@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
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  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 +1,820 @@
1
+ import { checkStopTokenThrottled, createStopTokenChecker, withStopTokenCheck, } from './stopToken.js';
2
+ import { createTimeGate } from './timeGate.js';
3
+ const openPhases = new WeakMap();
4
+ /**
5
+ * Open a phase on `cb`'s channel and return its close. The close emits the
6
+ * enclosing phase's label, or `''` when this was the outermost — which is what
7
+ * makes phases nest, so an inner phase cannot blank the label its caller set for
8
+ * the rest of the caller's work.
9
+ *
10
+ * `''` closing the outermost phase is what every consumer reads as "this phase
11
+ * is over": a {@link StatusWindow} thins it like any other status, and
12
+ * {@link aggregateStatus} reads it as "not in flight".
13
+ *
14
+ * The close takes the {@link PhaseOutcome}, because it is the one place that
15
+ * knows it — a phase that finished and a phase that threw retire the same label,
16
+ * and only the `finally` around the work can tell them apart.
17
+ */
18
+ function openPhase(cb, label) {
19
+ if (cb === undefined) {
20
+ return (_outcome) => { };
21
+ }
22
+ let stack = openPhases.get(cb);
23
+ if (stack === undefined) {
24
+ stack = [];
25
+ openPhases.set(cb, stack);
26
+ }
27
+ const phase = { label };
28
+ stack.push(phase);
29
+ return (outcome) => {
30
+ const index = stack.lastIndexOf(phase);
31
+ if (index !== -1) {
32
+ stack.splice(index, 1);
33
+ }
34
+ // the enclosing phase is restored whole, its source included: a nested
35
+ // phase ending does not stop the outer one waiting on the file it named
36
+ const restored = stack.at(-1)?.label ?? '';
37
+ cb(outcome === 'failed'
38
+ ? { message: phaseOf(restored), failed: true }
39
+ : restored);
40
+ };
41
+ }
42
+ /**
43
+ * Indeterminate phase: set `label` on the status channel, run `fn`, then restore
44
+ * whatever phase encloses it — `''` when there is none. Pass `stopToken` and the
45
+ * phase becomes a cancellation boundary too: this is the labelled form of
46
+ * {@link withStopTokenCheck}, so `fn` is checked on both sides of its await and
47
+ * neither check has to be remembered at the call site. The determinate
48
+ * counterpart is {@link withProgress}.
49
+ *
50
+ * Nests — see {@link openPhase}. An inner phase's close restores the enclosing
51
+ * label and not its bar; the enclosing phase's next `report()` re-establishes
52
+ * it, and one with none to send was indeterminate anyway.
53
+ *
54
+ * `msg` is a {@link StatusPhase} where the caller knows which file the phase is
55
+ * fetching — `downloadPhase(label, location)` builds one — and a plain string
56
+ * everywhere else. It nests and retires identically either way.
57
+ */
58
+ export async function updateStatus(msg, cb, fn, stopToken) {
59
+ const endPhase = openPhase(cb, msg);
60
+ // pessimistic, so anything leaving this scope other than a value — a throw, a
61
+ // cancel — retires the phase as unfinished
62
+ let outcome = 'failed';
63
+ // everything after the open is inside the try, the announcing write included,
64
+ // so a throw anywhere cannot leave this phase's label sitting on the channel
65
+ // forever — the error surfaces under a stale "Downloading file"
66
+ try {
67
+ cb?.(msg);
68
+ const result = await withStopTokenCheck(stopToken, fn);
69
+ outcome = 'completed';
70
+ return result;
71
+ }
72
+ finally {
73
+ endPhase(outcome);
74
+ }
75
+ }
76
+ function isPhaseFailure(status) {
77
+ return typeof status === 'object' && 'failed' in status;
78
+ }
79
+ /**
80
+ * The determinate reading in `status`, or undefined when there is none — a bare
81
+ * label, a {@link StatusPhase}, or the last word of a phase that threw. The one
82
+ * place the transport's union is narrowed to a `current`/`total`, so a consumer
83
+ * reading the numbers cannot mistake a label or a {@link PhaseFailure} for a
84
+ * measurement. It tests for the numbers themselves rather than excluding the
85
+ * shapes that lack them, so a shape added later is out until it opts in.
86
+ */
87
+ export function statusReading(status) {
88
+ return typeof status === 'object' && 'current' in status ? status : undefined;
89
+ }
90
+ /**
91
+ * What `status` says it is waiting on, or undefined when it names nothing — a
92
+ * label with no {@link StatusPhase} source, and every reading that arrived
93
+ * before one was attached. The URL is what a stalled phase has to show; see
94
+ * {@link StatusPhase}.
95
+ */
96
+ export function statusSource(status) {
97
+ return typeof status === 'object' && 'source' in status
98
+ ? status.source
99
+ : undefined;
100
+ }
101
+ /**
102
+ * The phase a status names, verbatim — its label, whichever shape it arrived in.
103
+ * The raw form, `''` and all, for the few places that have to reason about the
104
+ * sentinel itself, or that are rebuilding a phase around the label they were
105
+ * handed. Everywhere else wants {@link statusMessageText}.
106
+ */
107
+ export function phaseOf(status) {
108
+ return typeof status === 'object' ? status.message : status;
109
+ }
110
+ /**
111
+ * Extract the human-readable text from any status value, or `undefined` when
112
+ * there is none.
113
+ *
114
+ * `''` is none: it is the phase-over sentinel, not a label. Normalizing it here
115
+ * leaves one spelling of "nothing to show" for the three models that store a
116
+ * `statusMessage` (`assembly`, `BaseDisplayModel`, `FetchMixin`) — otherwise a
117
+ * reset's `undefined` and a phase's `''` read the same on screen
118
+ * (`message || 'Loading'`) and differently to everything else.
119
+ *
120
+ * The corollary binds anything that *transforms* a status: rewriting `''` into
121
+ * any other string — a prefix, a default — makes a phase that never ends, since
122
+ * a slot's last word is what {@link aggregateStatus} weighs. `levelStatusCallback`
123
+ * in `runDiagonalize.ts` is the one transformer in the tree.
124
+ */
125
+ export function statusMessageText(status) {
126
+ const text = status === undefined ? undefined : phaseOf(status);
127
+ return text === '' ? undefined : text;
128
+ }
129
+ /**
130
+ * Fraction complete in [0,1], or undefined when the status is indeterminate
131
+ * (a plain string, or a zero total).
132
+ */
133
+ export function statusFraction(status) {
134
+ const reading = statusReading(status);
135
+ return reading !== undefined && reading.total > 0
136
+ ? Math.min(1, reading.current / reading.total)
137
+ : undefined;
138
+ }
139
+ /**
140
+ * The shared state behind {@link createStatusFanOut} and {@link
141
+ * createStatusWindow}: N slots, the order the batch reached each phase in, and
142
+ * the last reading worth re-sending. Both of them are "several concurrent
143
+ * operations, one status" — the fan-out over the regions of one fetch, the
144
+ * window over the operations of one display — and the arbitration is the same
145
+ * either way, so it is written once.
146
+ *
147
+ * The two differ in what they do with the answer — the fan-out feeds a callback
148
+ * that has no way to say "nothing", the window owns a field it can blank — and
149
+ * in `holdLastReading`.
150
+ *
151
+ * **Hold only where the slots are raw reporters.** ADR-080's rule that a phase
152
+ * does not lose its bar because nothing is measuring it *this instant* is about
153
+ * one batch's peers sitting between reads. A slot fed by another aggregate has
154
+ * already had the rule applied to it: its bare label means "my children have no
155
+ * measurement", not "I am between reads", and holding over that puts back a
156
+ * percentage the child deliberately retired — the write ADR-071 exists to
157
+ * cancel. A window's slots are whole operations, and the commonest window has
158
+ * exactly one, where a held reading can only ever be older than what the slot
159
+ * just said.
160
+ */
161
+ function createStatusAggregate({ holdLastReading = false } = {}) {
162
+ const slots = [];
163
+ // every phase this batch has reached, against the order it reached them in,
164
+ // so a tie between two slots in different phases resolves the same way twice
165
+ const phaseRank = new Map();
166
+ // the current phase's last determinate reading — what a moment with nothing
167
+ // measuring it falls back to, rather than downgrading what we already know.
168
+ // Dropped the moment the batch is in some other phase, or in none.
169
+ let held;
170
+ // the last label of any kind, which outlives that: it is all there is to say
171
+ // once nothing is in flight, and saying it is what displaces the percentage
172
+ // queued behind the throttle
173
+ let lastMessage;
174
+ /**
175
+ * The best available answer to "what is this batch doing", in order: a
176
+ * reading we trust, whatever the aggregate says, the last label we saw.
177
+ * Undefined only while no slot has ever reported.
178
+ */
179
+ const derive = () => {
180
+ const aggregate = aggregateStatus(slots, phaseRank);
181
+ const message = statusMessageText(aggregate);
182
+ // A held reading describes one phase, and survives exactly as long as the
183
+ // batch is still in it. "Nothing in flight" is not that phase either: an
184
+ // empty aggregate is a batch with no work outstanding, and re-sending a
185
+ // percentage for work that has ENDED is the write ADR-071 exists to cancel.
186
+ // Both cases are one comparison, because an empty aggregate names no phase.
187
+ if (held?.message !== message) {
188
+ held = undefined;
189
+ }
190
+ const reading = statusReading(aggregate);
191
+ if (holdLastReading && reading !== undefined && !readsComplete(reading)) {
192
+ held = reading;
193
+ }
194
+ if (message !== undefined) {
195
+ lastMessage = message;
196
+ }
197
+ return held ?? aggregate ?? lastMessage;
198
+ };
199
+ return {
200
+ idle: () => slots.length === 0,
201
+ size: () => slots.length,
202
+ add() {
203
+ const slot = { status: undefined, completed: new Map() };
204
+ slots.push(slot);
205
+ return slot;
206
+ },
207
+ /**
208
+ * Retire a slot. Its finished phases go with it — one operation's bytes
209
+ * were never the denominator of another's, and a slot kept for its
210
+ * `completed` alone is the accumulation a long-lived aggregate cannot
211
+ * afford. Emptying resets the phase order too: idle is the batch boundary,
212
+ * and a rank recorded an hour ago has no business ordering today's phases.
213
+ */
214
+ remove(slot) {
215
+ const index = slots.indexOf(slot);
216
+ if (index !== -1) {
217
+ slots.splice(index, 1);
218
+ }
219
+ // a held reading describes an aggregate this slot was part of
220
+ held = undefined;
221
+ if (slots.length === 0) {
222
+ phaseRank.clear();
223
+ lastMessage = undefined;
224
+ }
225
+ },
226
+ /** Record one slot's status, then re-derive the shared value. */
227
+ update(slot, status) {
228
+ // what this slot just finished, credited at the total it retired at —
229
+ // only its own channel ever saw that number
230
+ const previous = statusReading(slot.status);
231
+ if (previous !== undefined && !continuesPhase(previous, status)) {
232
+ const { message, current, total } = previous;
233
+ // A phase that ENDED is charged its total: its `current` was only ever
234
+ // its total written twice, and undercharging it is what made the bar run
235
+ // backwards as a batch landed. A phase that THREW is charged what it
236
+ // transferred — the 900 bytes a dead socket will never carry are not
237
+ // work this batch completed, and crediting them walked the bar forward
238
+ // on a failure. Nothing in the readings separates the two, so
239
+ // {@link PhaseFailure} carries the difference.
240
+ slot.completed.set(message, finished(slot, message) + (isPhaseFailure(status) ? current : total));
241
+ }
242
+ // the marker is consumed here. From now on the slot is simply reporting
243
+ // the label the retire left behind, so nothing downstream — a parent
244
+ // channel, a display's field — has to know the shape exists.
245
+ slot.status = isPhaseFailure(status) ? status.message : status;
246
+ // every label, not only the determinate ones: an indeterminate phase that
247
+ // ties with another has to rank somewhere too, and it is the first slot to
248
+ // say the words that dates the phase either way
249
+ const phase = statusMessageText(status);
250
+ if (phase !== undefined && !phaseRank.has(phase)) {
251
+ phaseRank.set(phase, phaseRank.size);
252
+ }
253
+ return derive();
254
+ },
255
+ derive,
256
+ };
257
+ }
258
+ // An RPC statusCallback fires per progress event (often ~40/s), and each write
259
+ // to the observable statusMessage/statusProgress re-renders whatever loading
260
+ // indicator is up (and repositions its MUI Tooltip/Popper) — re-renders were
261
+ // measured outpacing the zoom animation's own frame rate before this. A progress
262
+ // indicator gains nothing from updating faster.
263
+ const STATUS_THROTTLE_MS = 100;
264
+ /**
265
+ * Thin one channel's status emits at the *source*, for a transport that pays
266
+ * per message.
267
+ *
268
+ * {@link createStatusWindow} already throttles what reaches a display's status
269
+ * field, but it runs on the main thread: every emit the worker made still cost
270
+ * a postMessage, a task and a structured clone to get there and be dropped. A
271
+ * scroll-zoom measured 9,668 of those in ten seconds — 23% of the main thread's
272
+ * busy time — for the ~100 statuses the window let through.
273
+ *
274
+ * What it drops is only ever an intermediate reading of a phase a later reading
275
+ * of the same phase supersedes, so {@link createStatusAggregate} is unaffected:
276
+ * it takes the latest reading per slot, and credits a phase its total only when
277
+ * the *label* changes. A change of label — including the `''` retire — and a
278
+ * {@link PhaseFailure} therefore go through untouched, and a reading queued
279
+ * behind the window is flushed ahead of the label that supersedes it so the
280
+ * transition still carries the phase's own last numbers.
281
+ */
282
+ export function throttleStatusEmits(emit) {
283
+ let lastEmitMs = 0;
284
+ let lastPhase;
285
+ let queued;
286
+ let timer;
287
+ const send = (status) => {
288
+ lastEmitMs = Date.now();
289
+ lastPhase = phaseOf(status);
290
+ emit(status);
291
+ };
292
+ const clearQueued = () => {
293
+ if (timer !== undefined) {
294
+ clearTimeout(timer);
295
+ timer = undefined;
296
+ }
297
+ queued = undefined;
298
+ };
299
+ return (status) => {
300
+ const wait = STATUS_THROTTLE_MS - (Date.now() - lastEmitMs);
301
+ if (wait > 0 && phaseOf(status) === lastPhase && !isPhaseFailure(status)) {
302
+ queued = status;
303
+ timer ??= setTimeout(() => {
304
+ timer = undefined;
305
+ // an assertion rather than a guard: the timer is scheduled in the same
306
+ // breath as the write to `queued`, and `clearQueued` drops the two
307
+ // together
308
+ const pending = queued;
309
+ queued = undefined;
310
+ send(pending);
311
+ }, wait);
312
+ }
313
+ else {
314
+ if (queued !== undefined) {
315
+ send(queued);
316
+ }
317
+ clearQueued();
318
+ send(status);
319
+ }
320
+ };
321
+ }
322
+ /**
323
+ * Open a {@link StatusWindow} over one status field. `write` is that field's
324
+ * **only** writer, statuses and the closing blank alike, so whatever guards it
325
+ * — `isAlive(self)`, a React `alive` flag — guards every one of them by
326
+ * construction rather than by a copy of the check at each `finally`.
327
+ *
328
+ * Leading-edge, so sparse updates pass straight through and dense bursts are
329
+ * thinned; trailing as well, so the last write of a phase always lands — it is
330
+ * the one that matters most and exactly the one a leading-edge-only gate drops.
331
+ *
332
+ * Create **one per owner** — a display, a dialog run, an assembly load — and
333
+ * take every one of that owner's status callbacks off it as a stream. The
334
+ * streams are slots in one aggregate, so the owner's two concurrent operations
335
+ * arbitrate for the field the same way one fetch's parallel regions do, and
336
+ * neither ends the other's label (ADR-081).
337
+ *
338
+ * Deliberately wraps only the *callback* path, never `setStatusMessage` itself
339
+ * — a display writing a phase label by hand ("Downloading" → "Parsing") is a
340
+ * sequence of distinct labels, and a trailing edge only guarantees the *last*
341
+ * of a burst, not each one in turn.
342
+ *
343
+ * Both fetch families own one: `FetchMixin` for the LGV displays, and
344
+ * `createStopTokenRotation` for the bare-autorun fetches (dotplot, synteny)
345
+ * that compose no fetch mixin — and a display that has both lends the mixin's
346
+ * to the rotation rather than opening a second on one field. A plain function
347
+ * rather than shared model state because the two families declare their status
348
+ * fields separately and one set shadows the other — see ADR-041.
349
+ */
350
+ export function createStatusWindow(write) {
351
+ let lastMs = 0;
352
+ let pending;
353
+ let timer;
354
+ const clearPending = () => {
355
+ if (timer !== undefined) {
356
+ clearTimeout(timer);
357
+ timer = undefined;
358
+ }
359
+ pending = undefined;
360
+ };
361
+ const run = (apply) => {
362
+ const now = Date.now();
363
+ const wait = STATUS_THROTTLE_MS - (now - lastMs);
364
+ if (wait <= 0) {
365
+ // a write passing on the leading edge supersedes anything queued behind
366
+ // it, so the trailing timer has nothing left to deliver
367
+ clearPending();
368
+ lastMs = now;
369
+ apply();
370
+ }
371
+ else {
372
+ // only the newest write of a burst survives — an older progress value
373
+ // is never what the user wants to be looking at
374
+ pending = apply;
375
+ timer ??= setTimeout(() => {
376
+ timer = undefined;
377
+ // an assertion, not a fallback: the timer is scheduled right after
378
+ // `pending` is set and `clearPending` drops the two together, so an
379
+ // `if (pending)` here would read as a reachable case and silently skip
380
+ // the `lastMs` bump
381
+ const queued = pending;
382
+ pending = undefined;
383
+ lastMs = Date.now();
384
+ queued();
385
+ }, wait);
386
+ }
387
+ };
388
+ const reset = () => {
389
+ clearPending();
390
+ lastMs = 0;
391
+ };
392
+ const aggregate = createStatusAggregate();
393
+ // never skipped: the value is `undefined` only before any slot has spoken,
394
+ // and a slot that has just spoken is one that has
395
+ const emit = (status) => {
396
+ if (status !== undefined) {
397
+ write(status);
398
+ }
399
+ };
400
+ return {
401
+ open({ isCurrent }) {
402
+ // an operation starting after a lull reports at once; one starting beside
403
+ // a running sibling waits its turn in the sibling's cadence
404
+ if (aggregate.idle()) {
405
+ reset();
406
+ }
407
+ const slot = aggregate.add();
408
+ warnOnSlotLeak(aggregate.size());
409
+ let live = true;
410
+ return {
411
+ statusCallback: status => {
412
+ if (live && isCurrent()) {
413
+ // recorded now, derived again when the write lands: a status that
414
+ // waited out the window would otherwise describe the slots as they
415
+ // were when it was queued, and a sibling may have retired since
416
+ aggregate.update(slot, status);
417
+ run(() => {
418
+ // re-read inside, because a trailing write fires on a timer and
419
+ // the operation it belongs to can be gone by then — a run that
420
+ // has since been stopped must not restore the label "Stopping"
421
+ // has already replaced
422
+ if (isCurrent()) {
423
+ emit(aggregate.derive());
424
+ }
425
+ });
426
+ }
427
+ },
428
+ clear() {
429
+ if (!live) {
430
+ return;
431
+ }
432
+ live = false;
433
+ aggregate.remove(slot);
434
+ if (aggregate.idle()) {
435
+ // the owner's last word, and nothing is coming to displace it
436
+ reset();
437
+ write(undefined);
438
+ }
439
+ else {
440
+ run(() => {
441
+ emit(aggregate.derive());
442
+ });
443
+ }
444
+ },
445
+ };
446
+ },
447
+ reset,
448
+ };
449
+ }
450
+ // An owner has a handful of concurrent operations at most — a display's three
451
+ // are the widest case in the tree — so a window past this is an operation that
452
+ // took a slot and never retired it, which pins a label up and goes on voting for
453
+ // a phase that is over. Silent otherwise, and `ChordVariantDisplay` was in
454
+ // exactly that shape from before ADR-081 gave the leak teeth.
455
+ const SLOT_LEAK_THRESHOLD = 16;
456
+ let warnedSlotLeak = false;
457
+ function warnOnSlotLeak(open) {
458
+ if (process.env.NODE_ENV === 'production' || warnedSlotLeak) {
459
+ return;
460
+ }
461
+ if (open > SLOT_LEAK_THRESHOLD) {
462
+ warnedSlotLeak = true;
463
+ console.error(`createStatusWindow: ${open} status streams open on one window. An ` +
464
+ `operation is not calling its stream's clear() — see ADR-081 and ` +
465
+ `agent-docs/reference/PROGRESS_REPORTING.md.`);
466
+ }
467
+ }
468
+ /**
469
+ * Format a phase label with a rounded percentage appended when a determinate
470
+ * `fraction` is present (e.g. `progressLabel('Downloading', 0.45)` →
471
+ * `"Downloading 45%"`). The single place the `X%` suffix is formatted: both
472
+ * {@link statusProgressLabel} (RpcStatus callers) and the loading
473
+ * overlays/indicators — which hold the message and fraction already split apart
474
+ * onto the model — route through it, so no caller hand-rolls `Math.round`.
475
+ */
476
+ export function progressLabel(message, fraction) {
477
+ const percent = fraction === undefined ? '' : `${Math.round(fraction * 100)}%`;
478
+ return [message, percent].filter(Boolean).join(' ');
479
+ }
480
+ /**
481
+ * {@link progressLabel} for an {@link RpcStatus}: the message, with a rounded
482
+ * percentage appended when the status is determinate (e.g. `"Downloading 45%"`).
483
+ * The form the loading dialogs use, holding the raw status object.
484
+ */
485
+ export function statusProgressLabel(status) {
486
+ return progressLabel(statusMessageText(status), statusFraction(status));
487
+ }
488
+ /**
489
+ * Adapt the byte-granularity download callback exposed by the readers
490
+ * (generic-filehandle2 `readFile`, @gmod/tabix `getLines`, @gmod/bam /
491
+ * @gmod/cram `getRecordsForRange`) to the structured {@link StatusCallback}
492
+ * transport, labelling each tick with `message`. Returns undefined when there's
493
+ * no `statusCallback`, so the reader can skip its progress bookkeeping entirely.
494
+ *
495
+ * **That skip is not a saving**, which is the opposite of what the shape
496
+ * suggests. Handed an `onProgress`, generic-filehandle2 streams the body into
497
+ * one pre-sized buffer; handed none it calls `res.bytes()` — and in a Chrome
498
+ * worker the streaming read is roughly 1.8x *faster* up to 10MB, giving that
499
+ * back only past ~25MB. So withholding this reporter honors a caller who asked
500
+ * for no reporting; it is never about speed. Numbers and the bench that retakes
501
+ * them:
502
+ * agent-docs/measurements/download-read-path.json.
503
+ *
504
+ * `total` is optional because not every reader knows the size up front
505
+ * (generic-filehandle2 omits it when the response has no Content-Length): with a
506
+ * total we emit a determinate bar, without one we emit just the label so the UI
507
+ * still shows the phase as an indeterminate spinner.
508
+ *
509
+ * Internal to this module — the only caller is {@link downloadStatus}, which is
510
+ * the API adapters use. Kept separate purely so the reporter logic reads on its
511
+ * own line.
512
+ */
513
+ function downloadStatusReporter(statusCallback, label) {
514
+ const message = phaseOf(label);
515
+ const source = statusSource(label);
516
+ return statusCallback
517
+ ? (current, total) => {
518
+ statusCallback(total === undefined ? label : { message, current, total, source });
519
+ }
520
+ : undefined;
521
+ }
522
+ /**
523
+ * Run a download phase whose reader counts its own progress. Shows `label`,
524
+ * hands `fn` the {@link downloadStatusReporter} to pass straight to the
525
+ * reader's `onProgress` (its ticks upgrade the same label to a determinate
526
+ * bar), then clears the status. Combines {@link updateStatus} with the reporter
527
+ * so the label is written in exactly one place — the phase label and the
528
+ * progress label can't drift apart.
529
+ *
530
+ * The unit is whatever the reader counts, and the caller does not have to know
531
+ * which: bytes for the index readers, blocks and expected-value chunks for
532
+ * `@gmod/hic`. All of them report `(current, total?)`.
533
+ *
534
+ * `stopToken` makes the phase a cancellation boundary, exactly as it does on
535
+ * {@link updateStatus} — `fn` is checked on both sides of its await.
536
+ *
537
+ * A {@link StatusPhase} `label` carries its source onto the readings too, so a
538
+ * download that stalls part-way through still names the file it was reading.
539
+ */
540
+ export async function downloadStatus(label, statusCallback, fn, stopToken) {
541
+ return updateStatus(label, statusCallback, () => fn(downloadStatusReporter(statusCallback, label)), stopToken);
542
+ }
543
+ /** How much of `message` this slot has already finished. */
544
+ function finished(slot, message) {
545
+ return slot.completed.get(message) ?? 0;
546
+ }
547
+ /**
548
+ * Does the batch have a measurement for this phase at all — one running now, or
549
+ * one it already retired? This is what separates a phase a region is still
550
+ * working through from one it has merely announced, and so what a tie between
551
+ * two phases turns on before their order does.
552
+ */
553
+ function measurable(vote) {
554
+ return vote.live > 0 || vote.anyFinished;
555
+ }
556
+ /**
557
+ * Combine the in-flight statuses of several concurrent operations (one RPC per
558
+ * visible region, say) into the single status the loading UI shows, so N regions
559
+ * read as one bar instead of each clobbering the shared field. Returns undefined
560
+ * when nothing is in flight.
561
+ *
562
+ * **Only operations in the same phase are summed.** `current`/`total` are
563
+ * additive within a phase — bytes with bytes, features with features — and
564
+ * incommensurable across one, so one phase wins and the rest are charged below
565
+ * (ADR-072). A fan-out whose slots share one phase, the common case, is a plain
566
+ * Σcurrent/Σtotal.
567
+ *
568
+ * **The phase that wins is the earliest one the batch is still in** (ADR-080). A
569
+ * batch is in every phase any of its operations is in — the phase that operation
570
+ * last *reported*, not the one it happens to be measuring this instant — and it
571
+ * leaves one when its LAST operation does. So the label moves forward once per
572
+ * phase, in order, and the bar under it is that phase's own.
573
+ *
574
+ * Rank alone would hand the label to a phase with nothing to say, so a phase the
575
+ * batch has anything to measure in — a reading now, or work already finished —
576
+ * beats one it does not. `phaseRank` is the fan-out's record of first
577
+ * appearance; with none, every phase ranks the same and the choice falls back to
578
+ * slot order.
579
+ *
580
+ * Each slot is then priced against the winning phase on its own, which is why
581
+ * this cannot be a Σ over two flat lists:
582
+ *
583
+ * - measuring it: its own `current`/`total`, plus whatever it already finished
584
+ * of that phase, in both halves.
585
+ * - not measuring it but having finished some: that finished work in both halves
586
+ * and **nothing more** — never the mean as well, or the bar falls every time a
587
+ * region moves on.
588
+ * - neither: in flight with nothing comparable to measure, so charged the mean
589
+ * of the totals we do know with nothing completed against it. That covers a
590
+ * response with no Content-Length and a slot in another phase alike; dropping
591
+ * either outright reads 100% while it is still downloading.
592
+ *
593
+ * A winning phase nothing is measuring right now comes back as its label alone —
594
+ * summing what its slots retired at reads 100% for a batch that is still
595
+ * working, and every slot being between reads is exactly when that happens.
596
+ * {@link createStatusFanOut} re-sends the phase's last real reading instead.
597
+ *
598
+ * A retired slot (`''` or nothing yet) never votes and is never charged the
599
+ * mean; charging it at zero is a bar that runs *backwards* as regions finish.
600
+ * Its finished work still counts, which is what keeps the fraction rising as the
601
+ * batch lands.
602
+ */
603
+ export function aggregateStatus(slots, phaseRank = new Map()) {
604
+ const inFlight = slots.filter((s) => s.status !== undefined && s.status !== '');
605
+ if (inFlight.length === 0) {
606
+ return undefined;
607
+ }
608
+ const votes = new Map();
609
+ for (const slot of inFlight) {
610
+ const message = phaseOf(slot.status);
611
+ let vote = votes.get(message);
612
+ if (vote === undefined) {
613
+ // an unseen phase ranks last, and with no record at all every phase ranks
614
+ // the same — which leaves the reduce below keeping its incumbent, the
615
+ // slot-order tie-break
616
+ vote = {
617
+ message,
618
+ live: 0,
619
+ liveTotal: 0,
620
+ rank: phaseRank.get(message) ?? phaseRank.size,
621
+ anyFinished: slots.some(s => finished(s, message) > 0),
622
+ };
623
+ votes.set(message, vote);
624
+ }
625
+ vote.source ??= statusSource(slot.status);
626
+ const reading = statusReading(slot.status);
627
+ if (reading !== undefined) {
628
+ vote.live++;
629
+ vote.liveTotal += reading.total;
630
+ }
631
+ }
632
+ // Whether the phase has anything to measure at all, and then how early the
633
+ // batch reached it. Not how many slots are in it: a count changes hands as
634
+ // regions cross, and the label went back and forth with it.
635
+ const better = (a, b) => measurable(a) !== measurable(b) ? measurable(a) : a.rank < b.rank;
636
+ const best = [...votes.values()].reduce((winner, vote) => better(vote, winner) ? vote : winner);
637
+ const { message, source } = best;
638
+ // nothing is measuring the winner, so its label alone goes out: summing what
639
+ // its slots retired at reads 100% for a batch that is still going
640
+ if (best.live === 0) {
641
+ return source === undefined ? message : { message, source };
642
+ }
643
+ const mean = best.liveTotal / best.live;
644
+ let current = 0;
645
+ let total = 0;
646
+ for (const slot of slots) {
647
+ // finished work is charged in full to both halves, which is what stops the
648
+ // denominator shrinking as regions land
649
+ const done = finished(slot, message);
650
+ current += done;
651
+ total += done;
652
+ const { status } = slot;
653
+ const reading = statusReading(status);
654
+ if (reading !== undefined && reading.message === message) {
655
+ current += reading.current;
656
+ total += reading.total;
657
+ }
658
+ else if (done === 0 && status !== undefined && status !== '') {
659
+ // in flight with nothing comparable to measure, so charged the mean — and
660
+ // only here. A slot already credited for this phase is not charged for it
661
+ // a second time, which is what made the bar fall as regions moved on.
662
+ total += mean;
663
+ }
664
+ }
665
+ return { message, current, total, source };
666
+ }
667
+ /**
668
+ * Fan one status field out to several concurrent operations that would
669
+ * otherwise fight over it. Each `slot()` returns a {@link StatusCallback}
670
+ * remembering its own latest value and how much of each phase it has been
671
+ * through; every write re-derives the shared status from all slots through
672
+ * {@link aggregateStatus}, so N concurrent downloads read as one bar instead of
673
+ * last-writer-wins — and the first one to finish (which writes the `''` every
674
+ * phase helper clears with) can't blank the label while the others are still
675
+ * running.
676
+ *
677
+ * Use it wherever several operations are handed one `statusCallback` at once —
678
+ * a `Promise.all`, an rxjs `merge`, or the per-region fan-out the LGV displays'
679
+ * `callEachRegion` builds over a fetch context. One fan-out per batch: slots are
680
+ * taken for the batch's lifetime and it is the batch that ends, so a long-lived
681
+ * one accumulates slots for work that is over.
682
+ *
683
+ * **A slot's finished phases are recorded here**, because only a slot's own
684
+ * channel ever sees the total it retired at, and they are what keep a landing
685
+ * batch's bar from walking backwards. A phase is over the moment the slot stops
686
+ * reporting it forward — see {@link continuesPhase}; the `''` it ends on is only
687
+ * one of the ways it can say so.
688
+ *
689
+ * **It never writes `''`.** A slot between two phases and a slot that is done
690
+ * both read as idle from here, so an empty aggregate means "no slot is reporting
691
+ * this instant", not "the batch is over". What goes out is the last label alone,
692
+ * with no bar — which is what that state is. The end of a batch is the owner's
693
+ * to declare (ADR-080): every one of them clears its field when its work ends.
694
+ *
695
+ * Something rather than nothing, because a write that lands is also how a
696
+ * phase's last progress value is *displaced* — statuses are throttled, so a
697
+ * percentage queued behind the window would otherwise fire after the work it
698
+ * measured had ended (ADR-071).
699
+ *
700
+ * **A phase does not lose its bar because nothing is measuring it this
701
+ * instant.** Between reads a slot reports the label alone, and when every slot
702
+ * is between reads at once the aggregate has no measurement — a determinate bar
703
+ * would drop to an indeterminate spinner and return a tick later. The phase's
704
+ * last reading is held and re-sent instead, and dropped the moment the phase
705
+ * changes.
706
+ */
707
+ export function createStatusFanOut(statusCallback) {
708
+ const aggregate = createStatusAggregate({ holdLastReading: true });
709
+ return () => {
710
+ const slot = aggregate.add();
711
+ return status => {
712
+ const out = aggregate.update(slot, status);
713
+ if (out !== undefined) {
714
+ statusCallback?.(out);
715
+ }
716
+ };
717
+ };
718
+ }
719
+ /**
720
+ * Does this reading say the work is finished? A fan-out's aggregate exists only
721
+ * while a slot is in flight, so a full one is never the truth: it is produced by
722
+ * a slot that has retired its read while another is still measuring, and the
723
+ * moment the retired one opens its next read the fraction falls back.
724
+ *
725
+ * So a complete reading is neither held nor shown when there is a real one to
726
+ * show instead; the phase ending is what moves the label on. Not a clamp on the
727
+ * arithmetic — {@link aggregateStatus} still reports what it computes, and a bar
728
+ * that falls because a region *joined* the batch still falls, which is true.
729
+ */
730
+ function readsComplete(status) {
731
+ return status.total > 0 && status.current >= status.total;
732
+ }
733
+ /**
734
+ * Is `status` the same determinate phase as `previous`, still running? Only a
735
+ * measurement of the same phase moving forward is; everything else retires it
736
+ * (ADR-080). Three shapes that are easy to miss, and all of them common:
737
+ *
738
+ * - the *enclosing* label a nested phase closes onto — a plain string, not `''`.
739
+ * The canvas feature fetch is exactly that, an adapter's byte-counted
740
+ * "Downloading features" inside the RPC's own.
741
+ * - a different phase's label, with no `''` between them.
742
+ * - a measurement moving *backwards* under the same label, which is a second
743
+ * phase of that name starting at zero. Tabix's redispatch does it when a
744
+ * feature overhangs the query.
745
+ * - a {@link PhaseFailure}, which retires the phase whatever label it carries.
746
+ */
747
+ function continuesPhase(previous, status) {
748
+ const reading = statusReading(status);
749
+ return (reading !== undefined &&
750
+ reading.message === previous.message &&
751
+ reading.current >= previous.current);
752
+ }
753
+ /**
754
+ * The single per-iteration callback for long synchronous worker loops. The
755
+ * returned `report(current)` is called once per outer-loop iteration and does
756
+ * two throttled jobs on each call:
757
+ *
758
+ * - checks the stop token via the existing throttled {@link checkStopTokenThrottled}
759
+ * machinery, so cancellation interrupts the loop within milliseconds instead
760
+ * of only at phase boundaries, and
761
+ * - emits a {@link StatusWithProgress} through `statusCallback` at most once per
762
+ * `throttleMs`, so the main thread gets a live percentage without flooding
763
+ * the postMessage channel.
764
+ *
765
+ * Both jobs are optional: with no `statusCallback`/`total` this is purely a
766
+ * throttled cancellation tick, so a loop has exactly one inner callback whether
767
+ * or not it drives the progress UI.
768
+ *
769
+ * Emission is gated on wall-clock time (`throttleMs`) through {@link
770
+ * createTimeGate}, which thins the `Date.now()` reads as well as the emits —
771
+ * see there for why its stride is learned rather than fixed. Keep the loop a
772
+ * plain `for` and call `report()` once per item (it owns the counter), or
773
+ * `report(n)` for an explicit position.
774
+ */
775
+ export function createProgressReporter({ label = '', total, statusCallback, stopToken, stopTokenCheck, throttleMs = 100, }) {
776
+ const checker = stopTokenCheck ?? createStopTokenChecker(stopToken);
777
+ const emitDue = createTimeGate();
778
+ let count = 0;
779
+ return (current = count) => {
780
+ count = current + 1;
781
+ checkStopTokenThrottled(checker);
782
+ if (statusCallback !== undefined &&
783
+ total !== undefined &&
784
+ emitDue(throttleMs)) {
785
+ statusCallback({ message: label, current, total });
786
+ }
787
+ };
788
+ }
789
+ /**
790
+ * Run a measurable phase: shows `label` at 0%, hands `fn` a {@link
791
+ * ProgressReporter} to drive during the work, then checks the stop token once
792
+ * more and restores the enclosing phase. The determinate counterpart to
793
+ * `updateStatus`, and it nests the same way — see {@link openPhase}.
794
+ */
795
+ export async function withProgress({ label, total, statusCallback, stopToken, }, fn) {
796
+ const report = createProgressReporter({
797
+ label,
798
+ total,
799
+ statusCallback,
800
+ stopToken,
801
+ });
802
+ const endPhase = openPhase(statusCallback, label);
803
+ // pessimistic for the same reason as `updateStatus`: a phase that leaves this
804
+ // scope any way other than returning did not finish its work
805
+ let outcome = 'failed';
806
+ try {
807
+ // inside the try, because `report` checks the stop token before it emits and
808
+ // so throws here on a token already stopped. Outside, that threw past the
809
+ // close and left the phase open on the channel — a slot whose last word is a
810
+ // label is one `aggregateStatus` counts as in flight for the rest of the
811
+ // batch.
812
+ report(0);
813
+ const result = await withStopTokenCheck(stopToken, () => fn(report));
814
+ outcome = 'completed';
815
+ return result;
816
+ }
817
+ finally {
818
+ endPhase(outcome);
819
+ }
820
+ }