@jbrowse/core 4.3.0 → 5.0.0-beta.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1140) hide show
  1. package/README.md +822 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +62 -93
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
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  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,59 @@
1
+ export declare const MAX_ZOOM_RATE_PER_MS: number;
2
+ export declare const SCROLL_ZOOM_FACTOR_DIVISOR = 500;
3
+ export declare function wheelZoomAccum(normalizedDeltaY: number, isCtrlZoom: boolean): number;
4
+ export declare function getZoomNormalizer(deltaY: number): 25 | 75 | 150 | 500;
5
+ export declare function normalizeWheelDelta(delta: number, deltaMode: number, pageHeight?: number): number;
6
+ export declare function wheelFrameElapsedMs(now: number, lastRafTime: number | null): number;
7
+ export declare function accumulateScroll(prev: number, deltaX: number): number;
8
+ export declare const ZOOM_ACTIVE_WINDOW_MS = 100;
9
+ export declare function isActivelyZooming(now: number, lastZoomTime: number | null): boolean;
10
+ export declare function applyZoomAccum(bpPerPx: number, zoomAccum: number, elapsedMs: number): number;
11
+ export interface WheelZoomView {
12
+ bpPerPx: number;
13
+ zoomTo: (bpPerPx: number, offset?: number) => void;
14
+ horizontalScroll: (delta: number) => void;
15
+ }
16
+ export interface WheelZoomTarget {
17
+ views: WheelZoomView[];
18
+ scrollZoom: boolean;
19
+ originElement: () => HTMLElement | undefined;
20
+ }
21
+ export interface WheelZoomControllerOptions {
22
+ element: HTMLElement;
23
+ resolveTarget: (event: WheelEvent) => WheelZoomTarget | undefined;
24
+ swallowUnhandled?: boolean;
25
+ /**
26
+ * Abandon the gesture once the pointer leaves `element`, rather than following
27
+ * the wheel events the browser keeps latching here (see trackPointerPresence).
28
+ *
29
+ * Only for an element large and stationary enough that "the pointer left" is a
30
+ * real exit. On a small or moving target it isn't: a zoom slides a thin svg
31
+ * ribbon out from under a stationary cursor, the browser fires mouseleave, and
32
+ * the gesture would die halfway through. So this is opt-in, not the default.
33
+ */
34
+ releaseOnPointerLeave?: boolean;
35
+ onEvent?: (event: WheelEvent) => void;
36
+ }
37
+ /**
38
+ * The one wheel gesture handler for linear views. Its decision matrix:
39
+ *
40
+ * - ctrl/meta+wheel, or (scrollZoom && |dy| >= |dx|) → zoom about the cursor
41
+ * - shift+wheel while scrollZoom is on → declined, we pass
42
+ * - a horizontal delta, unless one arrives mid-zoom → pan by dx
43
+ *
44
+ * Declining shift is what leaves a nested panel its own scroll
45
+ * (`usePanelVirtualScroll`) — it is not a way back to the page. Browsers turn
46
+ * shift+wheel into *horizontal* scrolling, so what a view declines here scrolls
47
+ * the page sideways or not at all. The vertical way out is spatial rather than
48
+ * modal: JBrowse binds this below the view's sticky header, leaving that header
49
+ * as a gutter the wheel still scrolls (LinearGenomeViewContainer's tracksRef).
50
+ *
51
+ * The listener is non-passive so it can preventDefault to suppress native scroll
52
+ * during a zoom. To pay for that it only accumulates deltas: every model write
53
+ * happens in one requestAnimationFrame, so a burst of events (fast trackpad,
54
+ * inertial scroll) collapses to a single update per frame instead of thrashing
55
+ * the views once per event.
56
+ *
57
+ * Returns its disposer.
58
+ */
59
+ export declare function createWheelZoomController({ element, resolveTarget, swallowUnhandled, releaseOnPointerLeave, onEvent, }: WheelZoomControllerOptions): () => void;
@@ -0,0 +1,231 @@
1
+ // Shared wheel-zoom math and event handling for linear genome views. The LGV
2
+ // wheel handler, the breakpoint-split overlay and the synteny canvas all zoom on
3
+ // ctrl/scroll-zoom wheel gestures and must behave identically, so the normalizer,
4
+ // the rate limit and the whole gesture decision matrix live here —
5
+ // createWheelZoomController below is what each of those three actually runs.
6
+ import { transaction } from 'mobx';
7
+ import { createFrameCoalescer } from './frameCoalescer.js';
8
+ import { trackPointerPresence } from './pointerPresence.js';
9
+ // max zoom delta per millisecond — equivalent to 0.2 per frame at 60fps
10
+ export const MAX_ZOOM_RATE_PER_MS = 0.2 / 16.67;
11
+ // Scroll-zoom (plain wheel with the scrollZoom preference on) divides by a fixed
12
+ // amount for a smooth proportional feel, rather than the adaptive
13
+ // getZoomNormalizer used for ctrl/pinch zoom where device deltas vary wildly.
14
+ export const SCROLL_ZOOM_FACTOR_DIVISOR = 500;
15
+ // The per-event contribution to the zoom accumulator, given a wheel delta
16
+ // already normalized to pixels via normalizeWheelDelta. ctrl/pinch zoom uses the
17
+ // adaptive normalizer; scroll-zoom uses the fixed divisor. Single source of the
18
+ // zoom-step feel so every wheel handler (LGV, breakpoint overlay, synteny)
19
+ // zooms identically for the same gesture.
20
+ export function wheelZoomAccum(normalizedDeltaY, isCtrlZoom) {
21
+ return (normalizedDeltaY /
22
+ (isCtrlZoom
23
+ ? getZoomNormalizer(normalizedDeltaY)
24
+ : SCROLL_ZOOM_FACTOR_DIVISOR));
25
+ }
26
+ // larger wheel deltas (e.g. mouse wheel notches) divide by more so a single
27
+ // notch produces a consistent zoom step regardless of device delta magnitude
28
+ export function getZoomNormalizer(deltaY) {
29
+ const abs = Math.abs(deltaY);
30
+ if (abs < 6) {
31
+ return 25;
32
+ }
33
+ if (abs > 150) {
34
+ return 500;
35
+ }
36
+ if (abs > 30) {
37
+ return 150;
38
+ }
39
+ return 75;
40
+ }
41
+ // One wheel notch in line mode (deltaMode 1) is roughly this many pixels, and a
42
+ // page (deltaMode 2) roughly WHEEL_PAGE_HEIGHT — the values Facebook's
43
+ // normalize-wheel uses, the de-facto cross-browser convention. Pixel mode (0),
44
+ // which trackpads and modern mice report, passes through untouched.
45
+ const WHEEL_LINE_HEIGHT = 40;
46
+ const WHEEL_PAGE_HEIGHT = 800;
47
+ // Convert a WheelEvent delta from its deltaMode units to pixels. Panel-scroll
48
+ // callers pass the viewport height as `pageHeight` so a page maps to exactly one
49
+ // screen; the zoom path omits it and takes the default. Single normalizer for
50
+ // both the zoom math here and the vertical-scroll handlers so a notch means the
51
+ // same thing everywhere.
52
+ export function normalizeWheelDelta(delta, deltaMode, pageHeight = WHEEL_PAGE_HEIGHT) {
53
+ return deltaMode === 1
54
+ ? delta * WHEEL_LINE_HEIGHT
55
+ : deltaMode === 2
56
+ ? delta * pageHeight
57
+ : delta;
58
+ }
59
+ // elapsed since the previous animation frame, clamped to 100ms and defaulting
60
+ // to one 60fps frame when there is no prior frame (first event or post-resume)
61
+ export function wheelFrameElapsedMs(now, lastRafTime) {
62
+ return Math.min(100, lastRafTime !== null ? now - lastRafTime : 16.67);
63
+ }
64
+ // Accumulate horizontal scroll across a frame, restarting from zero when the
65
+ // gesture reverses direction so a flick the opposite way isn't cancelled out by
66
+ // leftover momentum.
67
+ export function accumulateScroll(prev, deltaX) {
68
+ const reversed = prev !== 0 && Math.sign(deltaX) !== Math.sign(prev);
69
+ return (reversed ? 0 : prev) + deltaX;
70
+ }
71
+ // A pinch/scroll-zoom gesture fires a continuous stream of wheel events, so we
72
+ // treat the view as "actively zooming" until this many ms pass with no zoom
73
+ // event. While actively zooming, callers ignore horizontal deltas: trackpads
74
+ // emit an unintentional side-scroll mid-gesture that would otherwise pan the
75
+ // view out from under the user.
76
+ export const ZOOM_ACTIVE_WINDOW_MS = 100;
77
+ // `now` and `lastZoomTime` are both wheel-event timeStamps (same clock).
78
+ // lastZoomTime is null before any zoom has occurred.
79
+ export function isActivelyZooming(now, lastZoomTime) {
80
+ return lastZoomTime !== null && now - lastZoomTime < ZOOM_ACTIVE_WINDOW_MS;
81
+ }
82
+ // apply an accumulated zoom amount to bpPerPx, rate-limited so a burst of wheel
83
+ // events can't zoom faster than MAX_ZOOM_RATE_PER_MS over the frame's elapsed
84
+ export function applyZoomAccum(bpPerPx, zoomAccum, elapsedMs) {
85
+ const max = MAX_ZOOM_RATE_PER_MS * elapsedMs;
86
+ const d = Math.max(-max, Math.min(max, zoomAccum));
87
+ return d > 0 ? bpPerPx * (1 + d) : bpPerPx / (1 - d);
88
+ }
89
+ /**
90
+ * The one wheel gesture handler for linear views. Its decision matrix:
91
+ *
92
+ * - ctrl/meta+wheel, or (scrollZoom && |dy| >= |dx|) → zoom about the cursor
93
+ * - shift+wheel while scrollZoom is on → declined, we pass
94
+ * - a horizontal delta, unless one arrives mid-zoom → pan by dx
95
+ *
96
+ * Declining shift is what leaves a nested panel its own scroll
97
+ * (`usePanelVirtualScroll`) — it is not a way back to the page. Browsers turn
98
+ * shift+wheel into *horizontal* scrolling, so what a view declines here scrolls
99
+ * the page sideways or not at all. The vertical way out is spatial rather than
100
+ * modal: JBrowse binds this below the view's sticky header, leaving that header
101
+ * as a gutter the wheel still scrolls (LinearGenomeViewContainer's tracksRef).
102
+ *
103
+ * The listener is non-passive so it can preventDefault to suppress native scroll
104
+ * during a zoom. To pay for that it only accumulates deltas: every model write
105
+ * happens in one requestAnimationFrame, so a burst of events (fast trackpad,
106
+ * inertial scroll) collapses to a single update per frame instead of thrashing
107
+ * the views once per event.
108
+ *
109
+ * Returns its disposer.
110
+ */
111
+ export function createWheelZoomController({ element, resolveTarget, swallowUnhandled = false, releaseOnPointerLeave = false, onEvent, }) {
112
+ const frame = createFrameCoalescer();
113
+ const s = {
114
+ scrollDelta: 0,
115
+ zoomAccum: 0,
116
+ target: undefined,
117
+ lastClientX: 0,
118
+ originLeft: undefined,
119
+ lastRafTime: null,
120
+ lastZoomTime: null,
121
+ lastEventTime: null,
122
+ warnedNonCancelable: false,
123
+ };
124
+ // see releaseOnPointerLeave: drop any in-flight accumulation and stop consuming
125
+ // latched wheel events, so a continued gesture pans/zooms nothing and chains to
126
+ // the page instead of staying stuck to this element
127
+ const presence = releaseOnPointerLeave
128
+ ? trackPointerPresence(element, () => {
129
+ s.scrollDelta = 0;
130
+ s.zoomAccum = 0;
131
+ s.originLeft = undefined;
132
+ })
133
+ : undefined;
134
+ function flush(now) {
135
+ const elapsed = wheelFrameElapsedMs(now, s.lastRafTime);
136
+ s.lastRafTime = now;
137
+ const { target } = s;
138
+ if (target) {
139
+ const origin = target.originElement();
140
+ if (s.zoomAccum !== 0 && origin && s.originLeft === undefined) {
141
+ s.originLeft = origin.getBoundingClientRect().left;
142
+ }
143
+ const originLeft = s.originLeft;
144
+ transaction(() => {
145
+ if (s.zoomAccum !== 0 && originLeft !== undefined) {
146
+ const offset = s.lastClientX - originLeft;
147
+ for (const view of target.views) {
148
+ view.zoomTo(applyZoomAccum(view.bpPerPx, s.zoomAccum, elapsed), offset);
149
+ }
150
+ }
151
+ if (s.scrollDelta !== 0) {
152
+ for (const view of target.views) {
153
+ view.horizontalScroll(s.scrollDelta);
154
+ }
155
+ }
156
+ });
157
+ }
158
+ s.zoomAccum = 0;
159
+ s.scrollDelta = 0;
160
+ }
161
+ function onWheel(event) {
162
+ onEvent?.(event);
163
+ const gated = presence !== undefined && !presence.isOver;
164
+ const target = gated ? undefined : resolveTarget(event);
165
+ if (target && !(event.shiftKey && target.scrollZoom)) {
166
+ // a gap longer than the frame-elapsed clamp means this event starts a new
167
+ // gesture, so the previous frame time is meaningless — including when it
168
+ // predates a spell in a backgrounded tab, where a huge elapsed would
169
+ // otherwise lift the zoom rate limit on the first frame back
170
+ if (!isActivelyZooming(event.timeStamp, s.lastEventTime)) {
171
+ s.lastRafTime = null;
172
+ s.originLeft = undefined;
173
+ }
174
+ s.lastEventTime = event.timeStamp;
175
+ s.target = target;
176
+ const deltaY = normalizeWheelDelta(event.deltaY, event.deltaMode);
177
+ const deltaX = normalizeWheelDelta(event.deltaX, event.deltaMode);
178
+ const isCtrlZoom = event.ctrlKey || event.metaKey;
179
+ const isZoom = isCtrlZoom ||
180
+ (target.scrollZoom && Math.abs(deltaY) >= Math.abs(deltaX));
181
+ if (isZoom) {
182
+ // warn once per latched run, not once per event — a non-cancelable
183
+ // sequence fires ~100 events/sec and console.warn is not free
184
+ if (event.cancelable) {
185
+ s.warnedNonCancelable = false;
186
+ }
187
+ else if (!s.warnedNonCancelable) {
188
+ s.warnedNonCancelable = true;
189
+ console.warn('[wheelZoom] wheel event not cancelable — scroll sequence already in progress');
190
+ }
191
+ event.preventDefault();
192
+ s.zoomAccum += wheelZoomAccum(deltaY, isCtrlZoom);
193
+ s.lastClientX = event.clientX;
194
+ s.lastZoomTime = event.timeStamp;
195
+ // drop any side-scroll accumulated earlier this frame — we're zooming,
196
+ // and a deltaX that arrived just before the zoom is part of the same
197
+ // noisy gesture
198
+ s.scrollDelta = 0;
199
+ }
200
+ else if (isActivelyZooming(event.timeStamp, s.lastZoomTime)) {
201
+ // ignore stray horizontal deltas that arrive mid-zoom — trackpads emit
202
+ // an unintentional side-scroll during a pinch/scroll-zoom gesture that
203
+ // would otherwise pan the view away from where the user is zooming.
204
+ // preventDefault anyway so the page itself doesn't scroll instead.
205
+ event.preventDefault();
206
+ }
207
+ else {
208
+ // With scrollZoom on, swallow the gesture even though it fell outside
209
+ // the zoom threshold: without this, a diagonal trackpad gesture whose
210
+ // |deltaX| slightly exceeds |deltaY| slips through and scrolls the page
211
+ // (shift+wheel above is the deliberate exception). With scrollZoom
212
+ // off, only swallow what we are about to pan with, so a plain vertical
213
+ // wheel isn't silently eaten.
214
+ if (swallowUnhandled ||
215
+ target.scrollZoom ||
216
+ Math.abs(deltaX) > Math.abs(2 * deltaY)) {
217
+ event.preventDefault();
218
+ }
219
+ s.scrollDelta = accumulateScroll(s.scrollDelta, deltaX);
220
+ }
221
+ frame.schedule(flush);
222
+ }
223
+ }
224
+ element.addEventListener('wheel', onWheel, { passive: false });
225
+ return () => {
226
+ element.removeEventListener('wheel', onWheel);
227
+ presence?.dispose();
228
+ // so a flush can't fire against a detached view
229
+ frame.cancel();
230
+ };
231
+ }
@@ -0,0 +1,40 @@
1
+ /**
2
+ * Wait until a view has either initialized — launch blob consumed and all — or
3
+ * failed, and report which.
4
+ *
5
+ * `initialized` folds in a view's assemblies, so an assembly that fails to load
6
+ * leaves it false **forever**. A bare `when(() => view.initialized)` therefore
7
+ * does not fail — it never settles at all, and whatever the caller meant to do
8
+ * next simply never happens, with no error, no toast and a pending promise left
9
+ * behind. That has surfaced twice now as two different-looking bugs: an SVG
10
+ * export hung behind its dialog's spinner, and a launched breakpoint split view
11
+ * that opened but was never navigated or zoomed.
12
+ *
13
+ * `pendingLaunch` is the other half, and it matters because `initialized` can
14
+ * go true MID-launch: LGV's flips the moment displayedRegions land, while the
15
+ * same apply pass still has tracks to attach — so a caller acting there reads a
16
+ * positioned view with its tracks missing (an SVG export saves it that way).
17
+ * A launch failure cannot hang this: the state machine either clears the blob
18
+ * (materialized, reported as a snackbar) or sets the view's `error`
19
+ * (installInitAutorun's failure policy). A view with no launch machinery has no
20
+ * `pendingLaunch` and the term is vacuously satisfied.
21
+ *
22
+ * Every view exposes a resolved `error` beside `initialized`, so waiting on the
23
+ * pair turns the hang into something reportable. What to report is the caller's,
24
+ * because the vocabularies genuinely differ — an export says "cannot export"
25
+ * and attaches its failures for `awaitSvgRenders` to collect, while a launcher
26
+ * says the launch failed — which is why this returns the answer instead of
27
+ * throwing one wording at both.
28
+ *
29
+ * No time bound, deliberately: `(initialized && launch consumed) || error` is a
30
+ * terminal set, so a slow-but-healthy remote assembly is waited out rather than
31
+ * guessed at.
32
+ *
33
+ * @returns true if the view initialized (and consumed any launch), false if it
34
+ * settled on an error
35
+ */
36
+ export declare function whenViewSettled(view: {
37
+ initialized: boolean;
38
+ error: unknown;
39
+ pendingLaunch?: unknown;
40
+ }): Promise<boolean>;
@@ -0,0 +1,41 @@
1
+ import { when } from 'mobx';
2
+ /**
3
+ * Wait until a view has either initialized — launch blob consumed and all — or
4
+ * failed, and report which.
5
+ *
6
+ * `initialized` folds in a view's assemblies, so an assembly that fails to load
7
+ * leaves it false **forever**. A bare `when(() => view.initialized)` therefore
8
+ * does not fail — it never settles at all, and whatever the caller meant to do
9
+ * next simply never happens, with no error, no toast and a pending promise left
10
+ * behind. That has surfaced twice now as two different-looking bugs: an SVG
11
+ * export hung behind its dialog's spinner, and a launched breakpoint split view
12
+ * that opened but was never navigated or zoomed.
13
+ *
14
+ * `pendingLaunch` is the other half, and it matters because `initialized` can
15
+ * go true MID-launch: LGV's flips the moment displayedRegions land, while the
16
+ * same apply pass still has tracks to attach — so a caller acting there reads a
17
+ * positioned view with its tracks missing (an SVG export saves it that way).
18
+ * A launch failure cannot hang this: the state machine either clears the blob
19
+ * (materialized, reported as a snackbar) or sets the view's `error`
20
+ * (installInitAutorun's failure policy). A view with no launch machinery has no
21
+ * `pendingLaunch` and the term is vacuously satisfied.
22
+ *
23
+ * Every view exposes a resolved `error` beside `initialized`, so waiting on the
24
+ * pair turns the hang into something reportable. What to report is the caller's,
25
+ * because the vocabularies genuinely differ — an export says "cannot export"
26
+ * and attaches its failures for `awaitSvgRenders` to collect, while a launcher
27
+ * says the launch failed — which is why this returns the answer instead of
28
+ * throwing one wording at both.
29
+ *
30
+ * No time bound, deliberately: `(initialized && launch consumed) || error` is a
31
+ * terminal set, so a slow-but-healthy remote assembly is waited out rather than
32
+ * guessed at.
33
+ *
34
+ * @returns true if the view initialized (and consumed any launch), false if it
35
+ * settled on an error
36
+ */
37
+ export async function whenViewSettled(view) {
38
+ const ready = () => view.initialized && view.pendingLaunch === undefined;
39
+ await when(() => ready() || !!view.error);
40
+ return ready();
41
+ }
@@ -0,0 +1,34 @@
1
+ import type { Feature } from './simpleFeature.ts';
2
+ import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
3
+ /**
4
+ * Run `onFeat` on the feature a details lookup answers with, and say something
5
+ * when it answers with nothing.
6
+ *
7
+ * Every display paints from slim render arrays and re-fetches the whole feature
8
+ * on demand, so "click a feature, open its details" is always a round trip that
9
+ * can come back empty. Six call sites across three plugins had written that
10
+ * round trip out, and the shape they shared was
11
+ * `if (feature && isAlive(self)) { … }` — a guard that reads as defensive and is
12
+ * really the whole of what a click does when the lookup fails. Five of the six
13
+ * did nothing at all, which is the worst answer to a click: the user cannot tell
14
+ * a missing feature from a dead menu item.
15
+ *
16
+ * **The three outcomes are separated here because only here can they be told
17
+ * apart**, and conflating any two of them is a bug this replaces:
18
+ *
19
+ * - **threw** — reported with its own reason, through `notifyError`. A `fetch`
20
+ * passed in must therefore let its errors out; one that catches and answers
21
+ * `undefined` turns its failure into the miss below, and the user is told off
22
+ * twice for one click, the second time less usefully.
23
+ * - **answered nothing** — `onMiss`, which defaults to the shared sentence.
24
+ * - **the node died mid-flight** — nothing but the console. A track can be
25
+ * unticked while the fetch is in flight, and every branch below reaches
26
+ * `getSession(self)`, which throws on a detached node — inside a floating
27
+ * promise, where nothing catches it.
28
+ *
29
+ * `onMiss` is a parameter rather than fixed because one caller legitimately
30
+ * stays quiet: the pileup pre-warms the read behind a context menu before the
31
+ * user has asked for anything, so a miss there just leaves the menu without its
32
+ * feature items. Passing `() => {}` is how a call site says it is speculative.
33
+ */
34
+ export declare function withFeatureDetails(self: IStateTreeNode, fetch: () => Promise<Feature | undefined>, onFeat: (feat: Feature) => void, onMiss?: () => void): Promise<void>;
@@ -0,0 +1,59 @@
1
+ import { isAlive } from '@jbrowse/mobx-state-tree';
2
+ import { notifyFeatureDetailsMiss } from './openFeatureWidget.js';
3
+ import { getNotificationSink } from './sessionServices.js';
4
+ /**
5
+ * Run `onFeat` on the feature a details lookup answers with, and say something
6
+ * when it answers with nothing.
7
+ *
8
+ * Every display paints from slim render arrays and re-fetches the whole feature
9
+ * on demand, so "click a feature, open its details" is always a round trip that
10
+ * can come back empty. Six call sites across three plugins had written that
11
+ * round trip out, and the shape they shared was
12
+ * `if (feature && isAlive(self)) { … }` — a guard that reads as defensive and is
13
+ * really the whole of what a click does when the lookup fails. Five of the six
14
+ * did nothing at all, which is the worst answer to a click: the user cannot tell
15
+ * a missing feature from a dead menu item.
16
+ *
17
+ * **The three outcomes are separated here because only here can they be told
18
+ * apart**, and conflating any two of them is a bug this replaces:
19
+ *
20
+ * - **threw** — reported with its own reason, through `notifyError`. A `fetch`
21
+ * passed in must therefore let its errors out; one that catches and answers
22
+ * `undefined` turns its failure into the miss below, and the user is told off
23
+ * twice for one click, the second time less usefully.
24
+ * - **answered nothing** — `onMiss`, which defaults to the shared sentence.
25
+ * - **the node died mid-flight** — nothing but the console. A track can be
26
+ * unticked while the fetch is in flight, and every branch below reaches
27
+ * `getSession(self)`, which throws on a detached node — inside a floating
28
+ * promise, where nothing catches it.
29
+ *
30
+ * `onMiss` is a parameter rather than fixed because one caller legitimately
31
+ * stays quiet: the pileup pre-warms the read behind a context menu before the
32
+ * user has asked for anything, so a miss there just leaves the menu without its
33
+ * feature items. Passing `() => {}` is how a call site says it is speculative.
34
+ */
35
+ export async function withFeatureDetails(self, fetch, onFeat, onMiss = () => {
36
+ notifyFeatureDetailsMiss(self);
37
+ }) {
38
+ try {
39
+ const feature = await fetch();
40
+ if (!isAlive(self)) {
41
+ return;
42
+ }
43
+ if (feature) {
44
+ onFeat(feature);
45
+ }
46
+ else {
47
+ onMiss();
48
+ }
49
+ }
50
+ catch (e) {
51
+ // Logged whatever happened, and only toasted while the display is still
52
+ // there: `getSession` throws on a detached node, and a message naming a
53
+ // track the user has already closed is noise they cannot act on.
54
+ console.error(e);
55
+ if (isAlive(self)) {
56
+ getNotificationSink(self).notifyError(`${e}`, e);
57
+ }
58
+ }
59
+ }
@@ -0,0 +1,123 @@
1
+ export { legacyInitMessage, unknownKeysMessage } from './unknownSnapshotKeys.ts';
2
+ import type { IAnyModelType, IModelType, SnapshotIn } from '@jbrowse/mobx-state-tree';
3
+ /**
4
+ * How a launch key's value is told apart from the state property of the same
5
+ * name. A key whose name collides with nothing is `launch`; the rest name the
6
+ * discriminator that splits one authored array into the recipe entries the
7
+ * launcher resolves and the built snapshots MST restores.
8
+ *
9
+ * `replay` is the one that is not remapped at all: the value lands on its
10
+ * property, and a copy rides in the blob so the launcher can run the ordered
11
+ * imperative step the property write alone does not produce.
12
+ */
13
+ export type LaunchKeyKind = 'launch' | 'trackEntries' | 'rows' | 'highlightEntries' | 'replay';
14
+ export interface LaunchKeySpec {
15
+ kind: LaunchKeyKind;
16
+ }
17
+ export interface LaunchKeyRegistration<Commands, PassThrough extends string = never> {
18
+ keys: Record<string, LaunchKeySpec>;
19
+ passThrough: readonly PassThrough[];
20
+ /** never assigned; it carries `Commands` to `withLaunchInput`'s return type */
21
+ commands?: Commands;
22
+ }
23
+ /**
24
+ * The launch keys a view captured, plus what it has to report.
25
+ *
26
+ * `Commands` is not made partial: hand-authored JSON is what fills this, so a
27
+ * key the interface marks required is not a guarantee here either way, and the
28
+ * launcher already guards the ones it cannot proceed without.
29
+ */
30
+ export type LaunchInput<Commands> = Commands & {
31
+ unknown?: Record<string, unknown>;
32
+ malformed?: Record<string, unknown>;
33
+ legacyInit?: boolean;
34
+ };
35
+ /**
36
+ * The blob when it still holds something to apply, else undefined. A view's
37
+ * gates ask this rather than the raw property: a snapshot whose only launch
38
+ * content was a typo has nothing to launch, and a view that thinks otherwise
39
+ * waits on an assembly nobody named and never leaves the spinner.
40
+ *
41
+ * Returns the blob itself, never a copy — the launch autorun clears by
42
+ * identity, and a fresh object per read strands the init it just applied.
43
+ */
44
+ export declare function pendingLaunch<C>(launch: LaunchInput<C> | undefined): LaunchInput<C> | undefined;
45
+ /**
46
+ * A view's snapshot type, widened to the authored shape: every launch key is
47
+ * accepted beside the declared properties, and a key that is both takes either
48
+ * meaning. Excess-property checking then makes a misspelled key an error at
49
+ * every literal site — a `defaultSession` view, an `addView` call, a
50
+ * `createViewState` spec.
51
+ */
52
+ export type LaunchSnapshotIn<M extends IAnyModelType, Commands, PassThrough extends string = never> = Omit<SnapshotIn<M>, keyof Commands> & {
53
+ [K in keyof Commands]?: K extends keyof SnapshotIn<M> ? Commands[K] | SnapshotIn<M>[K] : Commands[K];
54
+ } & {
55
+ [K in PassThrough]?: unknown;
56
+ } & {
57
+ /**
58
+ * @deprecated v4's nesting. Write every setting directly on the view object;
59
+ * this is unwrapped on the way in and warns.
60
+ */
61
+ init?: Commands;
62
+ };
63
+ type ReservedKey = 'id' | 'type' | 'launch';
64
+ /**
65
+ * What a view can be launched with, derived: the keys its launcher interprets
66
+ * (`Commands`) plus every declared property of its state model, optional, in
67
+ * the property's own snapshot type. Nothing is restated, so a property is
68
+ * authorable — and TYPED — from the line that declares it.
69
+ *
70
+ * ```ts
71
+ * export type LinearSyntenyViewInit = ViewInit<
72
+ * LinearSyntenyViewStateModel,
73
+ * LinearSyntenyViewCommands
74
+ * >
75
+ * ```
76
+ *
77
+ * The twin of `LaunchSnapshotIn` above, from the other end: that one widens a
78
+ * snapshot type for a literal MST site, this one is what a caller BUILDING a
79
+ * spec annotates, so its commands stay required and its properties optional.
80
+ */
81
+ export type ViewInit<M extends IAnyModelType, Commands> = Commands & Partial<Omit<SnapshotIn<M>, keyof Commands | ReservedKey>>;
82
+ export type LaunchInputModel<M extends IAnyModelType, Commands, PassThrough extends string = never> = M extends IModelType<infer P, infer O, any, infer S> ? IModelType<P, O, LaunchSnapshotIn<M, Commands, PassThrough>, S> : never;
83
+ /**
84
+ * Declare one view's launch keys. The argument is
85
+ * `Record<keyof Commands, LaunchKeySpec>`, so a command the view interprets and
86
+ * nobody registered is a compile error rather than a key that partitions as a
87
+ * typo and warns.
88
+ *
89
+ * `passThrough` names keys that are neither a launch key nor a declared
90
+ * property and still belong on the snapshot — a legacy spelling the view's own
91
+ * `preProcessSnapshot` converts.
92
+ */
93
+ export declare function defineLaunchKeys<Commands>(): <const P extends readonly string[] = readonly never[]>(keys: Record<keyof Commands, LaunchKeySpec>, { passThrough }?: {
94
+ passThrough?: P;
95
+ }) => LaunchKeyRegistration<Commands, P[number]>;
96
+ /**
97
+ * Accept a view's settings written directly on the view object, and move the
98
+ * ones a launcher has to resolve into the internal `launch` property.
99
+ *
100
+ * The partition is a `preProcessSnapshot` and is PURE. A session's view type is
101
+ * a `types.union`, so MST runs every member's preprocessor against every
102
+ * candidate snapshot while deciding which one matches, and runs it about twice
103
+ * more per instantiation; a warning from in here fires against snapshots that
104
+ * are about to be rejected. `afterAttach` — reached only by a snapshot that won
105
+ * — reports what the partition captured.
106
+ *
107
+ * ORDER: MST runs preprocessors in the reverse of the order they were added, so
108
+ * this belongs on the chain BEFORE a view's own legacy-key preprocessor, where
109
+ * it partitions the snapshot MST finally consumes rather than a key that remap
110
+ * is about to convert.
111
+ *
112
+ * The widening cast is the LAST link that may change the creation type: it
113
+ * replaces `CustomC`, so a `.props()` added after it is invisible to
114
+ * `SnapshotIn`. Further `preProcessSnapshot`/`postProcessSnapshot` links are
115
+ * fine — both carry `CustomC` through.
116
+ *
117
+ * Not `types.snapshotProcessor`, which carries the same widened input and stops
118
+ * being a `ModelType`. `PluginManager.pluggableMstType` filters union members on
119
+ * `isModelType`, so a wrapped view is dropped from the session's view union
120
+ * without a word, and `ViewType.stateModel` and every `.properties`
121
+ * introspection site break with it.
122
+ */
123
+ export declare function withLaunchInput<M extends IAnyModelType, Commands, PassThrough extends string>(model: M, registration: LaunchKeyRegistration<Commands, PassThrough>): LaunchInputModel<M, Commands, PassThrough>;