@jbrowse/core 4.3.0 → 5.0.0-beta.1

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 (1124) hide show
  1. package/README.md +783 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +40 -40
  113. package/esm/PluginLoader.js +166 -82
  114. package/esm/PluginManager.d.ts +368 -55
  115. package/esm/PluginManager.js +326 -85
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +84 -65
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/TextSearch/BaseResults.d.ts +20 -21
  135. package/esm/TextSearch/BaseResults.js +8 -33
  136. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  137. package/esm/TextSearch/TextSearchManager.js +87 -34
  138. package/esm/assemblyManager/assembly.d.ts +307 -34
  139. package/esm/assemblyManager/assembly.js +551 -262
  140. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  141. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  142. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  143. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  144. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  145. package/esm/assemblyManager/assemblyManager.js +351 -46
  146. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  147. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  148. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  149. package/esm/assemblyManager/geneticCodes.js +47 -0
  150. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  151. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  152. package/esm/assemblyManager/index.d.ts +1 -1
  153. package/esm/assemblyManager/index.js +2 -2
  154. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  155. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  156. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  157. package/esm/assemblyManager/refNameColors.js +32 -0
  158. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  159. package/esm/assemblyManager/refNameMaps.js +87 -0
  160. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  161. package/esm/assemblyManager/refNameMismatch.js +66 -0
  162. package/esm/checkPlugins.d.ts +11 -0
  163. package/esm/checkPlugins.js +77 -0
  164. package/esm/configuration/configurationSchema.d.ts +154 -19
  165. package/esm/configuration/configurationSchema.js +359 -138
  166. package/esm/configuration/configurationSlot.d.ts +283 -30
  167. package/esm/configuration/configurationSlot.js +205 -226
  168. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  169. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  170. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  171. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  172. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  173. package/esm/configuration/fullConfSnapshot.js +66 -0
  174. package/esm/configuration/getConf.d.ts +88 -0
  175. package/esm/configuration/getConf.js +74 -0
  176. package/esm/configuration/index.d.ts +19 -3
  177. package/esm/configuration/index.js +19 -2
  178. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  179. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  180. package/esm/configuration/promotableDefaults.d.ts +199 -0
  181. package/esm/configuration/promotableDefaults.js +326 -0
  182. package/esm/configuration/promotablePin.d.ts +55 -0
  183. package/esm/configuration/promotableResolve.d.ts +108 -0
  184. package/esm/configuration/promotableResolve.js +117 -0
  185. package/esm/configuration/promotableSlots.d.ts +12 -0
  186. package/esm/configuration/promotableSlots.js +45 -0
  187. package/esm/configuration/readConfObject.d.ts +56 -0
  188. package/esm/configuration/readConfObject.js +161 -0
  189. package/esm/configuration/schemaRegistry.d.ts +35 -0
  190. package/esm/configuration/schemaRegistry.js +50 -0
  191. package/esm/configuration/schemaTypes.d.ts +23 -0
  192. package/esm/configuration/schemaTypes.js +94 -0
  193. package/esm/configuration/slotFacade.d.ts +82 -0
  194. package/esm/configuration/slotFacade.js +89 -0
  195. package/esm/configuration/slotShape.d.ts +12 -0
  196. package/esm/configuration/slotShape.js +84 -0
  197. package/esm/configuration/slotValueUtils.d.ts +17 -0
  198. package/esm/configuration/slotValueUtils.js +25 -0
  199. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  200. package/esm/configuration/tabixIndexFields.js +45 -0
  201. package/esm/configuration/tabixShorthand.d.ts +34 -0
  202. package/esm/configuration/tabixShorthand.js +45 -0
  203. package/esm/configuration/types.d.ts +170 -7
  204. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  205. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  206. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
  207. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
  208. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  209. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  210. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  211. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  212. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  213. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  214. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  215. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  216. package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
  217. package/esm/data_adapters/BaseAdapter/index.js +5 -5
  218. package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
  219. package/esm/data_adapters/BaseAdapter/stats.js +48 -22
  220. package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
  221. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  222. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  223. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  224. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  225. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  226. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  227. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  228. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  229. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  230. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  231. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  232. package/esm/data_adapters/dataAdapterCache.js +62 -22
  233. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  234. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  235. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  236. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  237. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  238. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  239. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  240. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  241. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  242. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  243. package/esm/pluggableElementTypes/DisplayType.d.ts +10 -0
  244. package/esm/pluggableElementTypes/DisplayType.js +14 -1
  245. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  246. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  247. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  248. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  249. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  250. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  251. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  252. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  253. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  254. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  255. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  256. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  257. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  258. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  259. package/esm/pluggableElementTypes/TrackType.js +1 -1
  260. package/esm/pluggableElementTypes/ViewType.d.ts +2 -1
  261. package/esm/pluggableElementTypes/ViewType.js +9 -2
  262. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  263. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  264. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  265. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  266. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  267. package/esm/pluggableElementTypes/extendElementType.js +68 -0
  268. package/esm/pluggableElementTypes/index.d.ts +7 -7
  269. package/esm/pluggableElementTypes/index.js +24 -14
  270. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  271. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  272. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
  273. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
  274. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
  275. package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
  276. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
  277. package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
  278. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  279. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  280. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  281. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  282. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
  283. package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
  284. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  285. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  286. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  287. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  288. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  289. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  290. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  291. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  292. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  293. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  294. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  295. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  296. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  297. package/esm/pluggableElementTypes/models/index.js +10 -8
  298. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  299. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  300. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  301. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  302. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
  303. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
  304. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
  305. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
  306. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
  307. package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
  308. package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
  309. package/esm/pluggableElementTypes/models/uriMatchesDomains.js +62 -0
  310. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts +5 -4
  311. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +20 -10
  312. package/esm/pluginDefinitions.d.ts +198 -0
  313. package/esm/pluginDefinitions.js +220 -0
  314. package/esm/rpc/BaseRpcDriver.d.ts +27 -35
  315. package/esm/rpc/BaseRpcDriver.js +74 -107
  316. package/esm/rpc/MainThreadRpcDriver.d.ts +9 -10
  317. package/esm/rpc/MainThreadRpcDriver.js +18 -29
  318. package/esm/rpc/RpcClient.d.ts +38 -0
  319. package/esm/rpc/RpcClient.js +154 -0
  320. package/esm/rpc/RpcManager.d.ts +116 -27
  321. package/esm/rpc/RpcManager.js +177 -50
  322. package/esm/rpc/RpcRegistry.d.ts +265 -0
  323. package/esm/rpc/RpcRegistry.js +1 -0
  324. package/esm/rpc/RpcServer.d.ts +41 -0
  325. package/esm/rpc/RpcServer.js +235 -0
  326. package/esm/rpc/WebWorkerRpcDriver.d.ts +71 -24
  327. package/esm/rpc/WebWorkerRpcDriver.js +312 -27
  328. package/esm/rpc/byteBudget.d.ts +49 -0
  329. package/esm/rpc/byteBudget.js +50 -0
  330. package/esm/rpc/configSchema.d.ts +27 -5
  331. package/esm/rpc/configSchema.js +40 -16
  332. package/esm/rpc/coreRpcMethods.d.ts +2 -5
  333. package/esm/rpc/coreRpcMethods.js +9 -12
  334. package/esm/rpc/explainTransferError.d.ts +35 -0
  335. package/esm/rpc/explainTransferError.js +158 -0
  336. package/esm/rpc/methods/CoreFreeResources.d.ts +19 -4
  337. package/esm/rpc/methods/CoreFreeResources.js +17 -6
  338. package/esm/rpc/methods/CoreGetExportData.d.ts +5 -18
  339. package/esm/rpc/methods/CoreGetExportData.js +26 -15
  340. package/esm/rpc/methods/CoreGetFeatures.d.ts +6 -15
  341. package/esm/rpc/methods/CoreGetFeatures.js +15 -17
  342. package/esm/rpc/methods/CoreGetInfo.d.ts +6 -0
  343. package/esm/rpc/methods/CoreGetInfo.js +12 -0
  344. package/esm/rpc/methods/CoreGetMetadata.d.ts +4 -7
  345. package/esm/rpc/methods/CoreGetMetadata.js +6 -9
  346. package/esm/rpc/methods/CoreGetRefNames.d.ts +4 -8
  347. package/esm/rpc/methods/CoreGetRefNames.js +24 -13
  348. package/esm/rpc/methods/CoreGetRegionByteEstimate.d.ts +6 -0
  349. package/esm/rpc/methods/CoreGetRegionByteEstimate.js +19 -0
  350. package/esm/rpc/methods/CoreGetRegions.d.ts +4 -6
  351. package/esm/rpc/methods/CoreGetRegions.js +6 -9
  352. package/esm/rpc/methods/CoreGetSequence.d.ts +4 -11
  353. package/esm/rpc/methods/CoreGetSequence.js +12 -13
  354. package/esm/rpc/serializeError/index.d.ts +9 -0
  355. package/esm/rpc/serializeError/index.js +86 -0
  356. package/esm/svg/SvgExport.d.ts +30 -0
  357. package/esm/svg/SvgExport.js +53 -0
  358. package/esm/svg/constants.d.ts +1 -0
  359. package/esm/svg/constants.js +5 -0
  360. package/esm/svg/saveSvgAsImage.d.ts +6 -0
  361. package/esm/svg/saveSvgAsImage.js +90 -0
  362. package/esm/svg/svgId.d.ts +42 -0
  363. package/esm/svg/svgId.js +84 -0
  364. package/esm/svg/svgReady.d.ts +136 -0
  365. package/esm/svg/svgReady.js +164 -0
  366. package/esm/svg/trackNames.d.ts +27 -0
  367. package/esm/svg/trackNames.js +31 -0
  368. package/esm/svg/wrapSvgExport.d.ts +12 -0
  369. package/esm/svg/wrapSvgExport.js +78 -0
  370. package/esm/ui/ActionLink.d.ts +7 -0
  371. package/esm/ui/ActionLink.js +9 -0
  372. package/esm/ui/AddCustomPluginDialog.d.ts +14 -0
  373. package/esm/ui/AddCustomPluginDialog.js +61 -0
  374. package/esm/ui/AddGenomePane.d.ts +8 -0
  375. package/esm/ui/AddGenomePane.js +228 -0
  376. package/esm/ui/AdvancedOptions.d.ts +6 -0
  377. package/esm/ui/AdvancedOptions.js +17 -0
  378. package/esm/ui/AppLogo.d.ts +1 -1
  379. package/esm/ui/AppLogo.js +2 -2
  380. package/esm/ui/AssemblySelector.d.ts +5 -8
  381. package/esm/ui/AssemblySelector.js +8 -26
  382. package/esm/ui/BaseExportSvgDialog.d.ts +16 -0
  383. package/esm/ui/BaseExportSvgDialog.js +84 -0
  384. package/esm/ui/BaseTooltip.d.ts +14 -3
  385. package/esm/ui/BaseTooltip.js +151 -34
  386. package/esm/ui/CascadingMenu.d.ts +9 -18
  387. package/esm/ui/CascadingMenu.js +368 -41
  388. package/esm/ui/CascadingMenuButton.d.ts +9 -11
  389. package/esm/ui/CascadingMenuButton.js +36 -18
  390. package/esm/ui/CascadingMenuHelpDialog.d.ts +2 -2
  391. package/esm/ui/CascadingMenuHelpDialog.js +4 -5
  392. package/esm/ui/CascadingMenuHelpIconButton.d.ts +2 -1
  393. package/esm/ui/CascadingMenuHelpIconButton.js +18 -9
  394. package/esm/ui/ColorPicker.d.ts +6 -9
  395. package/esm/ui/ColorPicker.js +36 -39
  396. package/esm/ui/ConfirmDialog.d.ts +2 -9
  397. package/esm/ui/ConfirmDialog.js +6 -9
  398. package/esm/ui/ContextMenu.d.ts +50 -0
  399. package/esm/ui/ContextMenu.js +55 -0
  400. package/esm/ui/CopyToClipboardButton.d.ts +10 -0
  401. package/esm/ui/CopyToClipboardButton.js +14 -0
  402. package/esm/ui/Crosshairs.d.ts +10 -0
  403. package/esm/ui/Crosshairs.js +15 -0
  404. package/esm/ui/DOMPurifySanitizedHTML.d.ts +1 -1
  405. package/esm/ui/DOMPurifySanitizedHTML.js +5 -5
  406. package/esm/ui/DataGridFlexContainer.d.ts +9 -2
  407. package/esm/ui/DataGridFlexContainer.js +4 -3
  408. package/esm/ui/Dialog.d.ts +5 -2
  409. package/esm/ui/Dialog.js +35 -27
  410. package/esm/ui/DraggableDialog.d.ts +3 -3
  411. package/esm/ui/DraggableDialog.js +50 -12
  412. package/esm/ui/DropDownMenu.d.ts +4 -2
  413. package/esm/ui/DropDownMenu.js +4 -4
  414. package/esm/ui/EditableTypography.d.ts +3 -1
  415. package/esm/ui/EditableTypography.js +34 -26
  416. package/esm/ui/ErrorActions.d.ts +24 -0
  417. package/esm/ui/ErrorActions.js +20 -0
  418. package/esm/ui/ErrorBanner.d.ts +7 -0
  419. package/esm/ui/ErrorBanner.js +35 -0
  420. package/esm/ui/ErrorBar.d.ts +6 -0
  421. package/esm/ui/ErrorBar.js +35 -0
  422. package/esm/ui/ErrorBoundary.d.ts +29 -5
  423. package/esm/ui/ErrorBoundary.js +32 -2
  424. package/esm/ui/ErrorMessage.d.ts +2 -4
  425. package/esm/ui/ErrorMessage.js +17 -52
  426. package/esm/ui/ErrorMessageStackTraceContents.d.ts +1 -1
  427. package/esm/ui/ErrorMessageStackTraceContents.js +3 -3
  428. package/esm/ui/ErrorMessageStackTraceDialog.d.ts +1 -1
  429. package/esm/ui/ErrorMessageStackTraceDialog.js +57 -96
  430. package/esm/ui/ErrorOverlay.d.ts +8 -0
  431. package/esm/ui/ErrorOverlay.js +5 -0
  432. package/esm/ui/ExportSvgDialog.d.ts +7 -0
  433. package/esm/ui/ExportSvgDialog.js +9 -0
  434. package/esm/ui/ExternalLink.d.ts +1 -1
  435. package/esm/ui/FactoryResetDialog.d.ts +1 -1
  436. package/esm/ui/FactoryResetDialog.js +6 -15
  437. package/esm/ui/FatalErrorDialog.d.ts +3 -2
  438. package/esm/ui/FatalErrorDialog.js +6 -5
  439. package/esm/ui/FileDropZone.d.ts +25 -0
  440. package/esm/ui/FileDropZone.js +128 -0
  441. package/esm/ui/FileSelector/FileSelector.d.ts +1 -1
  442. package/esm/ui/FileSelector/FileSelector.js +59 -30
  443. package/esm/ui/FileSelector/LocalFileChooser.d.ts +7 -2
  444. package/esm/ui/FileSelector/LocalFileChooser.js +61 -47
  445. package/esm/ui/FileSelector/LocationInput.d.ts +1 -1
  446. package/esm/ui/FileSelector/LocationInput.js +8 -12
  447. package/esm/ui/FileSelector/SourceTypeSelector.d.ts +5 -5
  448. package/esm/ui/FileSelector/SourceTypeSelector.js +9 -7
  449. package/esm/ui/FileSelector/UrlChooser.d.ts +1 -1
  450. package/esm/ui/FileSelector/UrlChooser.js +26 -2
  451. package/esm/ui/FileSelector/emptySourceType.d.ts +2 -0
  452. package/esm/ui/FileSelector/emptySourceType.js +14 -0
  453. package/esm/ui/FileSelector/useInternetAccounts.d.ts +383 -71
  454. package/esm/ui/FileSelector/useInternetAccounts.js +13 -6
  455. package/esm/ui/FileSelector/util.d.ts +58 -3
  456. package/esm/ui/FileSelector/util.js +128 -11
  457. package/esm/ui/GpuFallbackButton.d.ts +12 -0
  458. package/esm/ui/GpuFallbackButton.js +20 -0
  459. package/esm/ui/HoverMenu.d.ts +12 -3
  460. package/esm/ui/HoverMenu.js +31 -9
  461. package/esm/ui/HoverTooltip.d.ts +27 -0
  462. package/esm/ui/HoverTooltip.js +24 -0
  463. package/esm/ui/Icons.d.ts +6 -4
  464. package/esm/ui/Icons.js +9 -0
  465. package/esm/ui/InfoDialog.d.ts +7 -0
  466. package/esm/ui/InfoDialog.js +16 -0
  467. package/esm/ui/InlineMenuControls.d.ts +6 -0
  468. package/esm/ui/InlineMenuControls.js +17 -0
  469. package/esm/ui/JexlFilterDialog.d.ts +23 -0
  470. package/esm/ui/JexlFilterDialog.js +94 -0
  471. package/esm/ui/LabeledCheckbox.d.ts +9 -0
  472. package/esm/ui/LabeledCheckbox.js +7 -0
  473. package/esm/ui/LegendSwatchGlyph.d.ts +7 -0
  474. package/esm/ui/LegendSwatchGlyph.js +25 -0
  475. package/esm/ui/LoadingDots.d.ts +1 -0
  476. package/esm/ui/LoadingDots.js +30 -0
  477. package/esm/ui/LoadingEllipses.d.ts +17 -1
  478. package/esm/ui/LoadingEllipses.js +20 -29
  479. package/esm/ui/LoadingOverlay.d.ts +9 -0
  480. package/esm/ui/LoadingOverlay.js +137 -0
  481. package/esm/ui/LoadingProgress.d.ts +16 -0
  482. package/esm/ui/LoadingProgress.js +16 -0
  483. package/esm/ui/Logo.d.ts +2 -2
  484. package/esm/ui/Logo.js +23 -24
  485. package/esm/ui/Menu.js +1 -1
  486. package/esm/ui/MenuItemChevron.d.ts +3 -0
  487. package/esm/ui/MenuItemChevron.js +19 -0
  488. package/esm/ui/MenuItemEndDecoration.d.ts +4 -0
  489. package/esm/ui/MenuItemEndDecoration.js +28 -0
  490. package/esm/ui/MenuItemTrailing.d.ts +12 -0
  491. package/esm/ui/MenuItemTrailing.js +42 -0
  492. package/esm/ui/MenuTypes.d.ts +124 -4
  493. package/esm/ui/MenuTypes.js +13 -1
  494. package/esm/ui/MonospaceTextField.d.ts +9 -0
  495. package/esm/ui/MonospaceTextField.js +37 -0
  496. package/esm/ui/NumberTextField.d.ts +31 -0
  497. package/esm/ui/NumberTextField.js +33 -0
  498. package/esm/ui/PaletteContext.d.ts +85 -0
  499. package/esm/ui/PaletteContext.js +104 -0
  500. package/esm/ui/PinAdornment.d.ts +5 -0
  501. package/esm/ui/PinAdornment.js +79 -0
  502. package/esm/ui/PluggableComponent.d.ts +10 -0
  503. package/esm/ui/PluggableComponent.js +19 -0
  504. package/esm/ui/PluggableComponents.d.ts +29 -0
  505. package/esm/ui/PluggableComponents.js +28 -0
  506. package/esm/ui/PluggableElements.d.ts +23 -0
  507. package/esm/ui/PluggableElements.js +24 -0
  508. package/esm/ui/PluginStoreCard.d.ts +17 -0
  509. package/esm/ui/PluginStoreCard.js +45 -0
  510. package/esm/ui/PopoverPicker.d.ts +6 -0
  511. package/esm/ui/PopoverPicker.js +25 -0
  512. package/esm/ui/PrerenderedCanvas.d.ts +1 -1
  513. package/esm/ui/PrerenderedCanvas.js +5 -4
  514. package/esm/ui/ProgressChip.d.ts +37 -0
  515. package/esm/ui/ProgressChip.js +66 -0
  516. package/esm/ui/RedErrorMessageBox.d.ts +1 -1
  517. package/esm/ui/RedErrorMessageBox.js +9 -3
  518. package/esm/ui/RefNameAutocomplete/EndAdornment.d.ts +5 -0
  519. package/esm/ui/RefNameAutocomplete/EndAdornment.js +31 -0
  520. package/esm/ui/RefNameAutocomplete/HelpDialog.d.ts +3 -0
  521. package/esm/ui/RefNameAutocomplete/HelpDialog.js +7 -0
  522. package/esm/ui/RefNameAutocomplete/index.d.ts +22 -0
  523. package/esm/ui/RefNameAutocomplete/index.js +78 -0
  524. package/esm/ui/RefNameAutocomplete/util.d.ts +49 -0
  525. package/esm/ui/RefNameAutocomplete/util.js +168 -0
  526. package/esm/ui/ReplaceCurrentViewButton.d.ts +19 -0
  527. package/esm/ui/ReplaceCurrentViewButton.js +22 -0
  528. package/esm/ui/ResizeHandle.d.ts +13 -7
  529. package/esm/ui/ResizeHandle.js +42 -55
  530. package/esm/ui/ReturnToImportFormDialog.d.ts +1 -1
  531. package/esm/ui/ReturnToImportFormDialog.js +7 -9
  532. package/esm/ui/SanitizedHTML.d.ts +6 -1
  533. package/esm/ui/SanitizedHTML.js +7 -47
  534. package/esm/ui/ScrollEdgeShadow.d.ts +44 -0
  535. package/esm/ui/ScrollEdgeShadow.js +98 -0
  536. package/esm/ui/ScrollZoomToggle.d.ts +38 -0
  537. package/esm/ui/ScrollZoomToggle.js +92 -0
  538. package/esm/ui/SequenceAdapterInputs.d.ts +9 -0
  539. package/esm/ui/SequenceAdapterInputs.js +30 -0
  540. package/esm/ui/SettingsChangesTable.d.ts +14 -0
  541. package/esm/ui/SettingsChangesTable.js +49 -0
  542. package/esm/ui/ShareLinkField.d.ts +6 -0
  543. package/esm/ui/ShareLinkField.js +42 -0
  544. package/esm/ui/SingleSlider.d.ts +8 -0
  545. package/esm/ui/SingleSlider.js +11 -0
  546. package/esm/ui/SizeSliderRow.d.ts +16 -0
  547. package/esm/ui/SizeSliderRow.js +50 -0
  548. package/esm/ui/SliderTooltip.d.ts +2 -0
  549. package/esm/ui/SliderTooltip.js +17 -0
  550. package/esm/ui/Snackbar.d.ts +4 -2
  551. package/esm/ui/Snackbar.js +11 -8
  552. package/esm/ui/SnackbarContents.d.ts +1 -1
  553. package/esm/ui/SnackbarContents.js +21 -3
  554. package/esm/ui/SnackbarModel.d.ts +40 -0
  555. package/esm/ui/SnackbarModel.js +43 -11
  556. package/esm/ui/StackTraceButton.d.ts +5 -0
  557. package/esm/ui/StackTraceButton.js +16 -0
  558. package/esm/ui/StatusProgressBar.d.ts +37 -0
  559. package/esm/ui/StatusProgressBar.js +76 -0
  560. package/esm/ui/SubmitDialog.d.ts +6 -0
  561. package/esm/ui/SubmitDialog.js +9 -0
  562. package/esm/ui/SubmitForm.d.ts +23 -0
  563. package/esm/ui/SubmitForm.js +23 -0
  564. package/esm/ui/SvgColorLegend.d.ts +13 -0
  565. package/esm/ui/SvgColorLegend.js +65 -0
  566. package/esm/ui/SvgGradientLegend.d.ts +26 -0
  567. package/esm/ui/SvgGradientLegend.js +26 -0
  568. package/esm/ui/TagTextField.d.ts +40 -0
  569. package/esm/ui/TagTextField.js +32 -0
  570. package/esm/ui/VerticalScrollbar.d.ts +45 -0
  571. package/esm/ui/VerticalScrollbar.js +158 -0
  572. package/esm/ui/ViewLoadingScreen.d.ts +24 -0
  573. package/esm/ui/ViewLoadingScreen.js +76 -0
  574. package/esm/ui/addExtensionElement.d.ts +18 -0
  575. package/esm/ui/addExtensionElement.js +23 -0
  576. package/esm/ui/buildExtraTrackMenuItems.d.ts +22 -0
  577. package/esm/ui/buildExtraTrackMenuItems.js +14 -0
  578. package/esm/ui/colorSwatchStyle.d.ts +9 -0
  579. package/esm/ui/colorSwatchStyle.js +11 -0
  580. package/esm/ui/colors.d.ts +61 -8
  581. package/esm/ui/colors.js +135 -1
  582. package/esm/ui/extensionSelectors.d.ts +38 -0
  583. package/esm/ui/extensionSelectors.js +49 -0
  584. package/esm/ui/filterMenuItems.d.ts +112 -0
  585. package/esm/ui/filterMenuItems.js +86 -0
  586. package/esm/ui/formatErrorStack.d.ts +1 -0
  587. package/esm/ui/formatErrorStack.js +56 -0
  588. package/esm/ui/gpuFallback.d.ts +33 -0
  589. package/esm/ui/gpuFallback.js +39 -0
  590. package/esm/ui/highlightChipReveal.d.ts +32 -0
  591. package/esm/ui/highlightChipReveal.js +39 -0
  592. package/esm/ui/hoverBoxStyle.d.ts +11 -0
  593. package/esm/ui/hoverBoxStyle.js +13 -0
  594. package/esm/ui/index.d.ts +76 -4
  595. package/esm/ui/index.js +90 -19
  596. package/esm/ui/inlineMenuRowWidth.d.ts +1 -0
  597. package/esm/ui/inlineMenuRowWidth.js +8 -0
  598. package/esm/ui/launchTargetsMenuItem.d.ts +18 -0
  599. package/esm/ui/launchTargetsMenuItem.js +24 -0
  600. package/esm/ui/launchViewMenu.d.ts +4 -0
  601. package/esm/ui/launchViewMenu.js +36 -0
  602. package/esm/ui/legendMenuItem.d.ts +38 -0
  603. package/esm/ui/legendMenuItem.js +44 -0
  604. package/esm/ui/legendSpec.d.ts +62 -0
  605. package/esm/ui/legendSpec.js +78 -0
  606. package/esm/ui/loadingDotKeyframes.d.ts +18 -0
  607. package/esm/ui/loadingDotKeyframes.js +17 -0
  608. package/esm/ui/makeSizeMenu.d.ts +30 -0
  609. package/esm/ui/makeSizeMenu.js +82 -0
  610. package/esm/ui/mapStackTrace.d.ts +8 -0
  611. package/esm/ui/mapStackTrace.js +108 -0
  612. package/esm/ui/measureLegendText.d.ts +1 -0
  613. package/esm/ui/measureLegendText.js +8 -0
  614. package/esm/ui/menuItemAdornment.d.ts +33 -0
  615. package/esm/ui/menuItemAdornment.js +50 -0
  616. package/esm/ui/menuItems.d.ts +28 -0
  617. package/esm/ui/menuItems.js +26 -0
  618. package/esm/ui/menuLabels.d.ts +41 -0
  619. package/esm/ui/menuLabels.js +43 -0
  620. package/esm/ui/multiTrackMenuItems.d.ts +19 -0
  621. package/esm/ui/multiTrackMenuItems.js +15 -0
  622. package/esm/ui/palette.d.ts +559 -0
  623. package/esm/ui/palette.js +746 -0
  624. package/esm/ui/parseError.d.ts +4 -0
  625. package/esm/ui/parseError.js +18 -0
  626. package/esm/ui/persistentScrollbarStyle.d.ts +49 -0
  627. package/esm/ui/persistentScrollbarStyle.js +53 -0
  628. package/esm/ui/promotableMenuItems.d.ts +19 -0
  629. package/esm/ui/promotableMenuItems.js +89 -0
  630. package/esm/ui/promotablePinCoverage.d.ts +44 -0
  631. package/esm/ui/promotablePinCoverage.js +87 -0
  632. package/esm/ui/radioSubMenu.d.ts +33 -0
  633. package/esm/ui/radioSubMenu.js +32 -0
  634. package/esm/ui/react-colorful.js +5 -1
  635. package/esm/ui/replaceViewAction.d.ts +31 -0
  636. package/esm/ui/replaceViewAction.js +39 -0
  637. package/esm/ui/rewriteExternalAnchors.d.ts +1 -0
  638. package/esm/ui/rewriteExternalAnchors.js +8 -0
  639. package/esm/ui/scrollZoomLabels.d.ts +17 -0
  640. package/esm/ui/scrollZoomLabels.js +22 -0
  641. package/esm/ui/showSubMenu.d.ts +19 -0
  642. package/esm/ui/showSubMenu.js +30 -0
  643. package/esm/ui/sliderScale.d.ts +6 -0
  644. package/esm/ui/sliderScale.js +30 -0
  645. package/esm/ui/statusProgressKeyframes.d.ts +6 -0
  646. package/esm/ui/statusProgressKeyframes.js +14 -0
  647. package/esm/ui/stripStackTraceMessage.d.ts +1 -0
  648. package/esm/ui/stripStackTraceMessage.js +9 -0
  649. package/esm/ui/styleTheme.d.ts +158 -0
  650. package/esm/ui/styleTheme.js +115 -0
  651. package/esm/ui/submenuAim.d.ts +30 -0
  652. package/esm/ui/submenuAim.js +37 -0
  653. package/esm/ui/theme.d.ts +343 -29
  654. package/esm/ui/theme.js +258 -342
  655. package/esm/ui/toggleMenuItems.d.ts +44 -0
  656. package/esm/ui/toggleMenuItems.js +60 -0
  657. package/esm/ui/useAssemblySelection.d.ts +153 -0
  658. package/esm/ui/useAssemblySelection.js +54 -0
  659. package/esm/ui/useCoalescedPointer.d.ts +36 -0
  660. package/esm/ui/useCoalescedPointer.js +60 -0
  661. package/esm/ui/useCopyToClipboard.d.ts +15 -0
  662. package/esm/ui/useCopyToClipboard.js +41 -0
  663. package/esm/ui/useExportSvgPreference.d.ts +1 -0
  664. package/esm/ui/useExportSvgPreference.js +4 -0
  665. package/esm/ui/useMouseTracking.d.ts +71 -0
  666. package/esm/ui/useMouseTracking.js +179 -0
  667. package/esm/ui/useRecentLocations.d.ts +28 -0
  668. package/esm/ui/useRecentLocations.js +31 -0
  669. package/esm/ui/wrapComponent.d.ts +47 -0
  670. package/esm/ui/wrapComponent.js +58 -0
  671. package/esm/ui/zIndexes.d.ts +28 -0
  672. package/esm/ui/zIndexes.js +38 -0
  673. package/esm/util/Base1DUtils.d.ts +204 -16
  674. package/esm/util/Base1DUtils.js +310 -175
  675. package/esm/util/Base1DViewModel.d.ts +97 -20
  676. package/esm/util/Base1DViewModel.js +148 -39
  677. package/esm/util/FileSaver/index.d.ts +1 -0
  678. package/esm/util/FileSaver/index.js +27 -0
  679. package/esm/util/IntervalTree.d.ts +18 -39
  680. package/esm/util/IntervalTree.js +63 -244
  681. package/esm/util/SvgCanvas.d.ts +81 -0
  682. package/esm/util/SvgCanvas.js +500 -0
  683. package/esm/util/TimeTraveller.d.ts +12 -0
  684. package/esm/util/TimeTraveller.js +130 -27
  685. package/esm/util/aborting.d.ts +17 -4
  686. package/esm/util/aborting.js +30 -25
  687. package/esm/util/adapterMetadata.d.ts +20 -0
  688. package/esm/util/adapterMetadata.js +39 -0
  689. package/esm/util/addAndShowTrack.d.ts +22 -0
  690. package/esm/util/addAndShowTrack.js +23 -0
  691. package/esm/util/addRelativeUris.d.ts +17 -0
  692. package/esm/util/addRelativeUris.js +42 -0
  693. package/esm/util/addTrackComponent.d.ts +72 -0
  694. package/esm/util/addTrackComponent.js +53 -0
  695. package/esm/util/addTrackFromWidget.d.ts +94 -0
  696. package/esm/util/addTrackFromWidget.js +90 -0
  697. package/esm/util/analytics.d.ts +32 -3
  698. package/esm/util/analytics.js +102 -49
  699. package/esm/util/animationAllowed.d.ts +17 -0
  700. package/esm/util/animationAllowed.js +22 -0
  701. package/esm/util/applyInitSettings.d.ts +79 -0
  702. package/esm/util/applyInitSettings.js +91 -0
  703. package/esm/util/applyRowResizeWheel.d.ts +10 -0
  704. package/esm/util/applyRowResizeWheel.js +34 -0
  705. package/esm/util/assemblyConfigUtils.d.ts +144 -0
  706. package/esm/util/assemblyConfigUtils.js +498 -0
  707. package/esm/util/bandHeight.d.ts +53 -0
  708. package/esm/util/bandHeight.js +56 -0
  709. package/esm/util/bandLayout.d.ts +51 -0
  710. package/esm/util/bandLayout.js +36 -0
  711. package/esm/util/bezierConnector.d.ts +14 -0
  712. package/esm/util/bezierConnector.js +108 -0
  713. package/esm/util/bgzfWorkerPool.d.ts +78 -0
  714. package/esm/util/bgzfWorkerPool.js +81 -0
  715. package/esm/util/blockTypes.d.ts +64 -45
  716. package/esm/util/blockTypes.js +67 -74
  717. package/esm/util/bpUtils.d.ts +81 -0
  718. package/esm/util/bpUtils.js +103 -0
  719. package/esm/util/cacheBudgets.d.ts +52 -0
  720. package/esm/util/cacheBudgets.js +52 -0
  721. package/esm/util/cachedSetup.d.ts +51 -0
  722. package/esm/util/cachedSetup.js +87 -0
  723. package/esm/util/calculateDynamicBlocks.d.ts +5 -0
  724. package/esm/util/calculateDynamicBlocks.js +85 -82
  725. package/esm/util/calculateStaticBlocks.d.ts +2 -3
  726. package/esm/util/calculateStaticBlocks.js +48 -71
  727. package/esm/util/chooseGridPitch.d.ts +9 -0
  728. package/esm/util/chooseGridPitch.js +31 -0
  729. package/esm/util/clampToContig.d.ts +26 -0
  730. package/esm/util/clampToContig.js +28 -0
  731. package/esm/util/cmpStr.d.ts +1 -0
  732. package/esm/util/cmpStr.js +7 -0
  733. package/esm/util/coarseStripHTML.js +3 -15
  734. package/esm/util/color/cssColorsLevel4.js +6 -2
  735. package/esm/util/color/index.d.ts +81 -2
  736. package/esm/util/color/index.js +194 -25
  737. package/esm/util/color-bits/bit.d.ts +4 -0
  738. package/esm/util/color-bits/bit.js +37 -0
  739. package/esm/util/color-bits/convert.d.ts +23 -0
  740. package/esm/util/color-bits/convert.js +294 -0
  741. package/esm/util/color-bits/core.d.ts +34 -0
  742. package/esm/util/color-bits/core.js +67 -0
  743. package/esm/util/color-bits/format.d.ts +24 -0
  744. package/esm/util/color-bits/format.js +82 -0
  745. package/esm/util/color-bits/functions.d.ts +33 -0
  746. package/esm/util/color-bits/functions.js +70 -0
  747. package/esm/util/color-bits/index.d.ts +5 -0
  748. package/esm/util/color-bits/index.js +4 -0
  749. package/esm/util/color-bits/parse.d.ts +17 -0
  750. package/esm/util/color-bits/parse.js +382 -0
  751. package/esm/util/colorBits.d.ts +39 -0
  752. package/esm/util/colorBits.js +180 -0
  753. package/esm/util/colorRamp.d.ts +37 -0
  754. package/esm/util/colorRamp.js +93 -0
  755. package/esm/util/colord.d.ts +8 -0
  756. package/esm/util/colord.js +43 -191
  757. package/esm/util/convertCodingSequenceToPeptides.d.ts +17 -3
  758. package/esm/util/convertCodingSequenceToPeptides.js +51 -4
  759. package/esm/util/copyText.d.ts +18 -0
  760. package/esm/util/copyText.js +30 -0
  761. package/esm/util/copyToClipboard.d.ts +4 -0
  762. package/esm/util/copyToClipboard.js +58 -0
  763. package/esm/util/createStopTokenRotation.d.ts +117 -0
  764. package/esm/util/createStopTokenRotation.js +147 -0
  765. package/esm/util/createSvgRasterCanvas.d.ts +7 -0
  766. package/esm/util/createSvgRasterCanvas.js +22 -0
  767. package/esm/util/crypto.d.ts +24 -0
  768. package/esm/util/crypto.js +85 -2
  769. package/esm/util/dataGridUtils.d.ts +9 -0
  770. package/esm/util/dataGridUtils.js +36 -0
  771. package/esm/util/dedupe.js +1 -0
  772. package/esm/util/deepEqual.d.ts +8 -0
  773. package/esm/util/deepEqual.js +22 -0
  774. package/esm/util/deepMerge.d.ts +20 -0
  775. package/esm/util/deepMerge.js +44 -0
  776. package/esm/util/diagonalizeRegions.d.ts +23 -0
  777. package/esm/util/diagonalizeRegions.js +192 -0
  778. package/esm/util/environment.d.ts +4 -0
  779. package/esm/util/environment.js +43 -0
  780. package/esm/util/eventPoint.d.ts +32 -0
  781. package/esm/util/eventPoint.js +28 -0
  782. package/esm/util/fetchAndMaybeUnzip.d.ts +6 -0
  783. package/esm/util/fetchAndMaybeUnzip.js +64 -0
  784. package/esm/util/fetchContext.d.ts +82 -0
  785. package/esm/util/fetchContext.js +59 -0
  786. package/esm/util/fetchHub.d.ts +15 -0
  787. package/esm/util/fetchHub.js +31 -0
  788. package/esm/util/fetchJson.d.ts +1 -0
  789. package/esm/util/fetchJson.js +7 -0
  790. package/esm/util/fetchPhases.d.ts +77 -0
  791. package/esm/util/fetchPhases.js +1 -0
  792. package/esm/util/fetchSeq.d.ts +5 -1
  793. package/esm/util/fetchSeq.js +18 -6
  794. package/esm/util/fileHandleStore.d.ts +19 -2
  795. package/esm/util/fileHandleStore.js +95 -35
  796. package/esm/util/flatbush/index.d.ts +27 -6
  797. package/esm/util/flatbush/index.js +194 -218
  798. package/esm/util/formatBytes.d.ts +9 -0
  799. package/esm/util/formatBytes.js +18 -0
  800. package/esm/util/formatFastaStrings.d.ts +13 -0
  801. package/esm/util/formatFastaStrings.js +13 -0
  802. package/esm/util/formatGuessers.d.ts +30 -0
  803. package/esm/util/formatGuessers.js +69 -0
  804. package/esm/util/formatRelativeTime.d.ts +1 -0
  805. package/esm/util/formatRelativeTime.js +25 -0
  806. package/esm/util/frameCoalescer.d.ts +30 -0
  807. package/esm/util/frameCoalescer.js +22 -0
  808. package/esm/util/freezeDeep.d.ts +28 -0
  809. package/esm/util/freezeDeep.js +41 -0
  810. package/esm/util/geneticCodes.d.ts +56 -0
  811. package/esm/util/geneticCodes.js +371 -0
  812. package/esm/util/getFileName.d.ts +11 -0
  813. package/esm/util/getFileName.js +34 -0
  814. package/esm/util/getLocationUri.d.ts +49 -0
  815. package/esm/util/getLocationUri.js +63 -0
  816. package/esm/util/getRelativeX.d.ts +4 -0
  817. package/esm/util/getRelativeX.js +7 -0
  818. package/esm/util/getStr.d.ts +6 -0
  819. package/esm/util/getStr.js +15 -0
  820. package/esm/util/highlights.d.ts +21 -0
  821. package/esm/util/highlights.js +100 -0
  822. package/esm/util/hooks.d.ts +160 -0
  823. package/esm/util/hooks.js +416 -0
  824. package/esm/util/htmlText.d.ts +13 -0
  825. package/esm/util/htmlText.js +66 -0
  826. package/esm/util/idMaker.d.ts +1 -1
  827. package/esm/util/idMaker.js +31 -18
  828. package/esm/util/index.d.ts +82 -268
  829. package/esm/util/index.js +136 -853
  830. package/esm/util/indexCandidates.d.ts +50 -0
  831. package/esm/util/indexCandidates.js +101 -0
  832. package/esm/util/installClearHoverOnSurfaceMove.d.ts +40 -0
  833. package/esm/util/installClearHoverOnSurfaceMove.js +41 -0
  834. package/esm/util/installFetch.d.ts +194 -0
  835. package/esm/util/installFetch.js +178 -0
  836. package/esm/util/installInitAutorun.d.ts +62 -0
  837. package/esm/util/installInitAutorun.js +107 -0
  838. package/esm/util/intervals.d.ts +20 -0
  839. package/esm/util/intervals.js +37 -0
  840. package/esm/util/io/RemoteFileWithRangeCache.d.ts +10 -11
  841. package/esm/util/io/RemoteFileWithRangeCache.js +10 -148
  842. package/esm/util/io/index.d.ts +39 -2
  843. package/esm/util/io/index.js +115 -12
  844. package/esm/util/isDataCurrent.d.ts +7 -0
  845. package/esm/util/isDataCurrent.js +9 -0
  846. package/esm/util/isWebWorker.js +1 -2
  847. package/esm/util/iupac.d.ts +4 -0
  848. package/esm/util/iupac.js +59 -0
  849. package/esm/util/jexl.js +141 -17
  850. package/esm/util/jexlFilters.d.ts +75 -0
  851. package/esm/util/jexlFilters.js +49 -0
  852. package/esm/util/jexlStrings.d.ts +22 -1
  853. package/esm/util/jexlStrings.js +21 -14
  854. package/esm/util/layouts/GranularRectLayout.d.ts +13 -25
  855. package/esm/util/layouts/GranularRectLayout.js +99 -356
  856. package/esm/util/layouts/index.d.ts +1 -7
  857. package/esm/util/layouts/index.js +2 -6
  858. package/esm/util/layouts/intervalUtils.d.ts +12 -1
  859. package/esm/util/layouts/intervalUtils.js +13 -31
  860. package/esm/util/layouts/placeRect.d.ts +50 -0
  861. package/esm/util/layouts/placeRect.js +97 -0
  862. package/esm/util/leadingEdgeAutorun.d.ts +40 -0
  863. package/esm/util/leadingEdgeAutorun.js +51 -0
  864. package/esm/util/librpc.d.ts +5 -2
  865. package/esm/util/librpc.js +6 -1
  866. package/esm/util/linkify.js +2 -0
  867. package/esm/util/locString.d.ts +72 -0
  868. package/esm/util/locString.js +178 -7
  869. package/esm/util/locStringsToRegions.d.ts +10 -0
  870. package/esm/util/locStringsToRegions.js +35 -0
  871. package/esm/util/localStorage.d.ts +36 -0
  872. package/esm/util/localStorage.js +137 -0
  873. package/esm/util/makeAssembly.d.ts +54 -0
  874. package/esm/util/makeAssembly.js +52 -0
  875. package/esm/util/makeTrackId.d.ts +14 -0
  876. package/esm/util/makeTrackId.js +14 -0
  877. package/esm/util/matchTrackId.d.ts +11 -0
  878. package/esm/util/matchTrackId.js +14 -0
  879. package/esm/util/measureText.d.ts +24 -0
  880. package/esm/util/measureText.js +51 -0
  881. package/esm/util/mst-reflection.d.ts +14 -4
  882. package/esm/util/mst-reflection.js +33 -32
  883. package/esm/util/mstUtils.d.ts +89 -0
  884. package/esm/util/mstUtils.js +122 -0
  885. package/esm/util/nanoid.d.ts +0 -4
  886. package/esm/util/nanoid.js +10 -20
  887. package/esm/util/numericUtils.d.ts +20 -0
  888. package/esm/util/numericUtils.js +127 -0
  889. package/esm/util/objectUtils.d.ts +2 -0
  890. package/esm/util/objectUtils.js +9 -0
  891. package/esm/util/offscreenCanvasPonyfill.d.ts +5 -4
  892. package/esm/util/offscreenCanvasPonyfill.js +5 -47
  893. package/esm/util/openDisplays.d.ts +23 -0
  894. package/esm/util/openDisplays.js +79 -0
  895. package/esm/util/openFeatureWidget.d.ts +33 -0
  896. package/esm/util/openFeatureWidget.js +64 -0
  897. package/esm/util/paintLayer.d.ts +32 -0
  898. package/esm/util/paintLayer.js +33 -0
  899. package/esm/util/parentWalk.d.ts +32 -0
  900. package/esm/util/parentWalk.js +84 -0
  901. package/esm/util/parseLineByLine.d.ts +45 -2
  902. package/esm/util/parseLineByLine.js +156 -15
  903. package/esm/util/parseMotifList.d.ts +17 -0
  904. package/esm/util/parseMotifList.js +69 -0
  905. package/esm/util/pluginStore.d.ts +113 -0
  906. package/esm/util/pluginStore.js +253 -0
  907. package/esm/util/pointerPresence.d.ts +5 -0
  908. package/esm/util/pointerPresence.js +21 -0
  909. package/esm/util/progress.d.ts +459 -0
  910. package/esm/util/progress.js +820 -0
  911. package/esm/util/range.d.ts +42 -1
  912. package/esm/util/range.js +59 -2
  913. package/esm/util/renameRegions.d.ts +21 -0
  914. package/esm/util/renameRegions.js +129 -0
  915. package/esm/util/renderToStaticMarkup.d.ts +2 -0
  916. package/esm/util/renderToStaticMarkup.js +50 -0
  917. package/esm/util/reorder.d.ts +35 -0
  918. package/esm/util/reorder.js +83 -0
  919. package/esm/util/resolveRowHeight.d.ts +27 -0
  920. package/esm/util/resolveRowHeight.js +30 -0
  921. package/esm/util/revlist.d.ts +13 -0
  922. package/esm/util/revlist.js +14 -0
  923. package/esm/util/rowStackGeometry.d.ts +66 -0
  924. package/esm/util/rowStackGeometry.js +70 -0
  925. package/esm/util/rpc.d.ts +16 -1
  926. package/esm/util/rpc.js +12 -1
  927. package/esm/util/rxjs.d.ts +14 -1
  928. package/esm/util/rxjs.js +39 -10
  929. package/esm/util/sameStrings.d.ts +16 -0
  930. package/esm/util/sameStrings.js +20 -0
  931. package/esm/util/scrollLatch.d.ts +4 -0
  932. package/esm/util/scrollLatch.js +59 -0
  933. package/esm/util/selectNamedRegions.d.ts +136 -0
  934. package/esm/util/selectNamedRegions.js +222 -0
  935. package/esm/util/seqUtils.d.ts +17 -0
  936. package/esm/util/seqUtils.js +80 -0
  937. package/esm/util/sessionServices.d.ts +29 -0
  938. package/esm/util/sessionServices.js +46 -0
  939. package/esm/util/sessionSharing.d.ts +38 -0
  940. package/esm/util/sessionSharing.js +154 -0
  941. package/esm/util/sessionStorage.d.ts +1 -0
  942. package/esm/util/sessionStorage.js +15 -0
  943. package/esm/util/setStackTraceLimit.d.ts +6 -0
  944. package/esm/util/setStackTraceLimit.js +20 -0
  945. package/esm/util/simpleFeature.d.ts +112 -4
  946. package/esm/util/simpleFeature.js +181 -29
  947. package/esm/util/springAnimate.d.ts +20 -0
  948. package/esm/util/springAnimate.js +80 -0
  949. package/esm/util/stats.d.ts +25 -2
  950. package/esm/util/stats.js +39 -8
  951. package/esm/util/stopToken.d.ts +207 -15
  952. package/esm/util/stopToken.js +403 -55
  953. package/esm/util/stringUtils.d.ts +5 -0
  954. package/esm/util/stringUtils.js +34 -0
  955. package/esm/util/svgColorProps.d.ts +7 -0
  956. package/esm/util/svgColorProps.js +28 -0
  957. package/esm/util/tabix.d.ts +120 -0
  958. package/esm/util/tabix.js +143 -0
  959. package/esm/util/tags.d.ts +2 -0
  960. package/esm/util/tags.js +5 -0
  961. package/esm/util/temporaryAssembly.d.ts +21 -0
  962. package/esm/util/temporaryAssembly.js +29 -0
  963. package/esm/util/tickLabels.d.ts +36 -0
  964. package/esm/util/tickLabels.js +45 -0
  965. package/esm/util/timeGate.d.ts +26 -0
  966. package/esm/util/timeGate.js +79 -0
  967. package/esm/util/trackConfigDelta.d.ts +84 -0
  968. package/esm/util/trackConfigDelta.js +190 -0
  969. package/esm/util/tracks.d.ts +350 -30
  970. package/esm/util/tracks.js +574 -192
  971. package/esm/util/tss-react/cssAndCx.js +11 -66
  972. package/esm/util/tss-react/index.d.ts +11 -2
  973. package/esm/util/tss-react/index.js +9 -2
  974. package/esm/util/tss-react/makeStyles.js +7 -4
  975. package/esm/util/tss-react/mergeClasses.js +1 -0
  976. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  977. package/esm/util/tss-react/tools/classnames.js +3 -0
  978. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  979. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  980. package/esm/util/tss-react/types.d.ts +1 -1
  981. package/esm/util/tss-react/types.js +1 -6
  982. package/esm/util/types/ElementId.js +1 -1
  983. package/esm/util/types/data.d.ts +75 -0
  984. package/esm/util/types/data.js +41 -0
  985. package/esm/util/types/index.d.ts +358 -119
  986. package/esm/util/types/index.js +87 -64
  987. package/esm/util/types/isAny.d.ts +11 -0
  988. package/esm/util/types/isAny.js +1 -0
  989. package/esm/util/types/mst.d.ts +71 -47
  990. package/esm/util/types/mst.js +27 -22
  991. package/esm/util/types/predicate.d.ts +9 -0
  992. package/esm/util/types/predicate.js +1 -0
  993. package/esm/util/types/renderingServices.d.ts +16 -0
  994. package/esm/util/types/renderingServices.js +1 -0
  995. package/esm/util/types/services.d.ts +55 -0
  996. package/esm/util/types/services.js +10 -0
  997. package/esm/util/types/util.d.ts +8 -2
  998. package/esm/util/unzip.d.ts +1 -0
  999. package/esm/util/unzip.js +6 -0
  1000. package/esm/util/useEventCallback.d.ts +1 -0
  1001. package/esm/util/useEventCallback.js +16 -0
  1002. package/esm/util/useFeatureSequence.d.ts +13 -7
  1003. package/esm/util/useFeatureSequence.js +56 -78
  1004. package/esm/util/useFetch.d.ts +56 -0
  1005. package/esm/util/useFetch.js +188 -0
  1006. package/esm/util/useFetchPlugins.d.ts +12 -0
  1007. package/esm/util/useFetchPlugins.js +14 -0
  1008. package/esm/util/useMeasure.d.ts +11 -1
  1009. package/esm/util/useMeasure.js +20 -6
  1010. package/esm/util/usePanZoom.d.ts +75 -0
  1011. package/esm/util/usePanZoom.js +175 -0
  1012. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1013. package/esm/util/usePanelVirtualScroll.js +42 -0
  1014. package/esm/util/usePointerDrag.d.ts +37 -0
  1015. package/esm/util/usePointerDrag.js +61 -0
  1016. package/esm/util/useRafCommit.d.ts +4 -0
  1017. package/esm/util/useRafCommit.js +50 -0
  1018. package/esm/util/useResizeDrag.d.ts +91 -0
  1019. package/esm/util/useResizeDrag.js +105 -0
  1020. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1021. package/esm/util/useRowVirtualScroll.js +63 -0
  1022. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1023. package/esm/util/useVirtualScrollWheel.js +108 -0
  1024. package/esm/util/viewStatus.d.ts +58 -0
  1025. package/esm/util/viewStatus.js +20 -0
  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,174 @@
1
+ import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
2
+ /**
3
+ * Dev-only check that a display's fetch foundation attached it exactly once —
4
+ * the one ordering contract here that is a *state* rather than a declaration,
5
+ * so no selector can reach it. No-op in production.
6
+ *
7
+ * Called once per display from **whichever fetch foundation installed its
8
+ * autoruns** — `MultiRegionDisplayMixin`'s `afterAttach` for the per-region
9
+ * family, `installGlobalFetchAutorun` for the global one,
10
+ * `installComparativeFetchAutorun` for the comparative one. Landing here twice
11
+ * for one node means every autorun that foundation installs is installed twice:
12
+ * double fetches, double clears, and nothing anywhere says so.
13
+ *
14
+ * The named cause is a display that chains to `super` in its own `afterAttach`
15
+ * — our MST fork auto-chains lifecycle hooks, so the explicit call re-enters the
16
+ * foundation's hook. **That cause is a declaration and could be a lint selector;
17
+ * this check is not, because it is not the only cause**: composing two fetch
18
+ * foundations onto one display, or calling an installer from a display that
19
+ * already composes the mixin, arrives here the same way, through a composition
20
+ * assembled across files that no single one of them spells out. So the message
21
+ * leads with the common cause and then describes the state, not the syntax.
22
+ *
23
+ * `installedBy` names the caller so the message can describe the right thing;
24
+ * the WeakSet is shared, which is correct — a display composes one fetch
25
+ * foundation, so reaching here twice is the bug regardless of which.
26
+ *
27
+ * ARCHITECTURAL_LIMITS.md §"Ordering is the contract" is the authoritative
28
+ * account of which contracts report themselves at runtime, which are lint
29
+ * selectors and which are still silent; don't restate the split here, because
30
+ * this comment said "four places" against a heading that said five and a list
31
+ * that held six.
32
+ *
33
+ * Every message names the fix, not just the symptom — the failure modes here
34
+ * cost hours precisely because the symptom (a wedged display, a stale cache)
35
+ * points nowhere near the cause.
36
+ */
37
+ export declare function assertDisplayContract(self: IAnyStateTreeNode, installedBy?: string): void;
38
+ /** What one run of a display's fetch autorun did. */
39
+ export type FetchAutorunOutcome =
40
+ /** the display's own gate opened and a fetch started */
41
+ 'fetched'
42
+ /** the gate stayed shut, so this run did nothing */
43
+ | 'declined'
44
+ /** a foundation gate skipped the run before the display's own was consulted */
45
+ | 'gated'
46
+ /**
47
+ * The run stopped on something that re-wakes this autorun by itself, so it
48
+ * answers nothing either way — the same deferral `awaitingPrerequisite` gets,
49
+ * reached from inside the foundation rather than declared by the display. The
50
+ * per-region family's in-flight-fetch skip is the case: `reload()` signals the
51
+ * running fetch's stop token but `activeStopToken` clears in `runFetch`'s
52
+ * finally, so the very next run can still see `isLoading` — and that fetch
53
+ * ending bumps `fetchGeneration`, which the autorun tracks. Consuming the bump
54
+ * there would answer the retry with a run that predates it.
55
+ */
56
+ | 'deferred';
57
+ interface RetryContractHost {
58
+ reloadCounter: number;
59
+ fetchInert: boolean;
60
+ /**
61
+ * Optional: the comparative family has no two-stage fetch, so nothing there
62
+ * declares it. A family that grows one declares it and gets the deferral.
63
+ */
64
+ awaitingPrerequisite?: boolean;
65
+ /**
66
+ * Optional for the same reason: it is the LGV foundations' term for a view
67
+ * holding no content block, and a comparative display draws onto a shared
68
+ * surface that has no such state.
69
+ */
70
+ viewportEmpty?: boolean;
71
+ }
72
+ /** Called by `FetchMixin.runFetch`. Dev-only. */
73
+ export declare function noteFetchStarted(self: object): void;
74
+ /** Reads and clears the flag above, so each check starts from a known state. */
75
+ export declare function takeFetchStarted(self: object): boolean;
76
+ /**
77
+ * Dev-only check that a display's `reload()` can actually reach a fetch — the
78
+ * retry contract, which `DisplayErrorBar` depends on and which no type can
79
+ * state. No-op in production.
80
+ *
81
+ * **The button is the contract.** `DisplayErrorBar`'s only action is
82
+ * `model.reload()`, so every state that can raise the error bar has to be one
83
+ * `reload()` actually undoes; otherwise the button is present, looks live, and
84
+ * does nothing. It has failed three times, and the shape this catches is the one
85
+ * that recurs on its own: a gate that goes shut the moment data lands.
86
+ * `GlobalFetchMixin.reload()` clears the error and bumps `reloadCounter`,
87
+ * `installGlobalFetchAutorun` reads that counter unconditionally so the autorun
88
+ * re-runs — and then the gate declines, because from its point of view nothing
89
+ * has changed. Arc shipped exactly that: a `prepare` declining on `dataCurrent`,
90
+ * with the error clearing on click and no arcs ever coming back. The fix this
91
+ * message asks for is what `GlobalFetchMixin.reload()` now does for that whole
92
+ * family — drop `loadedFetchSignature`, so `dataCurrent` goes false and the
93
+ * gate opens.
94
+ *
95
+ * Detected at the moment it happens rather than statically, because the relation
96
+ * between `reload()` and the gate is semantic: a run that follows a
97
+ * `reloadCounter` bump and declines to fetch IS the dead button.
98
+ *
99
+ * **The bump is the only thing that arms this**, so a `reload()` override that
100
+ * neither bumps nor chains to super turns the whole check off for its display —
101
+ * silently, and for as long as nobody reads the override. Canvas shipped in that
102
+ * shape, which is two of the most-used displays in the product. What watches for
103
+ * the next one is `MultiRegionDisplayMixin`'s `reloadReachesCounter.test.ts`,
104
+ * which reads every `reload()` in the tree.
105
+ *
106
+ * **Both fetch foundations install it**, and what counts as the gate differs.
107
+ * The global family's `prepare()` returns the fetch's args or `undefined`, so
108
+ * its run classifies itself. The per-region family's gate is block coverage — a
109
+ * `reload()` that invalidates nothing leaves `needed` empty — plus the
110
+ * `fetchNeeded` override, which can decline inside an async body the foundation
111
+ * cannot read a return value from. So `MultiRegionDisplayMixin` classifies on
112
+ * whether the override reached `runFetch`, which every one of the nine does in
113
+ * its synchronous prefix. An override that awaits before fetching would read as a
114
+ * decline; there is no such override, and one added later gets a false report
115
+ * rather than a silent gap, which is the right way round.
116
+ *
117
+ * **A fetch also answers the retry on its own** (`noteFetchStarted`), because
118
+ * `reload()` may reach one without an autorun run in between: canvas's clears and
119
+ * calls `fetchNeeded` directly rather than waiting out the 600ms debounce, and
120
+ * the autorun's next run then finds the blocks covered.
121
+ *
122
+ * A display deliberately not fetching at all is the one exempt decline — LD with
123
+ * the triangle off, whose `reload()` correctly does nothing because there is
124
+ * nothing to load. That is already a named state: `fetchInert`, which the
125
+ * loading scrim reads for the same reason, so the exemption is not a second
126
+ * thing to remember. A display that suppresses the scrim and still wants the
127
+ * retry checked has the two questions genuinely apart and should say so here.
128
+ *
129
+ * `viewportEmpty` is the second exemption and the same shape once more, reached
130
+ * from the view rather than declared by the display: with no content block on
131
+ * screen there is no region to ask for, so every display in that view declines
132
+ * and every one of their Retry buttons is inert *because the viewport is*, not
133
+ * because a `reload()` forgot to invalidate anything. Reporting there would be
134
+ * true and useless — the fix the message names does not exist — and it would
135
+ * fire on every display at once, which is how a check stops being read. Same
136
+ * term the scrim, the export gate and `painted` read, so this is the fourth
137
+ * reader of one answer rather than a rule of its own.
138
+ *
139
+ * `awaitingPrerequisite` is not a second exemption — it is a *deferral*, and the
140
+ * difference is the point. A two-stage `reload()` bumps the counter, wakes a
141
+ * prerequisite fetch in another autorun, and declines here only until that
142
+ * lands. HiC is the case: the contacts autorun runs first and declines because
143
+ * `effectiveResolution` is still undefined, and the header arriving a moment
144
+ * later wakes it again through the tracked read that declined. So the bump is
145
+ * left outstanding instead of consumed, and the run after the prerequisite
146
+ * lands is the one that has to reach a fetch — if it declines too, the report
147
+ * lands then. A display cannot spend its retry on a decline it called
148
+ * preliminary, which is what an exemption here would have let it do.
149
+ * `fetchInert` is the wrong thing for HiC to say in any case, because it
150
+ * does want the scrim while the header is re-read.
151
+ *
152
+ * Both flags are read off the node, and both are declared once on `FetchMixin`
153
+ * — the one mixin all three display foundations compose. Neither foundation
154
+ * passes them in: the global family's three phases are autorun options because
155
+ * that is what they are, and these two are properties of the
156
+ * display, which is why an earlier arrangement that made this one an option
157
+ * there and a getter on the per-region mixin had one concept in two spellings.
158
+ *
159
+ * **The predicate has to be strictly narrower than the gate's own decline to be
160
+ * a deferral at all.** One that restates the gate's negation makes every decline a
161
+ * deferred one, so no run is ever judged and the display has opted out — an
162
+ * exemption by another name. HiC's is that shape, because its gate and its
163
+ * prerequisite are the same condition, and what covers HiC's retry instead is
164
+ * `LinearHicDisplay/infoFetchFailure.test.ts`. Say so at any call site that
165
+ * lands there, and pick a narrower predicate wherever one exists.
166
+ *
167
+ * **Everything it reads is `untracked`.** It runs inside the fetch autorun, so a
168
+ * tracked read of `fetchInert` — or of whatever `awaitingPrerequisite`
169
+ * reaches — would put that observable in the autorun's dependency set in dev and
170
+ * not in production, a display whose fetch re-fires only in development, which
171
+ * is worse than the bug being checked for.
172
+ */
173
+ export declare function makeRetryContractCheck(self: IAnyStateTreeNode & RetryContractHost): (outcome: FetchAutorunOutcome) => void;
174
+ export {};
@@ -0,0 +1,246 @@
1
+ import { getMembers } from '@jbrowse/mobx-state-tree';
2
+ import { untracked } from 'mobx';
3
+ // Nodes whose fetch foundation has already installed its autoruns. Keyed on the
4
+ // node rather than the model type: every display of a type would otherwise
5
+ // report from the second instance onward.
6
+ const attached = new WeakSet();
7
+ function report(message) {
8
+ // `console.error`, never `throw`: an error escaping `afterAttach` is read by
9
+ // the session loader as an invalid track and the display is silently dropped
10
+ // — which would hide the very contract violation this is reporting.
11
+ console.error(`[jbrowse display contract] ${message}`);
12
+ }
13
+ /**
14
+ * Dev-only check that a display's fetch foundation attached it exactly once —
15
+ * the one ordering contract here that is a *state* rather than a declaration,
16
+ * so no selector can reach it. No-op in production.
17
+ *
18
+ * Called once per display from **whichever fetch foundation installed its
19
+ * autoruns** — `MultiRegionDisplayMixin`'s `afterAttach` for the per-region
20
+ * family, `installGlobalFetchAutorun` for the global one,
21
+ * `installComparativeFetchAutorun` for the comparative one. Landing here twice
22
+ * for one node means every autorun that foundation installs is installed twice:
23
+ * double fetches, double clears, and nothing anywhere says so.
24
+ *
25
+ * The named cause is a display that chains to `super` in its own `afterAttach`
26
+ * — our MST fork auto-chains lifecycle hooks, so the explicit call re-enters the
27
+ * foundation's hook. **That cause is a declaration and could be a lint selector;
28
+ * this check is not, because it is not the only cause**: composing two fetch
29
+ * foundations onto one display, or calling an installer from a display that
30
+ * already composes the mixin, arrives here the same way, through a composition
31
+ * assembled across files that no single one of them spells out. So the message
32
+ * leads with the common cause and then describes the state, not the syntax.
33
+ *
34
+ * `installedBy` names the caller so the message can describe the right thing;
35
+ * the WeakSet is shared, which is correct — a display composes one fetch
36
+ * foundation, so reaching here twice is the bug regardless of which.
37
+ *
38
+ * ARCHITECTURAL_LIMITS.md §"Ordering is the contract" is the authoritative
39
+ * account of which contracts report themselves at runtime, which are lint
40
+ * selectors and which are still silent; don't restate the split here, because
41
+ * this comment said "four places" against a heading that said five and a list
42
+ * that held six.
43
+ *
44
+ * Every message names the fix, not just the symptom — the failure modes here
45
+ * cost hours precisely because the symptom (a wedged display, a stale cache)
46
+ * points nowhere near the cause.
47
+ */
48
+ export function assertDisplayContract(self, installedBy = "the per-region fetch foundation's afterAttach") {
49
+ if (process.env.NODE_ENV !== 'production') {
50
+ if (attached.has(self)) {
51
+ report(`${getMembers(self).name}: ${installedBy} ran twice on one display, ` +
52
+ `so its fetch autoruns are installed twice (double fetches, double ` +
53
+ `clears). Our MST fork auto-chains lifecycle hooks, so the usual ` +
54
+ `cause is a superAfterAttach() call in this display's afterAttach — ` +
55
+ `delete it. Otherwise this display composes two fetch foundations, ` +
56
+ `or calls an installer it already gets from a mixin. ` +
57
+ `See agent-docs/ARCHITECTURE.md §"What not to do".`);
58
+ }
59
+ else {
60
+ attached.add(self);
61
+ }
62
+ }
63
+ }
64
+ // Displays whose fetch has started since the last time the caller looked, and
65
+ // the ledger each of those nodes reports to. Both module-scope and keyed on the
66
+ // node for the same reason `attached` above is: the state is per display
67
+ // *instance*, and the code that needs it — `FetchMixin.runFetch`, a `.actions()`
68
+ // block, an `afterAttach` — cannot share a closure, because a mixin factory runs
69
+ // once per model type.
70
+ //
71
+ // The signal is `FetchMixin.runFetch`, the one place a fetch starts in every
72
+ // family, reached in the synchronous prefix of every one of the nine
73
+ // `fetchNeeded` overrides (directly, or through `fetchEachRegion` /
74
+ // `fetchAllRegions` / `fetchRegions`). The per-region foundation needs it because
75
+ // its gate is not a boolean it can read: `fetchNeeded` is an async action that
76
+ // returns the fetch's promise, and an override declines by returning early, which
77
+ // is indistinguishable from returning the promise of a fetch that has started.
78
+ //
79
+ // **A fetch answers an outstanding retry wherever `reload()` reached it from**,
80
+ // which is why `noteFetchStarted` tells the ledger rather than only setting a
81
+ // flag for the autorun to read. Canvas's `reload()` fetches directly — it clears
82
+ // and calls `fetchNeeded` itself instead of waiting out `FetchVisibleRegions`'
83
+ // 600ms debounce — so by the time that autorun runs, the blocks are covered and
84
+ // the run reads as a decline. Judging only from the autorun reports a dead button
85
+ // on the display with the liveliest one.
86
+ const fetchStarted = new WeakSet();
87
+ const ledgers = new WeakMap();
88
+ /** Called by `FetchMixin.runFetch`. Dev-only. */
89
+ export function noteFetchStarted(self) {
90
+ if (process.env.NODE_ENV === 'production') {
91
+ return;
92
+ }
93
+ fetchStarted.add(self);
94
+ ledgers.get(self)?.('fetched');
95
+ }
96
+ /** Reads and clears the flag above, so each check starts from a known state. */
97
+ export function takeFetchStarted(self) {
98
+ return fetchStarted.delete(self);
99
+ }
100
+ /**
101
+ * Dev-only check that a display's `reload()` can actually reach a fetch — the
102
+ * retry contract, which `DisplayErrorBar` depends on and which no type can
103
+ * state. No-op in production.
104
+ *
105
+ * **The button is the contract.** `DisplayErrorBar`'s only action is
106
+ * `model.reload()`, so every state that can raise the error bar has to be one
107
+ * `reload()` actually undoes; otherwise the button is present, looks live, and
108
+ * does nothing. It has failed three times, and the shape this catches is the one
109
+ * that recurs on its own: a gate that goes shut the moment data lands.
110
+ * `GlobalFetchMixin.reload()` clears the error and bumps `reloadCounter`,
111
+ * `installGlobalFetchAutorun` reads that counter unconditionally so the autorun
112
+ * re-runs — and then the gate declines, because from its point of view nothing
113
+ * has changed. Arc shipped exactly that: a `prepare` declining on `dataCurrent`,
114
+ * with the error clearing on click and no arcs ever coming back. The fix this
115
+ * message asks for is what `GlobalFetchMixin.reload()` now does for that whole
116
+ * family — drop `loadedFetchSignature`, so `dataCurrent` goes false and the
117
+ * gate opens.
118
+ *
119
+ * Detected at the moment it happens rather than statically, because the relation
120
+ * between `reload()` and the gate is semantic: a run that follows a
121
+ * `reloadCounter` bump and declines to fetch IS the dead button.
122
+ *
123
+ * **The bump is the only thing that arms this**, so a `reload()` override that
124
+ * neither bumps nor chains to super turns the whole check off for its display —
125
+ * silently, and for as long as nobody reads the override. Canvas shipped in that
126
+ * shape, which is two of the most-used displays in the product. What watches for
127
+ * the next one is `MultiRegionDisplayMixin`'s `reloadReachesCounter.test.ts`,
128
+ * which reads every `reload()` in the tree.
129
+ *
130
+ * **Both fetch foundations install it**, and what counts as the gate differs.
131
+ * The global family's `prepare()` returns the fetch's args or `undefined`, so
132
+ * its run classifies itself. The per-region family's gate is block coverage — a
133
+ * `reload()` that invalidates nothing leaves `needed` empty — plus the
134
+ * `fetchNeeded` override, which can decline inside an async body the foundation
135
+ * cannot read a return value from. So `MultiRegionDisplayMixin` classifies on
136
+ * whether the override reached `runFetch`, which every one of the nine does in
137
+ * its synchronous prefix. An override that awaits before fetching would read as a
138
+ * decline; there is no such override, and one added later gets a false report
139
+ * rather than a silent gap, which is the right way round.
140
+ *
141
+ * **A fetch also answers the retry on its own** (`noteFetchStarted`), because
142
+ * `reload()` may reach one without an autorun run in between: canvas's clears and
143
+ * calls `fetchNeeded` directly rather than waiting out the 600ms debounce, and
144
+ * the autorun's next run then finds the blocks covered.
145
+ *
146
+ * A display deliberately not fetching at all is the one exempt decline — LD with
147
+ * the triangle off, whose `reload()` correctly does nothing because there is
148
+ * nothing to load. That is already a named state: `fetchInert`, which the
149
+ * loading scrim reads for the same reason, so the exemption is not a second
150
+ * thing to remember. A display that suppresses the scrim and still wants the
151
+ * retry checked has the two questions genuinely apart and should say so here.
152
+ *
153
+ * `viewportEmpty` is the second exemption and the same shape once more, reached
154
+ * from the view rather than declared by the display: with no content block on
155
+ * screen there is no region to ask for, so every display in that view declines
156
+ * and every one of their Retry buttons is inert *because the viewport is*, not
157
+ * because a `reload()` forgot to invalidate anything. Reporting there would be
158
+ * true and useless — the fix the message names does not exist — and it would
159
+ * fire on every display at once, which is how a check stops being read. Same
160
+ * term the scrim, the export gate and `painted` read, so this is the fourth
161
+ * reader of one answer rather than a rule of its own.
162
+ *
163
+ * `awaitingPrerequisite` is not a second exemption — it is a *deferral*, and the
164
+ * difference is the point. A two-stage `reload()` bumps the counter, wakes a
165
+ * prerequisite fetch in another autorun, and declines here only until that
166
+ * lands. HiC is the case: the contacts autorun runs first and declines because
167
+ * `effectiveResolution` is still undefined, and the header arriving a moment
168
+ * later wakes it again through the tracked read that declined. So the bump is
169
+ * left outstanding instead of consumed, and the run after the prerequisite
170
+ * lands is the one that has to reach a fetch — if it declines too, the report
171
+ * lands then. A display cannot spend its retry on a decline it called
172
+ * preliminary, which is what an exemption here would have let it do.
173
+ * `fetchInert` is the wrong thing for HiC to say in any case, because it
174
+ * does want the scrim while the header is re-read.
175
+ *
176
+ * Both flags are read off the node, and both are declared once on `FetchMixin`
177
+ * — the one mixin all three display foundations compose. Neither foundation
178
+ * passes them in: the global family's three phases are autorun options because
179
+ * that is what they are, and these two are properties of the
180
+ * display, which is why an earlier arrangement that made this one an option
181
+ * there and a getter on the per-region mixin had one concept in two spellings.
182
+ *
183
+ * **The predicate has to be strictly narrower than the gate's own decline to be
184
+ * a deferral at all.** One that restates the gate's negation makes every decline a
185
+ * deferred one, so no run is ever judged and the display has opted out — an
186
+ * exemption by another name. HiC's is that shape, because its gate and its
187
+ * prerequisite are the same condition, and what covers HiC's retry instead is
188
+ * `LinearHicDisplay/infoFetchFailure.test.ts`. Say so at any call site that
189
+ * lands there, and pick a narrower predicate wherever one exists.
190
+ *
191
+ * **Everything it reads is `untracked`.** It runs inside the fetch autorun, so a
192
+ * tracked read of `fetchInert` — or of whatever `awaitingPrerequisite`
193
+ * reaches — would put that observable in the autorun's dependency set in dev and
194
+ * not in production, a display whose fetch re-fires only in development, which
195
+ * is worse than the bug being checked for.
196
+ */
197
+ export function makeRetryContractCheck(self) {
198
+ if (process.env.NODE_ENV === 'production') {
199
+ return () => { };
200
+ }
201
+ // eslint-disable-next-line no-restricted-syntax -- instrumentation
202
+ let lastCounter = untracked(() => self.reloadCounter);
203
+ function noteRetryContractOutcome(outcome) {
204
+ // eslint-disable-next-line no-restricted-syntax -- instrumentation
205
+ untracked(() => {
206
+ // A decline while a prerequisite is still in flight is a stage of the
207
+ // retry, so the bump stays OUTSTANDING rather than being either reported
208
+ // or forgotten — the run that follows the prerequisite landing is the one
209
+ // that answers it, and if that run declines too the report lands then.
210
+ // Deferring rather than exempting is what keeps the check's teeth here: a
211
+ // display cannot spend its retry on a decline it called preliminary.
212
+ if (outcome === 'deferred') {
213
+ return;
214
+ }
215
+ if (outcome === 'declined' && self.awaitingPrerequisite) {
216
+ return;
217
+ }
218
+ const retried = self.reloadCounter !== lastCounter;
219
+ // Consumed on every other outcome, `gated` included: a run the byte gate
220
+ // skipped answers the retry legitimately (that banner offers Force load,
221
+ // not Retry), and leaving the bump unconsumed would report against
222
+ // whichever unrelated run cleared the gate later.
223
+ lastCounter = self.reloadCounter;
224
+ if (retried &&
225
+ outcome === 'declined' &&
226
+ !self.fetchInert &&
227
+ !self.viewportEmpty) {
228
+ report(`${getMembers(self).name}: reload() bumped reloadCounter but the ` +
229
+ `fetch autorun's gate still declines, so Retry is a dead ` +
230
+ `button — it clears the error and nothing refetches. reload() has ` +
231
+ `to invalidate whatever that gate reads, not just bump the ` +
232
+ `counter (GlobalFetchMixin.reload drops loadedFetchSignature so ` +
233
+ `dataCurrent goes false). If this display is deliberately not ` +
234
+ `fetching, say so with fetchInert — the loading scrim and the SVG ` +
235
+ `export read it too; if this run declined only because a ` +
236
+ `prerequisite fetch in another autorun has not landed, say so with ` +
237
+ `awaitingPrerequisite and the retry is judged on the run after ` +
238
+ `it does. See DISPLAYCHROME.md §"The retry contract".`);
239
+ }
240
+ });
241
+ }
242
+ // So `noteFetchStarted` can answer an outstanding retry the moment a fetch
243
+ // begins, whether or not an autorun run is what began it.
244
+ ledgers.set(self, noteRetryContractOutcome);
245
+ return noteRetryContractOutcome;
246
+ }
@@ -1,14 +1,28 @@
1
1
  import type { Instance } from '@jbrowse/mobx-state-tree';
2
+ /**
3
+ * #config BaseConnection
4
+ * #gotcha A connection config is only a pointer: the hub's track list is
5
+ * fetched when the connection loads and held in memory, and is **not** written
6
+ * into a saved or shared session. Only a track you actually open is stored
7
+ * (under `connectionTrackConfigs`, keyed by `trackId`), which is what keeps a
8
+ * shared session small even against a very large hub.
9
+ */
2
10
  declare const BaseConnectionConfig: import("../../configuration/configurationSchema.ts").ConfigurationSchemaType<{
3
- name: {
4
- type: string;
5
- defaultValue: string;
6
- description: string;
11
+ /**
12
+ * #slot
13
+ */
14
+ readonly name: {
15
+ readonly type: "string";
16
+ readonly defaultValue: "nameOfConnection";
17
+ readonly description: "a unique name for this connection";
7
18
  };
8
- assemblyNames: {
9
- type: string;
10
- defaultValue: never[];
11
- description: string;
19
+ /**
20
+ * #slot
21
+ */
22
+ readonly assemblyNames: {
23
+ readonly type: "stringArray";
24
+ readonly defaultValue: readonly [];
25
+ readonly description: "optional list of names of assemblies in this connection";
12
26
  };
13
27
  }, import("../../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>;
14
28
  export default BaseConnectionConfig;
@@ -1,11 +1,24 @@
1
- import { ConfigurationSchema } from "../../configuration/index.js";
2
- function x() { }
1
+ import { ConfigurationSchema } from '../../configuration/index.js';
2
+ /**
3
+ * #config BaseConnection
4
+ * #gotcha A connection config is only a pointer: the hub's track list is
5
+ * fetched when the connection loads and held in memory, and is **not** written
6
+ * into a saved or shared session. Only a track you actually open is stored
7
+ * (under `connectionTrackConfigs`, keyed by `trackId`), which is what keeps a
8
+ * shared session small even against a very large hub.
9
+ */
3
10
  const BaseConnectionConfig = ConfigurationSchema('BaseConnection', {
11
+ /**
12
+ * #slot
13
+ */
4
14
  name: {
5
15
  type: 'string',
6
16
  defaultValue: 'nameOfConnection',
7
17
  description: 'a unique name for this connection',
8
18
  },
19
+ /**
20
+ * #slot
21
+ */
9
22
  assemblyNames: {
10
23
  type: 'stringArray',
11
24
  defaultValue: [],
@@ -13,6 +26,9 @@ const BaseConnectionConfig = ConfigurationSchema('BaseConnection', {
13
26
  },
14
27
  }, {
15
28
  explicitlyTyped: true,
29
+ /**
30
+ * #identifier
31
+ */
16
32
  explicitIdentifier: 'connectionId',
17
33
  });
18
34
  export default BaseConnectionConfig;
@@ -1,27 +1,46 @@
1
+ /**
2
+ * #config BaseInternetAccount
3
+ * the "base" internet account type
4
+ */
1
5
  export declare const BaseInternetAccountConfig: import("../../configuration/configurationSchema.ts").ConfigurationSchemaType<{
2
- name: {
3
- description: string;
4
- type: string;
5
- defaultValue: string;
6
+ /**
7
+ * #slot
8
+ */
9
+ readonly name: {
10
+ readonly description: "descriptive name of the internet account";
11
+ readonly type: "string";
12
+ readonly defaultValue: "";
6
13
  };
7
- description: {
8
- description: string;
9
- type: string;
10
- defaultValue: string;
14
+ /**
15
+ * #slot
16
+ */
17
+ readonly description: {
18
+ readonly description: "a description of the internet account";
19
+ readonly type: "string";
20
+ readonly defaultValue: "";
11
21
  };
12
- authHeader: {
13
- description: string;
14
- type: string;
15
- defaultValue: string;
22
+ /**
23
+ * #slot
24
+ */
25
+ readonly authHeader: {
26
+ readonly description: "request header for credentials";
27
+ readonly type: "string";
28
+ readonly defaultValue: "Authorization";
16
29
  };
17
- tokenType: {
18
- description: string;
19
- type: string;
20
- defaultValue: string;
30
+ /**
31
+ * #slot
32
+ */
33
+ readonly tokenType: {
34
+ readonly description: "a custom name for a token to include in the header";
35
+ readonly type: "string";
36
+ readonly defaultValue: "";
21
37
  };
22
- domains: {
23
- description: string;
24
- type: string;
25
- defaultValue: never[];
38
+ /**
39
+ * #slot
40
+ */
41
+ readonly domains: {
42
+ readonly description: "array of valid domains the url can contain to use this account";
43
+ readonly type: "stringArray";
44
+ readonly defaultValue: readonly [];
26
45
  };
27
46
  }, import("../../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "internetAccountId">>;
@@ -1,32 +1,53 @@
1
- import { ConfigurationSchema } from "../../configuration/index.js";
2
- function x() { }
1
+ import { ConfigurationSchema } from '../../configuration/index.js';
2
+ /**
3
+ * #config BaseInternetAccount
4
+ * the "base" internet account type
5
+ */
3
6
  export const BaseInternetAccountConfig = ConfigurationSchema('InternetAccount', {
7
+ /**
8
+ * #slot
9
+ */
4
10
  name: {
5
11
  description: 'descriptive name of the internet account',
6
12
  type: 'string',
7
13
  defaultValue: '',
8
14
  },
15
+ /**
16
+ * #slot
17
+ */
9
18
  description: {
10
19
  description: 'a description of the internet account',
11
20
  type: 'string',
12
21
  defaultValue: '',
13
22
  },
23
+ /**
24
+ * #slot
25
+ */
14
26
  authHeader: {
15
27
  description: 'request header for credentials',
16
28
  type: 'string',
17
29
  defaultValue: 'Authorization',
18
30
  },
31
+ /**
32
+ * #slot
33
+ */
19
34
  tokenType: {
20
35
  description: 'a custom name for a token to include in the header',
21
36
  type: 'string',
22
37
  defaultValue: '',
23
38
  },
39
+ /**
40
+ * #slot
41
+ */
24
42
  domains: {
25
43
  description: 'array of valid domains the url can contain to use this account',
26
44
  type: 'stringArray',
27
45
  defaultValue: [],
28
46
  },
29
47
  }, {
48
+ /**
49
+ * #identifier
50
+ */
30
51
  explicitIdentifier: 'internetAccountId',
31
52
  explicitlyTyped: true,
32
53
  });