDialog.js +56 -0
  422. package/esm/ui/AddGenomePane.d.ts +8 -0
  423. package/esm/ui/AddGenomePane.js +228 -0
  424. package/esm/ui/AdvancedOptions.d.ts +6 -0
  425. package/esm/ui/AdvancedOptions.js +17 -0
  426. package/esm/ui/AppLogo.d.ts +1 -1
  427. package/esm/ui/AppLogo.js +2 -2
  428. package/esm/ui/AppReadyMarker.d.ts +45 -0
  429. package/esm/ui/AppReadyMarker.js +89 -0
  430. package/esm/ui/AssemblySelector.d.ts +5 -8
  431. package/esm/ui/AssemblySelector.js +8 -26
  432. package/esm/ui/BaseExportSvgDialog.d.ts +16 -0
  433. package/esm/ui/BaseExportSvgDialog.js +84 -0
  434. package/esm/ui/BaseTooltip.d.ts +14 -3
  435. package/esm/ui/BaseTooltip.js +151 -34
  436. package/esm/ui/CascadingMenu.d.ts +9 -18
  437. package/esm/ui/CascadingMenu.js +446 -42
  438. package/esm/ui/CascadingMenuButton.d.ts +9 -11
  439. package/esm/ui/CascadingMenuButton.js +36 -18
  440. package/esm/ui/CascadingMenuHelpDialog.d.ts +2 -2
  441. package/esm/ui/CascadingMenuHelpDialog.js +4 -5
  442. package/esm/ui/CascadingMenuHelpIconButton.d.ts +2 -1
  443. package/esm/ui/CascadingMenuHelpIconButton.js +18 -9
  444. package/esm/ui/ColorPicker.d.ts +6 -9
  445. package/esm/ui/ColorPicker.js +36 -39
  446. package/esm/ui/ConfirmDialog.d.ts +2 -9
  447. package/esm/ui/ConfirmDialog.js +6 -9
  448. package/esm/ui/ContextMenu.d.ts +50 -0
  449. package/esm/ui/ContextMenu.js +55 -0
  450. package/esm/ui/CopyToClipboardButton.d.ts +10 -0
  451. package/esm/ui/CopyToClipboardButton.js +14 -0
  452. package/esm/ui/Crosshairs.d.ts +10 -0
  453. package/esm/ui/Crosshairs.js +15 -0
  454. package/esm/ui/DOMPurifySanitizedHTML.d.ts +1 -1
  455. package/esm/ui/DOMPurifySanitizedHTML.js +5 -5
  456. package/esm/ui/DataGridFlexContainer.d.ts +9 -2
  457. package/esm/ui/DataGridFlexContainer.js +4 -3
  458. package/esm/ui/Dialog.d.ts +5 -2
  459. package/esm/ui/Dialog.js +35 -27
  460. package/esm/ui/DraggableDialog.d.ts +3 -3
  461. package/esm/ui/DraggableDialog.js +50 -12
  462. package/esm/ui/DropDownMenu.d.ts +4 -2
  463. package/esm/ui/DropDownMenu.js +6 -5
  464. package/esm/ui/EditableTypography.d.ts +3 -1
  465. package/esm/ui/EditableTypography.js +34 -26
  466. package/esm/ui/ErrorActions.d.ts +24 -0
  467. package/esm/ui/ErrorActions.js +20 -0
  468. package/esm/ui/ErrorBanner.d.ts +7 -0
  469. package/esm/ui/ErrorBanner.js +35 -0
  470. package/esm/ui/ErrorBar.d.ts +6 -0
  471. package/esm/ui/ErrorBar.js +35 -0
  472. package/esm/ui/ErrorBoundary.d.ts +29 -5
  473. package/esm/ui/ErrorBoundary.js +32 -2
  474. package/esm/ui/ErrorMessage.d.ts +2 -4
  475. package/esm/ui/ErrorMessage.js +17 -52
  476. package/esm/ui/ErrorMessageStackTraceContents.d.ts +1 -1
  477. package/esm/ui/ErrorMessageStackTraceContents.js +5 -4
  478. package/esm/ui/ErrorMessageStackTraceDialog.d.ts +1 -1
  479. package/esm/ui/ErrorMessageStackTraceDialog.js +51 -96
  480. package/esm/ui/ErrorOverlay.d.ts +8 -0
  481. package/esm/ui/ErrorOverlay.js +5 -0
  482. package/esm/ui/ExportSvgDialog.d.ts +7 -0
  483. package/esm/ui/ExportSvgDialog.js +9 -0
  484. package/esm/ui/ExternalLink.d.ts +1 -1
  485. package/esm/ui/FactoryResetDialog.d.ts +1 -1
  486. package/esm/ui/FactoryResetDialog.js +6 -15
  487. package/esm/ui/FatalErrorDialog.d.ts +3 -2
  488. package/esm/ui/FatalErrorDialog.js +6 -5
  489. package/esm/ui/FileDropZone.d.ts +25 -0
  490. package/esm/ui/FileDropZone.js +129 -0
  491. package/esm/ui/FileSelector/FileSelector.d.ts +1 -1
  492. package/esm/ui/FileSelector/FileSelector.js +59 -30
  493. package/esm/ui/FileSelector/LocalFileChooser.d.ts +7 -2
  494. package/esm/ui/FileSelector/LocalFileChooser.js +61 -47
  495. package/esm/ui/FileSelector/LocationInput.d.ts +1 -1
  496. package/esm/ui/FileSelector/LocationInput.js +8 -12
  497. package/esm/ui/FileSelector/SourceTypeSelector.d.ts +5 -5
  498. package/esm/ui/FileSelector/SourceTypeSelector.js +9 -7
  499. package/esm/ui/FileSelector/UrlChooser.d.ts +1 -1
  500. package/esm/ui/FileSelector/UrlChooser.js +26 -2
  501. package/esm/ui/FileSelector/emptySourceType.d.ts +2 -0
  502. package/esm/ui/FileSelector/emptySourceType.js +14 -0
  503. package/esm/ui/FileSelector/useInternetAccounts.d.ts +436 -64
  504. package/esm/ui/FileSelector/useInternetAccounts.js +13 -6
  505. package/esm/ui/FileSelector/util.d.ts +58 -3
  506. package/esm/ui/FileSelector/util.js +128 -11
  507. package/esm/ui/GpuFallbackButton.d.ts +12 -0
  508. package/esm/ui/GpuFallbackButton.js +20 -0
  509. package/esm/ui/HoverMenu.d.ts +11 -3
  510. package/esm/ui/HoverMenu.js +34 -9
  511. package/esm/ui/HoverTooltip.d.ts +27 -0
  512. package/esm/ui/HoverTooltip.js +24 -0
  513. package/esm/ui/Icons.d.ts +6 -4
  514. package/esm/ui/Icons.js +9 -0
  515. package/esm/ui/InfoDialog.d.ts +7 -0
  516. package/esm/ui/InfoDialog.js +16 -0
  517. package/esm/ui/InlineMenuControls.d.ts +6 -0
  518. package/esm/ui/InlineMenuControls.js +17 -0
  519. package/esm/ui/JexlFilterDialog.d.ts +26 -0
  520. package/esm/ui/JexlFilterDialog.js +167 -0
  521. package/esm/ui/JexlFilterRowEditors.d.ts +15 -0
  522. package/esm/ui/JexlFilterRowEditors.js +90 -0
  523. package/esm/ui/LabeledCheckbox.d.ts +9 -0
  524. package/esm/ui/LabeledCheckbox.js +7 -0
  525. package/esm/ui/LazyBaseTooltip.d.ts +4 -0
  526. package/esm/ui/LazyBaseTooltip.js +9 -0
  527. package/esm/ui/LegendSwatchGlyph.d.ts +7 -0
  528. package/esm/ui/LegendSwatchGlyph.js +30 -0
  529. package/esm/ui/LoadingDots.d.ts +1 -0
  530. package/esm/ui/LoadingDots.js +30 -0
  531. package/esm/ui/LoadingEllipses.d.ts +17 -1
  532. package/esm/ui/LoadingEllipses.js +20 -29
  533. package/esm/ui/LoadingOverlay.d.ts +23 -0
  534. package/esm/ui/LoadingOverlay.js +139 -0
  535. package/esm/ui/LoadingProgress.d.ts +16 -0
  536. package/esm/ui/LoadingProgress.js +16 -0
  537. package/esm/ui/Logo.d.ts +2 -2
  538. package/esm/ui/Logo.js +23 -24
  539. package/esm/ui/Menu.js +1 -1
  540. package/esm/ui/MenuItemChevron.d.ts +3 -0
  541. package/esm/ui/MenuItemChevron.js +19 -0
  542. package/esm/ui/MenuItemEndDecoration.d.ts +4 -0
  543. package/esm/ui/MenuItemEndDecoration.js +28 -0
  544. package/esm/ui/MenuItemTrailing.d.ts +12 -0
  545. package/esm/ui/MenuItemTrailing.js +42 -0
  546. package/esm/ui/MenuTypes.d.ts +95 -5
  547. package/esm/ui/MenuTypes.js +16 -1
  548. package/esm/ui/MonospaceTextField.d.ts +10 -0
  549. package/esm/ui/MonospaceTextField.js +40 -0
  550. package/esm/ui/NumberTextField.d.ts +31 -0
  551. package/esm/ui/NumberTextField.js +33 -0
  552. package/esm/ui/PaletteContext.d.ts +90 -0
  553. package/esm/ui/PaletteContext.js +142 -0
  554. package/esm/ui/PluggableComponent.d.ts +10 -0
  555. package/esm/ui/PluggableComponent.js +19 -0
  556. package/esm/ui/PluggableComponents.d.ts +29 -0
  557. package/esm/ui/PluggableComponents.js +28 -0
  558. package/esm/ui/PluggableElements.d.ts +23 -0
  559. package/esm/ui/PluggableElements.js +24 -0
  560. package/esm/ui/PluginStoreCard.d.ts +17 -0
  561. package/esm/ui/PluginStoreCard.js +45 -0
  562. package/esm/ui/PopoverPicker.d.ts +6 -0
  563. package/esm/ui/PopoverPicker.js +25 -0
  564. package/esm/ui/PrerenderedCanvas.d.ts +1 -1
  565. package/esm/ui/PrerenderedCanvas.js +5 -4
  566. package/esm/ui/ProgressChip.d.ts +37 -0
  567. package/esm/ui/ProgressChip.js +66 -0
  568. package/esm/ui/RedErrorMessageBox.d.ts +1 -1
  569. package/esm/ui/RedErrorMessageBox.js +9 -3
  570. package/esm/ui/RefNameAutocomplete/EndAdornment.d.ts +5 -0
  571. package/esm/ui/RefNameAutocomplete/EndAdornment.js +31 -0
  572. package/esm/ui/RefNameAutocomplete/HelpDialog.d.ts +3 -0
  573. package/esm/ui/RefNameAutocomplete/HelpDialog.js +7 -0
  574. package/esm/ui/RefNameAutocomplete/SearchOption.d.ts +13 -0
  575. package/esm/ui/RefNameAutocomplete/SearchOption.js +45 -0
  576. package/esm/ui/RefNameAutocomplete/index.d.ts +21 -0
  577. package/esm/ui/RefNameAutocomplete/index.js +84 -0
  578. package/esm/ui/RefNameAutocomplete/util.d.ts +62 -0
  579. package/esm/ui/RefNameAutocomplete/util.js +209 -0
  580. package/esm/ui/ReplaceCurrentViewButton.d.ts +19 -0
  581. package/esm/ui/ReplaceCurrentViewButton.js +22 -0
  582. package/esm/ui/ResizeHandle.d.ts +15 -7
  583. package/esm/ui/ResizeHandle.js +73 -53
  584. package/esm/ui/ReturnToImportFormDialog.d.ts +1 -1
  585. package/esm/ui/ReturnToImportFormDialog.js +7 -9
  586. package/esm/ui/SanitizedHTML.d.ts +6 -1
  587. package/esm/ui/SanitizedHTML.js +7 -47
  588. package/esm/ui/ScrollChrome.d.ts +13 -0
  589. package/esm/ui/ScrollChrome.js +11 -0
  590. package/esm/ui/ScrollEdgeShadow.d.ts +41 -0
  591. package/esm/ui/ScrollEdgeShadow.js +77 -0
  592. package/esm/ui/ScrollZoomToggle.d.ts +15 -0
  593. package/esm/ui/ScrollZoomToggle.js +75 -0
  594. package/esm/ui/SequenceAdapterInputs.d.ts +9 -0
  595. package/esm/ui/SequenceAdapterInputs.js +30 -0
  596. package/esm/ui/SessionJsonPanel.d.ts +3 -0
  597. package/esm/ui/SessionJsonPanel.js +14 -0
  598. package/esm/ui/SettingsChangesTable.d.ts +15 -0
  599. package/esm/ui/SettingsChangesTable.js +87 -0
  600. package/esm/ui/ShareLinkField.d.ts +4 -0
  601. package/esm/ui/ShareLinkField.js +15 -0
  602. package/esm/ui/SingleSlider.d.ts +8 -0
  603. package/esm/ui/SingleSlider.js +11 -0
  604. package/esm/ui/SizeSliderRow.d.ts +14 -0
  605. package/esm/ui/SizeSliderRow.js +48 -0
  606. package/esm/ui/SliderTooltip.d.ts +2 -0
  607. package/esm/ui/SliderTooltip.js +17 -0
  608. package/esm/ui/Snackbar.d.ts +4 -2
  609. package/esm/ui/Snackbar.js +11 -8
  610. package/esm/ui/SnackbarContents.d.ts +1 -1
  611. package/esm/ui/SnackbarContents.js +21 -3
  612. package/esm/ui/SnackbarModel.d.ts +40 -0
  613. package/esm/ui/SnackbarModel.js +96 -52
  614. package/esm/ui/StackTraceButton.d.ts +5 -0
  615. package/esm/ui/StackTraceButton.js +16 -0
  616. package/esm/ui/StatusProgressBar.d.ts +37 -0
  617. package/esm/ui/StatusProgressBar.js +76 -0
  618. package/esm/ui/SubmitDialog.d.ts +6 -0
  619. package/esm/ui/SubmitDialog.js +9 -0
  620. package/esm/ui/SubmitForm.d.ts +23 -0
  621. package/esm/ui/SubmitForm.js +23 -0
  622. package/esm/ui/SvgColorLegend.d.ts +18 -0
  623. package/esm/ui/SvgColorLegend.js +106 -0
  624. package/esm/ui/TagTextField.d.ts +40 -0
  625. package/esm/ui/TagTextField.js +32 -0
  626. package/esm/ui/VerticalScrollbar.d.ts +24 -0
  627. package/esm/ui/VerticalScrollbar.js +104 -0
  628. package/esm/ui/ViewLoadingScreen.d.ts +25 -0
  629. package/esm/ui/ViewLoadingScreen.js +52 -0
  630. package/esm/ui/addExtensionElement.d.ts +18 -0
  631. package/esm/ui/addExtensionElement.js +23 -0
  632. package/esm/ui/buildExtraTrackMenuItems.d.ts +22 -0
  633. package/esm/ui/buildExtraTrackMenuItems.js +14 -0
  634. package/esm/ui/colorScale.d.ts +92 -0
  635. package/esm/ui/colorScale.js +72 -0
  636. package/esm/ui/colorSwatchStyle.d.ts +9 -0
  637. package/esm/ui/colorSwatchStyle.js +11 -0
  638. package/esm/ui/colors.d.ts +125 -8
  639. package/esm/ui/colors.js +364 -1
  640. package/esm/ui/extensionSelectors.d.ts +38 -0
  641. package/esm/ui/extensionSelectors.js +49 -0
  642. package/esm/ui/filterMenuItems.d.ts +112 -0
  643. package/esm/ui/filterMenuItems.js +86 -0
  644. package/esm/ui/formatErrorStack.d.ts +1 -0
  645. package/esm/ui/formatErrorStack.js +56 -0
  646. package/esm/ui/gpuFallback.d.ts +33 -0
  647. package/esm/ui/gpuFallback.js +39 -0
  648. package/esm/ui/hoverBoxStyle.d.ts +23 -0
  649. package/esm/ui/hoverBoxStyle.js +28 -0
  650. package/esm/ui/index.d.ts +77 -5
  651. package/esm/ui/index.js +83 -20
  652. package/esm/ui/inlineMenuRowWidth.d.ts +1 -0
  653. package/esm/ui/inlineMenuRowWidth.js +8 -0
  654. package/esm/ui/launchTargetsMenuItem.d.ts +18 -0
  655. package/esm/ui/launchTargetsMenuItem.js +24 -0
  656. package/esm/ui/launchViewMenu.d.ts +4 -0
  657. package/esm/ui/launchViewMenu.js +46 -0
  658. package/esm/ui/legendMenuItem.d.ts +16 -0
  659. package/esm/ui/legendMenuItem.js +17 -0
  660. package/esm/ui/legendSpec.d.ts +69 -0
  661. package/esm/ui/legendSpec.js +69 -0
  662. package/esm/ui/loadingDotKeyframes.d.ts +18 -0
  663. package/esm/ui/loadingDotKeyframes.js +17 -0
  664. package/esm/ui/makeSizeMenu.d.ts +24 -0
  665. package/esm/ui/makeSizeMenu.js +58 -0
  666. package/esm/ui/mapStackTrace.d.ts +8 -0
  667. package/esm/ui/mapStackTrace.js +108 -0
  668. package/esm/ui/measureLegendText.d.ts +1 -0
  669. package/esm/ui/measureLegendText.js +8 -0
  670. package/esm/ui/menuItemAdornment.d.ts +22 -0
  671. package/esm/ui/menuItemAdornment.js +28 -0
  672. package/esm/ui/menuItems.d.ts +23 -0
  673. package/esm/ui/menuItems.js +21 -0
  674. package/esm/ui/menuLabels.d.ts +41 -0
  675. package/esm/ui/menuLabels.js +43 -0
  676. package/esm/ui/multiTrackMenuItems.d.ts +25 -0
  677. package/esm/ui/multiTrackMenuItems.js +15 -0
  678. package/esm/ui/palette.d.ts +561 -0
  679. package/esm/ui/palette.js +785 -0
  680. package/esm/ui/parseError.d.ts +4 -0
  681. package/esm/ui/parseError.js +18 -0
  682. package/esm/ui/persistentScrollbarStyle.d.ts +49 -0
  683. package/esm/ui/persistentScrollbarStyle.js +53 -0
  684. package/esm/ui/radioSubMenu.d.ts +33 -0
  685. package/esm/ui/radioSubMenu.js +32 -0
  686. package/esm/ui/react-colorful.js +5 -1
  687. package/esm/ui/replaceViewAction.d.ts +31 -0
  688. package/esm/ui/replaceViewAction.js +39 -0
  689. package/esm/ui/rewriteExternalAnchors.d.ts +1 -0
  690. package/esm/ui/rewriteExternalAnchors.js +8 -0
  691. package/esm/ui/scrollZoomLabels.d.ts +17 -0
  692. package/esm/ui/scrollZoomLabels.js +22 -0
  693. package/esm/ui/showSubMenu.d.ts +19 -0
  694. package/esm/ui/showSubMenu.js +30 -0
  695. package/esm/ui/sliderScale.d.ts +6 -0
  696. package/esm/ui/sliderScale.js +30 -0
  697. package/esm/ui/statusProgressKeyframes.d.ts +6 -0
  698. package/esm/ui/statusProgressKeyframes.js +14 -0
  699. package/esm/ui/stripStackTraceMessage.d.ts +1 -0
  700. package/esm/ui/stripStackTraceMessage.js +9 -0
  701. package/esm/ui/styleTheme.d.ts +158 -0
  702. package/esm/ui/styleTheme.js +115 -0
  703. package/esm/ui/submenuAim.d.ts +30 -0
  704. package/esm/ui/submenuAim.js +37 -0
  705. package/esm/ui/theme.d.ts +268 -30
  706. package/esm/ui/theme.js +250 -350
  707. package/esm/ui/toggleMenuItems.d.ts +42 -0
  708. package/esm/ui/toggleMenuItems.js +61 -0
  709. package/esm/ui/useAssemblySelection.d.ts +153 -0
  710. package/esm/ui/useAssemblySelection.js +54 -0
  711. package/esm/ui/useCoalescedPointer.d.ts +36 -0
  712. package/esm/ui/useCoalescedPointer.js +60 -0
  713. package/esm/ui/useCopyToClipboard.d.ts +15 -0
  714. package/esm/ui/useCopyToClipboard.js +41 -0
  715. package/esm/ui/useExportSvgPreference.d.ts +1 -0
  716. package/esm/ui/useExportSvgPreference.js +4 -0
  717. package/esm/ui/useMouseTracking.d.ts +71 -0
  718. package/esm/ui/useMouseTracking.js +179 -0
  719. package/esm/ui/useRecentLocations.d.ts +28 -0
  720. package/esm/ui/useRecentLocations.js +31 -0
  721. package/esm/ui/viewHeaderHeight.d.ts +1 -0
  722. package/esm/ui/viewHeaderHeight.js +1 -0
  723. package/esm/ui/wrapComponent.d.ts +47 -0
  724. package/esm/ui/wrapComponent.js +58 -0
  725. package/esm/ui/zIndexes.d.ts +28 -0
  726. package/esm/ui/zIndexes.js +38 -0
  727. package/esm/util/Base1DUtils.d.ts +207 -17
  728. package/esm/util/Base1DUtils.js +316 -173
  729. package/esm/util/Base1DViewModel.d.ts +99 -21
  730. package/esm/util/Base1DViewModel.js +151 -41
  731. package/esm/util/FileSaver/index.d.ts +1 -0
  732. package/esm/util/FileSaver/index.js +27 -0
  733. package/esm/util/IntervalTree.d.ts +18 -39
  734. package/esm/util/IntervalTree.js +63 -244
  735. package/esm/util/SvgCanvas.d.ts +83 -0
  736. package/esm/util/SvgCanvas.js +520 -0
  737. package/esm/util/TimeTraveller.d.ts +12 -0
  738. package/esm/util/TimeTraveller.js +130 -27
  739. package/esm/util/aborting.d.ts +56 -4
  740. package/esm/util/aborting.js +112 -25
  741. package/esm/util/adapterMetadata.d.ts +20 -0
  742. package/esm/util/adapterMetadata.js +40 -0
  743. package/esm/util/addAndShowTrack.d.ts +19 -0
  744. package/esm/util/addAndShowTrack.js +27 -0
  745. package/esm/util/addRelativeUris.d.ts +29 -0
  746. package/esm/util/addRelativeUris.js +78 -0
  747. package/esm/util/addTrackComponent.d.ts +72 -0
  748. package/esm/util/addTrackComponent.js +53 -0
  749. package/esm/util/addTrackFromWidget.d.ts +91 -0
  750. package/esm/util/addTrackFromWidget.js +91 -0
  751. package/esm/util/aggregateFieldName.d.ts +10 -0
  752. package/esm/util/aggregateFieldName.js +8 -0
  753. package/esm/util/analytics.d.ts +32 -3
  754. package/esm/util/analytics.js +135 -49
  755. package/esm/util/animationAllowed.d.ts +26 -0
  756. package/esm/util/animationAllowed.js +35 -0
  757. package/esm/util/applyRowResizeWheel.d.ts +15 -0
  758. package/esm/util/applyRowResizeWheel.js +23 -0
  759. package/esm/util/assemblyConfigUtils.d.ts +144 -0
  760. package/esm/util/assemblyConfigUtils.js +498 -0
  761. package/esm/util/bandHeight.d.ts +63 -0
  762. package/esm/util/bandHeight.js +85 -0
  763. package/esm/util/bandLayout.d.ts +51 -0
  764. package/esm/util/bandLayout.js +36 -0
  765. package/esm/util/bezierConnector.d.ts +15 -0
  766. package/esm/util/bezierConnector.js +101 -0
  767. package/esm/util/bgzfWorkerPool.d.ts +24 -0
  768. package/esm/util/bgzfWorkerPool.js +27 -0
  769. package/esm/util/binnedAggregate.d.ts +17 -0
  770. package/esm/util/binnedAggregate.js +275 -0
  771. package/esm/util/blockTypes.d.ts +64 -45
  772. package/esm/util/blockTypes.js +67 -74
  773. package/esm/util/bpUtils.d.ts +81 -0
  774. package/esm/util/bpUtils.js +103 -0
  775. package/esm/util/cacheBudgets.d.ts +55 -0
  776. package/esm/util/cacheBudgets.js +55 -0
  777. package/esm/util/cachedSetup.d.ts +51 -0
  778. package/esm/util/cachedSetup.js +87 -0
  779. package/esm/util/calculateDynamicBlocks.d.ts +5 -0
  780. package/esm/util/calculateDynamicBlocks.js +85 -82
  781. package/esm/util/calculateStaticBlocks.d.ts +2 -3
  782. package/esm/util/calculateStaticBlocks.js +48 -71
  783. package/esm/util/categoricalField.d.ts +56 -0
  784. package/esm/util/categoricalField.js +73 -0
  785. package/esm/util/chooseGridPitch.d.ts +9 -0
  786. package/esm/util/chooseGridPitch.js +31 -0
  787. package/esm/util/clampToContig.d.ts +43 -0
  788. package/esm/util/clampToContig.js +47 -0
  789. package/esm/util/cmpStr.d.ts +1 -0
  790. package/esm/util/cmpStr.js +7 -0
  791. package/esm/util/coarseStripHTML.js +2 -15
  792. package/esm/util/color/cssColorsLevel4.d.ts +1 -0
  793. package/esm/util/color/cssColorsLevel4.js +7 -2
  794. package/esm/util/color/index.d.ts +84 -3
  795. package/esm/util/color/index.js +197 -25
  796. package/esm/util/color-bits/bit.d.ts +4 -0
  797. package/esm/util/color-bits/bit.js +37 -0
  798. package/esm/util/color-bits/convert.d.ts +23 -0
  799. package/esm/util/color-bits/convert.js +294 -0
  800. package/esm/util/color-bits/core.d.ts +34 -0
  801. package/esm/util/color-bits/core.js +67 -0
  802. package/esm/util/color-bits/format.d.ts +24 -0
  803. package/esm/util/color-bits/format.js +82 -0
  804. package/esm/util/color-bits/functions.d.ts +33 -0
  805. package/esm/util/color-bits/functions.js +70 -0
  806. package/esm/util/color-bits/index.d.ts +5 -0
  807. package/esm/util/color-bits/index.js +4 -0
  808. package/esm/util/color-bits/parse.d.ts +17 -0
  809. package/esm/util/color-bits/parse.js +382 -0
  810. package/esm/util/colorBits.d.ts +39 -0
  811. package/esm/util/colorBits.js +155 -0
  812. package/esm/util/colorRamp.d.ts +81 -0
  813. package/esm/util/colorRamp.js +244 -0
  814. package/esm/util/colorScale.d.ts +156 -0
  815. package/esm/util/colorScale.js +243 -0
  816. package/esm/util/colorSchemes.d.ts +21 -0
  817. package/esm/util/colorSchemes.js +30 -0
  818. package/esm/util/colord.d.ts +8 -0
  819. package/esm/util/colord.js +43 -191
  820. package/esm/util/convertCodingSequenceToPeptides.d.ts +17 -3
  821. package/esm/util/convertCodingSequenceToPeptides.js +51 -4
  822. package/esm/util/copyText.d.ts +18 -0
  823. package/esm/util/copyText.js +30 -0
  824. package/esm/util/copyToClipboard.d.ts +4 -0
  825. package/esm/util/copyToClipboard.js +58 -0
  826. package/esm/util/createAbortRotation.d.ts +115 -0
  827. package/esm/util/createAbortRotation.js +116 -0
  828. package/esm/util/createSvgRasterCanvas.d.ts +17 -0
  829. package/esm/util/createSvgRasterCanvas.js +22 -0
  830. package/esm/util/crypto.d.ts +24 -0
  831. package/esm/util/crypto.js +85 -2
  832. package/esm/util/cssColorParse.d.ts +15 -0
  833. package/esm/util/cssColorParse.js +53 -0
  834. package/esm/util/dataGridUtils.d.ts +9 -0
  835. package/esm/util/dataGridUtils.js +36 -0
  836. package/esm/util/dedupe.js +1 -0
  837. package/esm/util/deepEqual.d.ts +8 -0
  838. package/esm/util/deepEqual.js +22 -0
  839. package/esm/util/deepMerge.d.ts +20 -0
  840. package/esm/util/deepMerge.js +44 -0
  841. package/esm/util/diagonalizeRegions.d.ts +22 -0
  842. package/esm/util/diagonalizeRegions.js +187 -0
  843. package/esm/util/environment.d.ts +4 -0
  844. package/esm/util/environment.js +43 -0
  845. package/esm/util/eventPoint.d.ts +32 -0
  846. package/esm/util/eventPoint.js +28 -0
  847. package/esm/util/expandLooseSearchIndex.d.ts +19 -0
  848. package/esm/util/expandLooseSearchIndex.js +29 -0
  849. package/esm/util/featureTable.d.ts +224 -0
  850. package/esm/util/featureTable.js +366 -0
  851. package/esm/util/featureTransforms.d.ts +80 -0
  852. package/esm/util/featureTransforms.js +1579 -0
  853. package/esm/util/featureTypes.d.ts +24 -0
  854. package/esm/util/featureTypes.js +35 -0
  855. package/esm/util/fetchAndMaybeUnzip.d.ts +6 -0
  856. package/esm/util/fetchAndMaybeUnzip.js +71 -0
  857. package/esm/util/fetchContext.d.ts +81 -0
  858. package/esm/util/fetchContext.js +59 -0
  859. package/esm/util/fetchHub.d.ts +17 -0
  860. package/esm/util/fetchHub.js +31 -0
  861. package/esm/util/fetchJson.d.ts +1 -0
  862. package/esm/util/fetchJson.js +7 -0
  863. package/esm/util/fetchPhases.d.ts +77 -0
  864. package/esm/util/fetchPhases.js +1 -0
  865. package/esm/util/fetchSeq.d.ts +4 -1
  866. package/esm/util/fetchSeq.js +18 -6
  867. package/esm/util/fieldReader.d.ts +17 -0
  868. package/esm/util/fieldReader.js +62 -0
  869. package/esm/util/fileHandleStore.d.ts +19 -2
  870. package/esm/util/fileHandleStore.js +95 -35
  871. package/esm/util/flatbush/index.d.ts +27 -6
  872. package/esm/util/flatbush/index.js +194 -218
  873. package/esm/util/formatBytes.d.ts +9 -0
  874. package/esm/util/formatBytes.js +18 -0
  875. package/esm/util/formatFastaStrings.d.ts +13 -0
  876. package/esm/util/formatFastaStrings.js +13 -0
  877. package/esm/util/formatGuessers.d.ts +30 -0
  878. package/esm/util/formatGuessers.js +69 -0
  879. package/esm/util/formatRelativeTime.d.ts +1 -0
  880. package/esm/util/formatRelativeTime.js +25 -0
  881. package/esm/util/frameCoalescer.d.ts +30 -0
  882. package/esm/util/frameCoalescer.js +22 -0
  883. package/esm/util/freezeDeep.d.ts +26 -0
  884. package/esm/util/freezeDeep.js +39 -0
  885. package/esm/util/geneticCodes.d.ts +56 -0
  886. package/esm/util/geneticCodes.js +371 -0
  887. package/esm/util/getFileName.d.ts +11 -0
  888. package/esm/util/getFileName.js +34 -0
  889. package/esm/util/getLocationUri.d.ts +49 -0
  890. package/esm/util/getLocationUri.js +63 -0
  891. package/esm/util/getRelativeX.d.ts +4 -0
  892. package/esm/util/getRelativeX.js +7 -0
  893. package/esm/util/getStr.d.ts +6 -0
  894. package/esm/util/getStr.js +15 -0
  895. package/esm/util/groupKeys.d.ts +77 -0
  896. package/esm/util/groupKeys.js +155 -0
  897. package/esm/util/highlights.d.ts +25 -0
  898. package/esm/util/highlights.js +87 -0
  899. package/esm/util/hooks.d.ts +189 -0
  900. package/esm/util/hooks.js +485 -0
  901. package/esm/util/htmlText.d.ts +13 -0
  902. package/esm/util/htmlText.js +66 -0
  903. package/esm/util/idMaker.d.ts +1 -1
  904. package/esm/util/idMaker.js +31 -18
  905. package/esm/util/index.d.ts +82 -268
  906. package/esm/util/index.js +137 -853
  907. package/esm/util/indexCandidates.d.ts +20 -0
  908. package/esm/util/indexCandidates.js +43 -0
  909. package/esm/util/installClearHoverOnSurfaceMove.d.ts +40 -0
  910. package/esm/util/installClearHoverOnSurfaceMove.js +41 -0
  911. package/esm/util/installFetch.d.ts +234 -0
  912. package/esm/util/installFetch.js +205 -0
  913. package/esm/util/installInitAutorun.d.ts +63 -0
  914. package/esm/util/installInitAutorun.js +107 -0
  915. package/esm/util/installPrerequisiteFetch.d.ts +115 -0
  916. package/esm/util/installPrerequisiteFetch.js +111 -0
  917. package/esm/util/intervals.d.ts +20 -0
  918. package/esm/util/intervals.js +37 -0
  919. package/esm/util/io/RemoteFileWithRangeCache.d.ts +10 -11
  920. package/esm/util/io/RemoteFileWithRangeCache.js +10 -148
  921. package/esm/util/io/index.d.ts +39 -2
  922. package/esm/util/io/index.js +120 -12
  923. package/esm/util/isDataCurrent.d.ts +9 -0
  924. package/esm/util/isDataCurrent.js +12 -0
  925. package/esm/util/isTextEntryFocused.d.ts +7 -0
  926. package/esm/util/isTextEntryFocused.js +16 -0
  927. package/esm/util/isWebWorker.js +1 -2
  928. package/esm/util/iupac.d.ts +4 -0
  929. package/esm/util/iupac.js +59 -0
  930. package/esm/util/jexl.js +146 -19
  931. package/esm/util/jexlFilterRows.d.ts +89 -0
  932. package/esm/util/jexlFilterRows.js +252 -0
  933. package/esm/util/jexlFilters.d.ts +68 -0
  934. package/esm/util/jexlFilters.js +61 -0
  935. package/esm/util/jexlStrings.d.ts +21 -1
  936. package/esm/util/jexlStrings.js +20 -14
  937. package/esm/util/layouts/GranularRectLayout.d.ts +20 -25
  938. package/esm/util/layouts/GranularRectLayout.js +116 -356
  939. package/esm/util/layouts/index.d.ts +1 -7
  940. package/esm/util/layouts/index.js +2 -6
  941. package/esm/util/layouts/intervalUtils.d.ts +12 -1
  942. package/esm/util/layouts/intervalUtils.js +13 -31
  943. package/esm/util/layouts/placeRect.d.ts +50 -0
  944. package/esm/util/layouts/placeRect.js +97 -0
  945. package/esm/util/lazyAfterAttach.d.ts +13 -0
  946. package/esm/util/lazyAfterAttach.js +31 -0
  947. package/esm/util/lazyWithPreload.d.ts +19 -0
  948. package/esm/util/lazyWithPreload.js +27 -0
  949. package/esm/util/leadingEdgeAutorun.d.ts +40 -0
  950. package/esm/util/leadingEdgeAutorun.js +51 -0
  951. package/esm/util/legendCandidates.d.ts +72 -0
  952. package/esm/util/legendCandidates.js +138 -0
  953. package/esm/util/librpc.d.ts +5 -2
  954. package/esm/util/librpc.js +6 -1
  955. package/esm/util/linkify.js +2 -0
  956. package/esm/util/locString.d.ts +72 -0
  957. package/esm/util/locString.js +178 -7
  958. package/esm/util/locStringsToRegions.d.ts +10 -0
  959. package/esm/util/locStringsToRegions.js +35 -0
  960. package/esm/util/localStorage.d.ts +36 -0
  961. package/esm/util/localStorage.js +137 -0
  962. package/esm/util/makeAssembly.d.ts +54 -0
  963. package/esm/util/makeAssembly.js +52 -0
  964. package/esm/util/makeTrackId.d.ts +14 -0
  965. package/esm/util/makeTrackId.js +14 -0
  966. package/esm/util/markEncoding.d.ts +150 -0
  967. package/esm/util/markEncoding.js +845 -0
  968. package/esm/util/markEncodingTypes.d.ts +588 -0
  969. package/esm/util/markEncodingTypes.js +8 -0
  970. package/esm/util/matchTrackId.d.ts +11 -0
  971. package/esm/util/matchTrackId.js +14 -0
  972. package/esm/util/measureText.d.ts +24 -0
  973. package/esm/util/measureText.js +51 -0
  974. package/esm/util/mst-reflection.d.ts +3 -11
  975. package/esm/util/mst-reflection.js +3 -52
  976. package/esm/util/mstUtils.d.ts +97 -0
  977. package/esm/util/mstUtils.js +137 -0
  978. package/esm/util/nanoid.d.ts +0 -4
  979. package/esm/util/nanoid.js +10 -20
  980. package/esm/util/numericUtils.d.ts +27 -0
  981. package/esm/util/numericUtils.js +143 -0
  982. package/esm/util/numericValue.d.ts +14 -0
  983. package/esm/util/numericValue.js +34 -0
  984. package/esm/util/objectUtils.d.ts +2 -0
  985. package/esm/util/objectUtils.js +9 -0
  986. package/esm/util/offscreenCanvasPonyfill.d.ts +5 -4
  987. package/esm/util/offscreenCanvasPonyfill.js +5 -47
  988. package/esm/util/openFeatureWidget.d.ts +38 -0
  989. package/esm/util/openFeatureWidget.js +64 -0
  990. package/esm/util/openViews.d.ts +17 -0
  991. package/esm/util/openViews.js +22 -0
  992. package/esm/util/paintLayer.d.ts +32 -0
  993. package/esm/util/paintLayer.js +33 -0
  994. package/esm/util/parentWalk.d.ts +32 -0
  995. package/esm/util/parentWalk.js +84 -0
  996. package/esm/util/parseLineByLine.d.ts +44 -2
  997. package/esm/util/parseLineByLine.js +150 -15
  998. package/esm/util/parseMotifList.d.ts +17 -0
  999. package/esm/util/parseMotifList.js +69 -0
  1000. package/esm/util/pluginStore.d.ts +111 -0
  1001. package/esm/util/pluginStore.js +254 -0
  1002. package/esm/util/pointerPresence.d.ts +5 -0
  1003. package/esm/util/pointerPresence.js +21 -0
  1004. package/esm/util/preloadComponent.d.ts +5 -0
  1005. package/esm/util/preloadComponent.js +11 -0
  1006. package/esm/util/progress.d.ts +459 -0
  1007. package/esm/util/progress.js +821 -0
  1008. package/esm/util/quantileExtent.d.ts +49 -0
  1009. package/esm/util/quantileExtent.js +162 -0
  1010. package/esm/util/range.d.ts +46 -1
  1011. package/esm/util/range.js +68 -2
  1012. package/esm/util/renameRegions.d.ts +41 -0
  1013. package/esm/util/renameRegions.js +143 -0
  1014. package/esm/util/renderToStaticMarkup.d.ts +2 -0
  1015. package/esm/util/renderToStaticMarkup.js +60 -0
  1016. package/esm/util/reorder.d.ts +35 -0
  1017. package/esm/util/reorder.js +83 -0
  1018. package/esm/util/resolveRowHeight.d.ts +27 -0
  1019. package/esm/util/resolveRowHeight.js +30 -0
  1020. package/esm/util/revlist.d.ts +13 -0
  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
  1023. package/esm/util/rowStackGeometry.js +70 -0
  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
  1071. package/esm/util/systemColorScheme.js +27 -0
  1072. package/esm/util/tabix.d.ts +125 -0
  1073. package/esm/util/tabix.js +148 -0
  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
  1076. package/esm/util/temporaryAssembly.d.ts +21 -0
  1077. package/esm/util/temporaryAssembly.js +29 -0
  1078. package/esm/util/thresholdScale.d.ts +91 -0
  1079. package/esm/util/thresholdScale.js +166 -0
  1080. package/esm/util/tickLabels.d.ts +36 -0
  1081. package/esm/util/tickLabels.js +45 -0
  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
  1121. package/esm/util/unzip.d.ts +1 -0
  1122. package/esm/util/unzip.js +6 -0
  1123. package/esm/util/useEventCallback.d.ts +1 -0
  1124. package/esm/util/useEventCallback.js +16 -0
  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
  1126. package/esm/util/useFeatureSequence.js +55 -77
  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
  1130. package/esm/util/useFetchPlugins.js +18 -0
  1131. package/esm/util/useMeasure.d.ts +11 -1
  1132. package/esm/util/useMeasure.js +20 -6
  1133. package/esm/util/usePanZoom.d.ts +75 -0
  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
  1136. package/esm/util/usePanelVirtualScroll.js +15 -0
  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
  1144. package/esm/util/useRowVirtualScroll.js +22 -0
  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
  1148. package/esm/util/viewHighlights.js +5 -0
  1149. package/esm/util/viewStatus.d.ts +90 -0
  1150. package/esm/util/viewStatus.js +54 -0
  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
  1160. package/esm/util/withFeatureDetails.js +59 -0
  1161. package/esm/util/withLaunchInput.d.ts +174 -0
  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  1170. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  1171. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
  1172. package/esm/ReExports/BaseFeatureDetails.js +0 -9
  1173. package/esm/ReExports/DataGrid.d.ts +0 -1
  1174. package/esm/ReExports/DataGrid.js +0 -1
  1175. package/esm/ReExports/index.d.ts +0 -1
  1176. package/esm/ReExports/index.js +0 -1
  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
  1181. package/esm/data_adapters/util.js +0 -6
  1182. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1183. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1184. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1185. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1186. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1187. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1188. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1189. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1190. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1191. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1192. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1193. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1194. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1195. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1196. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1197. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1198. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1199. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1200. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1201. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1202. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1203. package/esm/rpc/baseRpcConfig.js +0 -10
  1204. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1205. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1206. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1207. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1208. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1209. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1210. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1211. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1212. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1213. package/esm/rpc/methods/CoreRender.js +0 -40
  1214. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1215. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1216. package/esm/rpc/methods/util.d.ts +0 -15
  1217. package/esm/rpc/methods/util.js +0 -7
  1218. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1219. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1220. package/esm/ui/MenuButton.d.ts +0 -1
  1221. package/esm/ui/MenuButton.js +0 -1
  1222. package/esm/ui/MenuItems.d.ts +0 -15
  1223. package/esm/ui/MenuItems.js +0 -59
  1224. package/esm/ui/useEvent.d.ts +0 -1
  1225. package/esm/ui/useEvent.js +0 -10
  1226. package/esm/util/blobToDataURL.d.ts +0 -1
  1227. package/esm/util/blobToDataURL.js +0 -14
  1228. package/esm/util/compositeMap.d.ts +0 -11
  1229. package/esm/util/compositeMap.js +0 -59
  1230. package/esm/util/flatqueue/index.d.ts +0 -11
  1231. package/esm/util/flatqueue/index.js +0 -61
  1232. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1233. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1234. package/esm/util/layouts/MultiLayout.js +0 -40
  1235. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1236. package/esm/util/layouts/PileupLayout.js +0 -202
  1237. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1238. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1239. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1240. package/esm/util/layouts/SceneGraph.js +0 -121
  1241. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1242. package/esm/util/makeAbortableReaction.js +0 -47
  1243. package/esm/util/map-obj/index.d.ts +0 -13
  1244. package/esm/util/map-obj/index.js +0 -92
  1245. package/esm/util/nextTick.d.ts +0 -1
  1246. package/esm/util/nextTick.js +0 -3
  1247. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1248. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1249. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1250. package/esm/util/offscreenCanvasUtils.js +0 -19
  1251. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1252. package/esm/util/renderToAbstractCanvas.js +0 -53
  1253. package/esm/util/stopToken.d.ts +0 -19
  1254. package/esm/util/stopToken.js +0 -90
  1255. package/esm/util/transferables.d.ts +0 -2
  1256. package/esm/util/transferables.js +0 -35
  1257. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1258. package/esm/util/tss-react/mui/index.js +0 -1
  1259. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1260. package/esm/util/tss-react/mui/mui.js +0 -5
  1261. package/esm/util/when.d.ts +0 -1
  1262. package/esm/util/when.js +0 -1
  1263. /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -1,107 +1,277 @@
1
- import { getParent, types } from '@jbrowse/mobx-state-tree';
2
- import { getConf } from "../../configuration/index.js";
3
- import { getContainingTrack, getContainingView, getEnv, } from "../../util/index.js";
4
- import { getParentRenderProps } from "../../util/tracks.js";
5
- import { ElementId } from "../../util/types/mst.js";
1
+ import { hasParent, isAlive, types } from '@jbrowse/mobx-state-tree';
2
+ import { applyConfSettings, getConf } from '../../configuration/index.js';
3
+ import { getContainingTrack, getEnv, statusFraction, statusMessageText, } from '../../util/index.js';
4
+ import { ElementId } from '../../util/types/mst.js';
5
+ import { displaySetterName } from '../../util/unknownSnapshotKeys.js';
6
+ /**
7
+ * #stateModel BaseDisplay
8
+ * #category display
9
+ */
6
10
  function stateModelFactory() {
7
11
  return types
8
12
  .model('BaseDisplay', {
13
+ /**
14
+ * #property
15
+ */
9
16
  id: ElementId,
17
+ /**
18
+ * #property
19
+ */
10
20
  type: types.string,
11
- rpcDriverName: types.maybe(types.string),
12
21
  })
13
22
  .volatile(() => ({
14
- rendererTypeName: '',
23
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
15
24
  error: undefined,
16
25
  statusMessage: undefined,
26
+ /**
27
+ * #volatile
28
+ * determinate progress fraction [0,1] for the current status, or
29
+ * undefined when the in-flight phase is indeterminate. Set alongside
30
+ * `statusMessage` by `setStatusMessage`; a display that never shows a
31
+ * bar simply leaves it undefined.
32
+ */
33
+ statusProgress: undefined,
17
34
  }))
18
35
  .views(self => ({
36
+ /**
37
+ * #getter
38
+ */
39
+ get parentTrack() {
40
+ if (!hasParent(self)) {
41
+ console.warn(`[BaseDisplayModel] parentTrack accessed with no parent: alive=${isAlive(self)} type=${self.type}`);
42
+ }
43
+ return getContainingTrack(self);
44
+ },
45
+ }))
46
+ .views(self => ({
47
+ /**
48
+ * #getter
49
+ */
19
50
  get RenderingComponent() {
20
51
  const { pluginManager } = getEnv(self);
21
52
  return pluginManager.getDisplayType(self.type)
22
53
  .ReactComponent;
23
54
  },
55
+ /**
56
+ * #getter
57
+ */
24
58
  get DisplayBlurb() {
25
59
  return null;
26
60
  },
61
+ /**
62
+ * #getter
63
+ */
27
64
  get adapterConfig() {
28
- return getConf(this.parentTrack, 'adapter');
29
- },
30
- get parentTrack() {
31
- return getContainingTrack(self);
65
+ // `Record<string, unknown>` is as narrow as this can honestly get: which
66
+ // adapter a track uses is open-ended, so the *contents* are
67
+ // unpredictable. The *shape* is not, and that is the part worth
68
+ // declaring. Leaving it to infer `getConf`'s `any` was the status quo and
69
+ // it propagated: every consumer's RPC arg and adapter spec takes
70
+ // `Record<string, unknown>`, so they accepted whatever they were handed,
71
+ // and two displays re-declared this getter locally just to annotate it.
72
+ //
73
+ // Not `| undefined` — see `BaseTrackModel.adapterConfig` for the probe
74
+ // showing the slot always materializes an object.
75
+ //
76
+ // This is a snapshot, so read a specific slot with an array path off the
77
+ // live node (`getConf(track, ['adapter', 'x'])`) rather than off this —
78
+ // `types.stripDefault` omits a slot at its default. See
79
+ // ../../configuration/CLAUDE.md.
80
+ return getConf(self.parentTrack, 'adapter');
32
81
  },
82
+ /**
83
+ * #getter
84
+ * Returns true if the parent track is minimized. Used to skip
85
+ * expensive operations like autoruns when track is not visible.
86
+ */
33
87
  get isMinimized() {
34
- return this.parentTrack.minimized;
88
+ return self.parentTrack.minimized;
35
89
  },
36
- get parentDisplay() {
37
- try {
38
- const parent = getParent(self);
39
- const parentType = parent?.type;
40
- if (typeof parentType === 'string' &&
41
- parentType.endsWith('Display')) {
42
- return parent;
43
- }
44
- }
45
- catch {
46
- }
90
+ /**
91
+ * #getter
92
+ * Overridable hook (default `undefined`): what the pointer is currently
93
+ * over, for readers **outside** the display. `LinearGenomeViewContainer`
94
+ * publishes it to `session.hovered`, the view-wide "what is the user
95
+ * pointing at" channel a plugin can subscribe to.
96
+ *
97
+ * Declared here because a cross-display consumer can only read a name the
98
+ * base declares — the same reason `FetchMixin.fetchInert` is a
99
+ * hook rather than a getter each display invents. The container used to
100
+ * read `featureUnderMouse`, which only the wiggle, alignments and
101
+ * Manhattan families spelled that way — canvas said `hoveredFeature`,
102
+ * variants `hoveredGenotype` — so the channel carried a hover from a third
103
+ * of the display types and nothing said which. It also asked only
104
+ * `displays[0]` of each track.
105
+ *
106
+ * `unknown` because the payload genuinely differs — a read, a wiggle bin,
107
+ * a SNP, a genotype cell — and `session.hovered` is typed to match ("can
108
+ * be anything; code that wants to deal with this should examine it").
109
+ * Narrow it in the override.
110
+ */
111
+ get hoveredFeature() {
47
112
  return undefined;
48
113
  },
49
- get effectiveRpcDriverName() {
50
- if (self.rpcDriverName) {
51
- return self.rpcDriverName;
52
- }
53
- if (this.parentDisplay?.effectiveRpcDriverName) {
54
- return this.parentDisplay.effectiveRpcDriverName;
55
- }
56
- try {
57
- return getConf(this.parentTrack, 'rpcDriverName') || undefined;
58
- }
59
- catch {
60
- return undefined;
61
- }
114
+ /**
115
+ * #getter
116
+ * Overridable hook (default `'feature'`): the SINGULAR word for one of
117
+ * the things this display draws, as a menu row or a chip says it —
118
+ * "Hide this read", "Showing 3 variants".
119
+ *
120
+ * Declared here for the same reason as `hoveredFeature` above: it is read
121
+ * across the display boundary, by chrome that has no idea which display
122
+ * it is drawing for (`SoloSelectionChip`, alignments' group-label
123
+ * overlay), and a name only the base declares is a name every such
124
+ * consumer can rely on. Two displays declared it independently and one of
125
+ * those declarations WAS this default.
126
+ *
127
+ * **A control keeps the generic word; content takes this one.** "Variant
128
+ * height" reads as a different setting from "Feature height" when it is
129
+ * the same one, so the shared menus stay on "feature" however the display
130
+ * answers here, and the noun varies where it names what the user is
131
+ * looking at — "Showing 3 variants", "Hide this read". A display drawing
132
+ * something the generic word already fits is right to leave this alone.
133
+ *
134
+ * Distinct from the per-hit noun a context menu takes off the clicked
135
+ * item's own `type` ("mRNA", "gene"); that names one annotation, this
136
+ * names what the track holds. The hit noun falls back to this.
137
+ */
138
+ get featureNoun() {
139
+ return 'feature';
62
140
  },
63
- }))
64
- .views(self => ({
65
- renderProps() {
141
+ /**
142
+ * #getter
143
+ * The widget `openFeatureWidget` opens for one of this display's
144
+ * features. Displays may override it. The default is the generic feature
145
+ * widget, for displays drawing plain features.
146
+ *
147
+ * Displays whose features are a specific kind (a read, a variant, a
148
+ * synteny block) override it, including the `id`: two displays naming
149
+ * one id share the drawer panel, which suits two displays showing the
150
+ * same kind of feature.
151
+ */
152
+ get featureWidgetType() {
66
153
  return {
67
- ...getParentRenderProps(self),
68
- notReady: self.isMinimized || getContainingView(self).minimized,
69
- rpcDriverName: self.effectiveRpcDriverName,
154
+ type: 'BaseFeatureWidget',
155
+ id: 'baseFeature',
70
156
  };
71
157
  },
158
+ }))
159
+ .views(self => ({
160
+ /**
161
+ * #method
162
+ * props passed to the renderer's React "Rendering" component.
163
+ * these are client-side only and never sent to the worker.
164
+ * includes displayModel and callbacks
165
+ */
72
166
  renderingProps() {
73
167
  return {
74
168
  displayModel: self,
75
169
  };
76
170
  },
77
- get rendererType() {
78
- const { pluginManager } = getEnv(self);
79
- return pluginManager.getRendererType(self.rendererTypeName);
80
- },
81
- get DisplayMessageComponent() {
82
- return undefined;
83
- },
171
+ /**
172
+ * #method
173
+ */
84
174
  trackMenuItems() {
85
175
  return [];
86
176
  },
87
- get viewMenuActions() {
88
- return [];
89
- },
90
- regionCannotBeRendered() {
91
- return null;
92
- },
93
177
  }))
94
178
  .actions(self => ({
95
- setStatusMessage(arg) {
96
- self.statusMessage = arg;
179
+ /**
180
+ * #action
181
+ */
182
+ setStatusMessage(status) {
183
+ // derive the indeterminate label and the determinate fraction from the
184
+ // one status transport; displays with no bar just ignore statusProgress
185
+ self.statusMessage = statusMessageText(status);
186
+ self.statusProgress = statusFraction(status);
97
187
  },
188
+ /**
189
+ * #action
190
+ */
98
191
  setError(error) {
99
192
  self.error = error;
100
193
  },
101
- setRpcDriverName(rpcDriverName) {
102
- self.rpcDriverName = rpcDriverName;
103
- },
194
+ /**
195
+ * #action
196
+ * Overridable hook (default no-op): drop whatever `hoveredFeature`
197
+ * reports. The writing twin of that getter, and what
198
+ * `installClearHoverOnViewportChange` calls.
199
+ *
200
+ * A display that STORES its hover owes an override; one that derives it
201
+ * from the live pointer (MAF, Hi-C, LD) owes nothing, and the default
202
+ * costs it nothing. Declared here so the clear can be installed for every
203
+ * display rather than remembered per display — forgetting it is the
204
+ * failure ARCHITECTURE.md's stored-hover section is about, and it used to
205
+ * be six closures at six call sites, which is six chances to omit one.
206
+ */
207
+ clearHoveredFeature() { },
208
+ /**
209
+ * #action
210
+ * base display reload does nothing, see specialized displays for details
211
+ */
104
212
  reload() { },
213
+ /**
214
+ * #action
215
+ * Apply a set of display settings to the live display, and report which
216
+ * were applied. Each key runs through the display config schema's
217
+ * `preProcessSnapshot` (shorthand expansions and legacy-key migrations,
218
+ * as `showTrackGeneric` applies to a session spec's inline track keys),
219
+ * then writes the matching config slot. A key naming a sub-schema
220
+ * (`facet`, `color`) replaces the whole object, its string shorthand
221
+ * lifted by that schema, and `null` clears it. Keys that are not slots
222
+ * come back in `unapplied` as `{ key, reason }`, so a caller can tell a
223
+ * misspelling from a key that has an action instead of a slot.
224
+ *
225
+ * `allowSetters` also routes a non-slot key to a single-argument action
226
+ * named `set<Key>`. It is off by default because session specs, share
227
+ * links and embeds pass untyped JSON here, and a default fallback would
228
+ * let them call internal setters (`setError`, `setScrollTop`, ...) and
229
+ * call multi-argument setters with one argument. A caller that wants a
230
+ * specific action can call it directly.
231
+ *
232
+ * A key whose write threw is reported in `failed`. Only `failed` means
233
+ * the caller passed a bad value. `unapplied` needs the caller's own
234
+ * context to read: `showTrackGeneric` spreads the same settings into the
235
+ * display's snapshot, so a declared prop (`resolution`) has already
236
+ * landed by the time it reports here, while the restyle path spreads
237
+ * nothing and every entry there did nothing.
238
+ *
239
+ * A per-key error does not abort the remaining keys. A caller
240
+ * mid-`showTrack` has already pushed the track, and one rejected value
241
+ * should not leave it half-configured.
242
+ */
243
+ applyDisplaySettings(settings, options) {
244
+ // configuration is the reference every concrete display adds at
245
+ // instantiation (see DisplayModel below); the base model composes
246
+ // before it exists, hence the cast rather than a prop
247
+ const { configuration } = self;
248
+ const { applied, undeclared, failed } = applyConfSettings(configuration, settings);
249
+ const unapplied = [];
250
+ for (const [key, value] of Object.entries(undeclared)) {
251
+ if (!key || key === 'type') {
252
+ unapplied.push({ key, reason: key ? 'display-type' : 'no-slot' });
253
+ continue;
254
+ }
255
+ const setter = self[displaySetterName(key)];
256
+ if (typeof setter !== 'function') {
257
+ unapplied.push({ key, reason: 'no-slot' });
258
+ }
259
+ else if (!options?.allowSetters) {
260
+ unapplied.push({ key, reason: 'setter-only' });
261
+ }
262
+ else {
263
+ try {
264
+ ;
265
+ setter(value);
266
+ applied.push(`${key} (via setter)`);
267
+ }
268
+ catch (e) {
269
+ failed.push({ key, error: `${e}` });
270
+ }
271
+ }
272
+ }
273
+ return { applied, unapplied, failed };
274
+ },
105
275
  }));
106
276
  }
107
277
  export const BaseDisplay = stateModelFactory();
@@ -1,55 +1,264 @@
1
1
  import type PluginManager from '../../PluginManager.ts';
2
- import type { FileTypeExporter } from './saveTrackFileTypes/types.ts';
3
- import type { AnyConfigurationSchemaType } from '../../configuration/index.ts';
2
+ import type { RefNameMismatch } from '../../assemblyManager/refNameMismatch.ts';
3
+ import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '../../configuration/index.ts';
4
4
  import type { MenuItem } from '../../ui/index.ts';
5
- import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
6
- export declare function getCompatibleDisplays(self: IAnyStateTreeNode): ({
7
- [x: string]: any;
8
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
9
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
10
- [x: string]: any;
11
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
12
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>)[];
5
+ import type { DisplayModel } from './BaseDisplayModel.tsx';
6
+ import type { FileTypeExporter } from './saveTrackFileTypes/types.ts';
7
+ import type { IType, Instance } from '@jbrowse/mobx-state-tree';
8
+ /**
9
+ * #stateModel BaseTrackModel
10
+ * #category track
11
+ *
12
+ * these MST models only exist for tracks that are *shown*. they should contain
13
+ * only UI state for the track, and have a reference to a track configuration.
14
+ * note that multiple displayed tracks could use the same configuration.
15
+ */
13
16
  export declare function createBaseTrackModel(pm: PluginManager, trackType: string, baseTrackConfig: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
17
+ /**
18
+ * #property
19
+ */
14
20
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
15
- type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
16
- configuration: AnyConfigurationSchemaType;
17
- minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
18
- pinned: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
19
- displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
21
+ /**
22
+ * #property
23
+ */
24
+ type: import("@jbrowse/mobx-state-tree").ILiteralType<string>;
25
+ /**
26
+ * #property
27
+ */
28
+ configuration: import("../../configuration/configurationSchema.ts").IConfigurationReference<AnyConfigurationSchemaType>;
29
+ /**
30
+ * #property
31
+ */
32
+ minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
33
+ /**
34
+ * #property
35
+ */
36
+ pinned: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
37
+ /**
38
+ * #property
39
+ * The runtime plugin union (`pluggableMstType`) is typed only as
40
+ * `IAnyType`, erasing the element to `any`. Assert the concrete
41
+ * `DisplayModel` instance every registered display satisfies so reads
42
+ * (`activeDisplay`, `trackMenuItems`) are checked;
43
+ * create/snapshot stay `unknown` since the union's snapshot shape is
44
+ * genuinely dynamic (`replaceDisplay` writes a partial snapshot).
45
+ */
46
+ displays: import("@jbrowse/mobx-state-tree").IArrayType<IType<unknown, unknown, DisplayModel>>;
20
47
  }, {
48
+ /**
49
+ * Whether a height-resize gesture is in progress on this track. Set by
50
+ * whichever handle owns the drag — the view's track resize handle, or a
51
+ * handle a display draws inside itself — and read by displays that sit an
52
+ * expensive per-frame layer out of the gesture.
53
+ *
54
+ * On the track rather than the display because the gesture belongs to the
55
+ * container running it, not to whatever display happens to be active: the
56
+ * view can bracket a drag without knowing which display it landed on, and
57
+ * two handles on one track share one flag rather than racing to clear
58
+ * each other's.
59
+ */
60
+ resizing: boolean;
61
+ } & {
62
+ /**
63
+ * #getter
64
+ */
21
65
  readonly trackId: string;
66
+ /**
67
+ * #getter
68
+ * determines which webworker to send the track to, currently based on trackId
69
+ */
22
70
  readonly rpcSessionId: string;
23
- readonly name: any;
71
+ /**
72
+ * #getter
73
+ */
74
+ readonly name: string;
75
+ /**
76
+ * #getter
77
+ * this track's own name-search index, from the `textSearching`
78
+ * sub-config. `undefined` when the track has none.
79
+ *
80
+ * The path, not a bare `'textSearchAdapter'`: the slot is
81
+ * `textSearching.textSearchAdapter` (`baseTrackConfig.ts`), and a bare
82
+ * read of a name no schema declares returns `undefined` and reports
83
+ * nothing at any layer, so this getter answered `undefined` for every
84
+ * track ever configured with one. `TextSearchManager` reads the same slot
85
+ * by hand-walking `conf.textSearching.textSearchAdapter`, which is why
86
+ * nothing noticed.
87
+ */
24
88
  readonly textSearchAdapter: any;
25
- readonly adapterConfig: any;
26
- readonly viewMenuActions: MenuItem[];
27
- readonly canConfigure: boolean | ({
28
- [x: string]: any;
29
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
30
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
31
- [x: string]: any;
32
- } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
33
- } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>) | undefined;
89
+ /**
90
+ * #getter
91
+ */
92
+ readonly adapterConfig: Record<string, unknown>;
93
+ /**
94
+ * #getter
95
+ * a shown track always has at least one display
96
+ */
97
+ readonly activeDisplay: DisplayModel & import("@jbrowse/mobx-state-tree").IStateTreeNode<IType<unknown, unknown, DisplayModel>>;
98
+ /**
99
+ * #getter
100
+ * the configured displays the CONTAINING VIEW can draw and the track's
101
+ * adapter feeds, which is the set `replaceDisplay` will accept
102
+ *
103
+ * `configuration.displays` is not that set: baseTrackConfig injects one
104
+ * entry per display type registered for the track TYPE, across every
105
+ * view type, so a VariantTrack carries a ChordVariantDisplay a linear
106
+ * view cannot draw. The track menu's own "Display types" submenu has
107
+ * always filtered them; this exposes the same list to code, because the
108
+ * alternative is every caller re-deriving it from the plugin manager.
109
+ */
110
+ readonly compatibleDisplays: AnyConfigurationModel[];
34
111
  } & {
35
- readonly adapterType: import("../AdapterType.ts").default;
112
+ /**
113
+ * #getter
114
+ * Set when this track's file and one of its assemblies share no reference
115
+ * name at all — the `1/2/3` file loaded against a `chr1/chr2/chr3`
116
+ * assembly, which otherwise draws an empty track and says nothing.
117
+ *
118
+ * The verdict is reached in `loadRefNameMap`, which is the only place both
119
+ * name sets are in scope, and recorded on the *assembly* because nothing
120
+ * in the assembly manager can reach a track (the session is a sibling
121
+ * subtree, so `getSession` from there finds only the root). The lookup
122
+ * inverts that: the record is keyed by adapter cache key, which is exactly
123
+ * what `rpcSessionId` already is, so a track finds its own with no
124
+ * plumbing in between.
125
+ *
126
+ * The names come from `getConfAssemblyNamesOrNone`, not from a raw
127
+ * `assemblyNames` slot read: this model is shared by every track type, and
128
+ * `ReferenceSequenceTrack`'s schema does not declare that slot — it names
129
+ * its assembly by being the `sequence` of one. A raw read there returns
130
+ * `undefined` with no diagnostic at any layer, so the getter was inert for
131
+ * that one track type while looking like it worked. The `OrNone` half is
132
+ * what keeps this total: it runs on every render of every track label, and
133
+ * an unanswerable question must not become a thrown getter.
134
+ *
135
+ * Diagnostic only. It gates nothing, and a track carrying one still loads,
136
+ * still fetches and still draws whatever it can.
137
+ */
138
+ readonly refNameMismatch: RefNameMismatch | undefined;
139
+ /**
140
+ * #getter
141
+ */
142
+ readonly adapterType: import("../AdapterType.ts").default<any>;
36
143
  } & {
144
+ /**
145
+ * #action
146
+ * Write the config to the session now rather than after the 400 ms
147
+ * wait, for an edit that has to be undoable the moment it lands.
148
+ */
149
+ persistConfigurationNow(): void;
150
+ /**
151
+ * #action
152
+ */
37
153
  setPinned(flag: boolean): void;
154
+ /**
155
+ * #action
156
+ */
38
157
  setMinimized(flag: boolean): void;
39
- showDisplay(displayId: string, initialSnapshot?: {}): void;
40
- hideDisplay(displayId: string): number;
41
- replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: {}): void;
158
+ /**
159
+ * #action
160
+ */
161
+ setResizing(flag: boolean): void;
162
+ /**
163
+ * #action
164
+ * `applyDisplaySettings` on the display being drawn (`activeDisplay`,
165
+ * which a shown track always has — this is not meaningful on a bare
166
+ * config node) — the track-level entry for "restyle this track in
167
+ * place" (a session spec's inline keys, an agent's settings bag). Only
168
+ * that one display: settings vocabularies are per display type, so
169
+ * broadcasting one bag across a track's other displays would mis-route
170
+ * keys; address a non-active display directly if that is what you mean.
171
+ * See BaseDisplayModel for the routing and the `allowSetters` opt-in.
172
+ */
173
+ applyDisplaySettings(settings: Record<string, unknown>, options?: {
174
+ allowSetters?: boolean;
175
+ }): {
176
+ applied: string[];
177
+ unapplied: import("../../util/unknownSnapshotKeys.ts").UnappliedSetting[];
178
+ failed: {
179
+ key: string;
180
+ error: string;
181
+ }[];
182
+ };
183
+ /**
184
+ * #action
185
+ */
186
+ replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: any): void;
187
+ /**
188
+ * #action
189
+ * Persist any config-schema mutation (quick track-menu edits calling
190
+ * `setSlot` directly, or the full Settings dialog) back to the session,
191
+ * debounced, mirroring ConfigurationEditorWidget's own save. Both savers
192
+ * intentionally coexist — this one covers direct setSlot edits on a shown
193
+ * track, the widget covers an unshown track edited from the selector (no
194
+ * BaseTrackModel). When both fire they compute an identical delta, deduped
195
+ * in updateTrackConfiguration; don't drop one to "simplify". `reaction`
196
+ * (not `autorun`) on purpose: `self.configuration` is defined
197
+ * immediately on attach, unlike ConfigurationEditorWidget's `target`
198
+ * (which starts undefined), so an autorun's guaranteed first run would
199
+ * otherwise schedule a spurious flush for every track ever shown, even
200
+ * completely untouched ones — `reaction` only fires on an actual change.
201
+ *
202
+ * `equals: compareStructural` is load-bearing, not an optimization:
203
+ * `self.configuration` is a re-resolving reference, and persisting a save
204
+ * can swap the resolved node identity (the delta path reconciles in place
205
+ * but still churns once, and a session without deltas replaces the frozen
206
+ * `jbrowse.tracks` entry, rehydrating a brand-new MST node every write).
207
+ * Referential comparison would treat every such swap as a fresh change
208
+ * and re-fire the save, an unbounded debounced loop. Structural
209
+ * comparison settles once the content stops changing.
210
+ */
211
+ afterAttach(): void;
42
212
  } & {
213
+ /**
214
+ * #action
215
+ * The awaitable sibling of `replaceDisplay`: loads the target display's
216
+ * state model, then swaps to it carrying whatever settings the outgoing
217
+ * display can hand over.
218
+ *
219
+ * `replaceDisplay` stays a plain sync action and ASSERTS the model is
220
+ * loaded, and every display state model in this tree is a dynamic import
221
+ * until something shows one — so a caller that has not already shown the
222
+ * target needs this. Named like `launchTrack`, which is the same problem
223
+ * one level up.
224
+ */
225
+ launchDisplay(displayId: string): Promise<void>;
226
+ } & {
227
+ /**
228
+ * #getter
229
+ * Whether this track's adapter writes an export format itself, rather
230
+ * than the save dialog rebuilding one out of rendered features. A claim
231
+ * about the adapter type, not about a given format — the fetch still
232
+ * falls back when the adapter declines the one that was asked for.
233
+ */
234
+ readonly exportsDataViaAdapter: boolean;
235
+ /**
236
+ * #getter
237
+ * The size in bytes above which "Save track data" asks for confirmation
238
+ * before fetching. Uses the adapter's `fetchSizeLimit` where it declares
239
+ * one, so a save asks at the same size at which the track's display
240
+ * refuses to render; otherwise a default. The default is generous
241
+ * because exceeding it only prompts for confirmation, and the user
242
+ * explicitly requested the data.
243
+ */
244
+ readonly exportByteLimit: number;
245
+ /**
246
+ * #method
247
+ */
43
248
  saveTrackFileFormatOptions(): Record<string, FileTypeExporter>;
44
249
  } & {
250
+ /**
251
+ * #getter
252
+ * the "Save track data" menu entry. Kept separate from trackMenuItems so
253
+ * consumers (e.g. the LGV track-label menu) can place it alongside the
254
+ * session's Settings/Copy/Delete track actions without fishing it back out
255
+ * of the general list
256
+ */
257
+ readonly saveTrackDataMenuItem: MenuItem;
258
+ /**
259
+ * #method
260
+ */
45
261
  trackMenuItems(): MenuItem[];
46
- }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
47
- id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
48
- type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
49
- configuration: AnyConfigurationSchemaType;
50
- minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
51
- pinned: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
52
- displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
53
- }>>;
262
+ }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
54
263
  export type BaseTrackStateModel = ReturnType<typeof createBaseTrackModel>;
55
264
  export type BaseTrackModel = Instance<BaseTrackStateModel>;