@jbrowse/core 4.2.1 → 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 +196 -55
  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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  1025. package/esm/util/viewStatus.js +20 -0
  1026. package/esm/util/virtualRange.d.ts +36 -0
  1027. package/esm/util/virtualRange.js +26 -0
  1028. package/esm/util/webStorage.d.ts +26 -0
  1029. package/esm/util/webStorage.js +92 -0
  1030. package/esm/util/wheelZoom.d.ts +59 -0
  1031. package/esm/util/wheelZoom.js +231 -0
  1032. package/esm/util/whenViewSettled.d.ts +27 -0
  1033. package/esm/util/whenViewSettled.js +28 -0
  1034. package/esm/util/withFeatureDetails.d.ts +34 -0
  1035. package/esm/util/withFeatureDetails.js +59 -0
  1036. package/package.json +240 -820
  1037. package/esm/ReExports/DataGrid.d.ts +0 -1
  1038. package/esm/ReExports/DataGrid.js +0 -1
  1039. package/esm/configuration/util.d.ts +0 -10
  1040. package/esm/configuration/util.js +0 -123
  1041. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1042. package/esm/data_adapters/util.d.ts +0 -1
  1043. package/esm/data_adapters/util.js +0 -6
  1044. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1045. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1046. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1047. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1048. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1049. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1050. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1051. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1052. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1053. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1054. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1055. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1056. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1057. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1058. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1059. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1060. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1061. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1062. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1063. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1064. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1065. package/esm/rpc/baseRpcConfig.js +0 -10
  1066. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1067. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1068. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1069. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1070. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1071. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1072. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1073. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1074. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1075. package/esm/rpc/methods/CoreRender.js +0 -40
  1076. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1077. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1078. package/esm/rpc/methods/util.d.ts +0 -15
  1079. package/esm/rpc/methods/util.js +0 -7
  1080. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1082. package/esm/ui/MenuButton.d.ts +0 -1
  1083. package/esm/ui/MenuButton.js +0 -1
  1084. package/esm/ui/MenuItems.d.ts +0 -15
  1085. package/esm/ui/MenuItems.js +0 -59
  1086. package/esm/ui/useEvent.d.ts +0 -1
  1087. package/esm/ui/useEvent.js +0 -10
  1088. package/esm/util/blobToDataURL.d.ts +0 -1
  1089. package/esm/util/blobToDataURL.js +0 -14
  1090. package/esm/util/compositeMap.d.ts +0 -11
  1091. package/esm/util/compositeMap.js +0 -59
  1092. package/esm/util/flatqueue/index.d.ts +0 -11
  1093. package/esm/util/flatqueue/index.js +0 -61
  1094. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1095. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1096. package/esm/util/layouts/MultiLayout.js +0 -40
  1097. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1098. package/esm/util/layouts/PileupLayout.js +0 -202
  1099. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1100. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1101. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1102. package/esm/util/layouts/SceneGraph.js +0 -121
  1103. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1104. package/esm/util/makeAbortableReaction.js +0 -47
  1105. package/esm/util/map-obj/index.d.ts +0 -13
  1106. package/esm/util/map-obj/index.js +0 -92
  1107. package/esm/util/nextTick.d.ts +0 -1
  1108. package/esm/util/nextTick.js +0 -3
  1109. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1110. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1111. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1112. package/esm/util/offscreenCanvasUtils.js +0 -19
  1113. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1114. package/esm/util/renderToAbstractCanvas.js +0 -53
  1115. package/esm/util/transferables.d.ts +0 -2
  1116. package/esm/util/transferables.js +0 -35
  1117. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1118. package/esm/util/tss-react/mui/index.js +0 -1
  1119. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1120. package/esm/util/tss-react/mui/mui.js +0 -5
  1121. package/esm/util/when.d.ts +0 -1
  1122. package/esm/util/when.js +0 -1
  1123. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1124. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -0,0 +1,122 @@
1
+ import { getEnv as getEnvMST } from '@jbrowse/mobx-state-tree';
2
+ import { cachedParent, findParentThatIs } from './parentWalk.js';
3
+ import { isDisplayModel, isSessionModel, isTrackModel, isViewModel, } from './types/index.js';
4
+ export { findParentThat, findParentThatIs, getRpcSessionId, } from './parentWalk.js';
5
+ const containingDisplayCache = new WeakMap();
6
+ const containingTrackCache = new WeakMap();
7
+ const containingViewCache = new WeakMap();
8
+ const sessionCache = new WeakMap();
9
+ /**
10
+ * #api core/util
11
+ * Returns the JBrowse session model for any node in the state tree. Throws if
12
+ * the node has no session ancestor.
13
+ */
14
+ export function getSession(node) {
15
+ return cachedParent(sessionCache, node, () => findParentThatIs(node, isSessionModel), 'no session model found!');
16
+ }
17
+ /**
18
+ * #api core/util
19
+ * Returns the view model that contains the given node. Throws if the node has no
20
+ * containing view.
21
+ */
22
+ export function getContainingView(node) {
23
+ return cachedParent(containingViewCache, node, () => findParentThatIs(node, isViewModel), 'no containing view found');
24
+ }
25
+ /**
26
+ * #api core/util
27
+ * Returns the track model that contains the given node. Throws if the node has
28
+ * no containing track.
29
+ */
30
+ export function getContainingTrack(node) {
31
+ return cachedParent(containingTrackCache, node, () => findParentThatIs(node, isTrackModel), 'no containing track found');
32
+ }
33
+ /**
34
+ * #api core/util
35
+ * Returns the display model that contains the given node. Throws if the node has
36
+ * no containing display.
37
+ */
38
+ export function getContainingDisplay(node) {
39
+ return cachedParent(containingDisplayCache, node, () => findParentThatIs(node, isDisplayModel), 'no containing display found');
40
+ }
41
+ /**
42
+ * #api core/util
43
+ * The host's assembly manager, for a module that resolves names and nothing
44
+ * else.
45
+ *
46
+ * Unlike the accessors in `sessionServices.ts` this one buys the caller no
47
+ * smaller type graph — an `AssemblyManager` is an MST model a `PluginManager`
48
+ * built, so naming it costs what naming a session costs. It is here to say
49
+ * which service is wanted, and because that cost is the finding: the assembly
50
+ * manager is the one thing on `AbstractSessionModel` a third-party host cannot
51
+ * simply implement.
52
+ */
53
+ export function getAssemblyHost(node) {
54
+ return getSession(node);
55
+ }
56
+ /**
57
+ * #api core/util
58
+ * Everything a display needs of its host in order to draw a region: the
59
+ * assemblies, the RPC entry point and the colors.
60
+ */
61
+ export function getRenderingServices(node) {
62
+ return getSession(node);
63
+ }
64
+ /**
65
+ * #api core/util
66
+ * Resolve user-authored refName text against the assembly of the view
67
+ * containing `node` — the one normalization layer, which resolves aliases and
68
+ * casing together. Falls back to the input when the assembly is absent or its
69
+ * aliases have not loaded.
70
+ *
71
+ * Keyed off the VIEW's assembly rather than the track's, because the view is
72
+ * what the comparison is against: displayed regions, loaded regions and blocks
73
+ * all carry the refNames the view laid out.
74
+ *
75
+ * Reach for this wherever a refName a *person* wrote is about to be compared
76
+ * against regions, features or blocks, which carry the assembly's canonical
77
+ * name. A refName a display copied off a region is canonical already and needs
78
+ * nothing; one that arrived in a session spec, a config slot or a URL is
79
+ * whatever the author read out of the location box.
80
+ *
81
+ * Skipping it fails silently and, worse, assembly-dependently: `chr12` matches
82
+ * on an assembly canonicalized `chr12` and matches nothing on one canonicalized
83
+ * `12`, so the same spec key works on one config and quietly does nothing on
84
+ * the next, with no error for anyone to act on.
85
+ *
86
+ * Resolves through `getCanonicalRefName2`, whose fallback is what keeps a spec
87
+ * read before the alias file has loaded from throwing — and the getters that
88
+ * read user specs do run from the first render.
89
+ *
90
+ * Takes a refName, not a spec that might hold one: the resolver reads
91
+ * `refName.toLowerCase()`, so anything else throws once the aliases are there,
92
+ * and a caller reading an untyped `frozen` slot has to establish that it names
93
+ * a refName at all before this is the right question to ask of it.
94
+ */
95
+ export function canonicalizeViewRefName(node, refName) {
96
+ const { assemblyManager } = getSession(node);
97
+ const name = getContainingView(node).assemblyNames?.[0];
98
+ const assembly = name ? assemblyManager.get(name) : undefined;
99
+ return assembly?.getCanonicalRefName2(refName) ?? refName;
100
+ }
101
+ /**
102
+ * #api core/util
103
+ * Returns the MST environment for a node, which carries the `pluginManager`.
104
+ */
105
+ export function getEnv(obj) {
106
+ return getEnvMST(obj);
107
+ }
108
+ export function hashCode(str) {
109
+ let hash = 0;
110
+ if (str.length === 0) {
111
+ return hash;
112
+ }
113
+ for (let i = 0; i < str.length; i++) {
114
+ const chr = str.charCodeAt(i);
115
+ hash = (hash << 5) - hash + chr;
116
+ hash |= 0;
117
+ }
118
+ return hash;
119
+ }
120
+ export function objectHash(obj) {
121
+ return `${hashCode(JSON.stringify(obj))}`;
122
+ }
@@ -1,5 +1 @@
1
- export declare const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
2
- export declare const random: (bytes: number) => Uint8Array<ArrayBuffer>;
3
- export declare const customRandom: (alphabet: string, defaultSize: number, getRandom: (bytes: number) => Uint8Array) => (size?: number) => string;
4
- export declare const customAlphabet: (alphabet: string, size?: number) => (size?: number) => string;
5
1
  export declare const nanoid: (size?: number) => string;
@@ -1,29 +1,19 @@
1
- export const urlAlphabet = 'useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict';
2
- export const random = (bytes) => crypto.getRandomValues(new Uint8Array(bytes));
3
- export const customRandom = (alphabet, defaultSize, getRandom) => {
4
- const mask = (2 << (Math.log(alphabet.length - 1) / Math.LN2)) - 1;
5
- const step = -~((1.6 * mask * defaultSize) / alphabet.length);
6
- return (size = defaultSize) => {
7
- let id = '';
8
- while (true) {
9
- const bytes = getRandom(step);
10
- let j = step;
11
- while (j--) {
12
- id += alphabet[bytes[j] & mask] || '';
13
- if (id.length === size) {
14
- return id;
15
- }
16
- }
17
- }
18
- };
19
- };
20
- export const customAlphabet = (alphabet, size = 21) => customRandom(alphabet, size, random);
1
+ // The web-crypto branch of nanoid (https://github.com/ai/nanoid, MIT), reduced
2
+ // to the one generator we call. The custom-alphabet machinery was carried along
3
+ // unused; restore it from upstream if a non-default alphabet is ever needed.
21
4
  export const nanoid = (size = 21) => crypto.getRandomValues(new Uint8Array(size)).reduce((id, byte) => {
5
+ // It is incorrect to use bytes exceeding the alphabet size.
6
+ // The following mask reduces the random byte in the 0-255 value
7
+ // range to the 0-63 value range. Therefore, adding hacks, such
8
+ // as empty string fallback or magic numbers, is unnecessary because
9
+ // the bitmask trims bytes down to the alphabet size.
22
10
  byte &= 63;
23
11
  if (byte < 36) {
12
+ // `0-9a-z`
24
13
  id += byte.toString(36);
25
14
  }
26
15
  else if (byte < 62) {
16
+ // `A-Z`
27
17
  id += (byte - 26).toString(36).toUpperCase();
28
18
  }
29
19
  else if (byte > 62) {
@@ -0,0 +1,20 @@
1
+ export declare function clamp(num: number, min: number, max: number): number;
2
+ export declare function minmax(a: number, b: number): readonly [number, number];
3
+ export declare function max(arr: ArrayLike<number>, init?: number): number;
4
+ export declare function maxFinite(arr: ArrayLike<number>, init?: number): number;
5
+ export declare function min(arr: ArrayLike<number>, init?: number): number;
6
+ export declare function sum(arr: ArrayLike<number>): number;
7
+ export declare function avg(arr: ArrayLike<number>): number;
8
+ export declare function setNumberGrouping(enabled: boolean): void;
9
+ export declare function getNumberGrouping(): boolean;
10
+ export declare function toLocale(n: number): string;
11
+ export declare function toPrecision(s: number, n?: number): number;
12
+ export declare function reducePrecision(s: number, n?: number): string;
13
+ /**
14
+ * A byte count as a person reads it. Shared by the region-too-large banner and
15
+ * the save-track-data dialog, which quote the same index estimate and would
16
+ * otherwise word the same number two ways.
17
+ */
18
+ export declare function getDisplayStr(totalBytes: number): string;
19
+ export declare function radToDeg(radians: number): number;
20
+ export declare function polarToCartesian(rho: number, theta: number): [number, number];
@@ -0,0 +1,127 @@
1
+ export function clamp(num, min, max) {
2
+ if (num < min) {
3
+ return min;
4
+ }
5
+ if (num > max) {
6
+ return max;
7
+ }
8
+ return num;
9
+ }
10
+ export function minmax(a, b) {
11
+ return [Math.min(a, b), Math.max(a, b)];
12
+ }
13
+ // Index iteration so these accept both arrays and typed arrays (e.g.
14
+ // Float32Array) without requiring Iterable.
15
+ export function max(arr, init = Number.NEGATIVE_INFINITY) {
16
+ let max = init;
17
+ for (let i = 0; i < arr.length; i++) {
18
+ max = Math.max(arr[i], max);
19
+ }
20
+ return max;
21
+ }
22
+ // Like max() but skips NaN/Infinity entries rather than propagating them (a
23
+ // single NaN poisons Math.max). Used where an array can legitimately carry
24
+ // gaps, e.g. a score series with unmeasured bins in it.
25
+ export function maxFinite(arr, init = Number.NEGATIVE_INFINITY) {
26
+ let max = init;
27
+ for (let i = 0; i < arr.length; i++) {
28
+ const v = arr[i];
29
+ if (Number.isFinite(v) && v > max) {
30
+ max = v;
31
+ }
32
+ }
33
+ return max;
34
+ }
35
+ export function min(arr, init = Number.POSITIVE_INFINITY) {
36
+ let min = init;
37
+ for (let i = 0; i < arr.length; i++) {
38
+ min = Math.min(arr[i], min);
39
+ }
40
+ return min;
41
+ }
42
+ export function sum(arr) {
43
+ let sum = 0;
44
+ for (let i = 0; i < arr.length; i++) {
45
+ sum += arr[i];
46
+ }
47
+ return sum;
48
+ }
49
+ export function avg(arr) {
50
+ return sum(arr) / arr.length;
51
+ }
52
+ // Thousand separators are a display convention, not part of the number. They
53
+ // make a coordinate readable, but they survive a copy-paste into tools that
54
+ // then choke on them, so users who copy coordinates out of the app more than
55
+ // they read them can turn them off (the `numberGrouping` preference).
56
+ //
57
+ // A plain variable rather than an observable, because every number the app
58
+ // displays funnels through here — including strings built worker-side, where a
59
+ // jexl `mouseover` slot formats a tooltip against the full feature. A
60
+ // main-thread-only reactive value would leave those stale, so the app would sit
61
+ // half-formatted until every track refetched. Instead each realm sets this once
62
+ // at startup (the worker gets it in its boot configuration, see RpcManager) and
63
+ // the preference asks for a reload, which buys uniformity for one page load.
64
+ let numberGrouping = true;
65
+ export function setNumberGrouping(enabled) {
66
+ numberGrouping = enabled;
67
+ }
68
+ // read when handing the setting to another realm; not a display path
69
+ export function getNumberGrouping() {
70
+ return numberGrouping;
71
+ }
72
+ // Fast number formatter with thousand separators.
73
+ // Benchmarked at 5-67x faster than toLocaleString('en-US')
74
+ export function toLocale(n) {
75
+ const abs = Math.abs(n);
76
+ // `!(abs >= 1000)` also covers NaN, which has no digits to group, and
77
+ // String() switches to exponential form at 1e21 and for Infinity, where a
78
+ // thousands separator is meaningless
79
+ if (!numberGrouping || !(abs >= 1000) || abs >= 1e21) {
80
+ return String(n);
81
+ }
82
+ const str = String(abs);
83
+ // separators count from the decimal point, not the end of the string
84
+ const intLen = Number.isInteger(abs) ? str.length : str.indexOf('.');
85
+ let result = n < 0 ? '-' : '';
86
+ for (let i = 0; i < intLen; i++) {
87
+ if (i > 0 && (intLen - i) % 3 === 0) {
88
+ result += ',';
89
+ }
90
+ result += str[i];
91
+ }
92
+ return intLen === str.length ? result : result + str.slice(intLen);
93
+ }
94
+ // numeric significant-figure rounding; reducePrecision is the formatted form
95
+ export function toPrecision(s, n = 3) {
96
+ return Number.parseFloat(s.toPrecision(n));
97
+ }
98
+ export function reducePrecision(s, n = 3) {
99
+ return toLocale(toPrecision(s, n));
100
+ }
101
+ /**
102
+ * A byte count as a person reads it. Shared by the region-too-large banner and
103
+ * the save-track-data dialog, which quote the same index estimate and would
104
+ * otherwise word the same number two ways.
105
+ */
106
+ export function getDisplayStr(totalBytes) {
107
+ // pick the unit from the rounded value so e.g. 999,999 bytes reads "1 Mb"
108
+ // rather than "1000 Kb"
109
+ const mb = toPrecision(totalBytes / 1_000_000);
110
+ const kb = toPrecision(totalBytes / 1000);
111
+ if (mb >= 1) {
112
+ return `${mb} Mb`;
113
+ }
114
+ else if (kb >= 1) {
115
+ return `${kb} Kb`;
116
+ }
117
+ else {
118
+ return `${Math.floor(totalBytes)} bytes`;
119
+ }
120
+ }
121
+ const oneEightyOverPi = 180 / Math.PI;
122
+ export function radToDeg(radians) {
123
+ return (radians * oneEightyOverPi) % 360;
124
+ }
125
+ export function polarToCartesian(rho, theta) {
126
+ return [rho * Math.cos(theta), rho * Math.sin(theta)];
127
+ }
@@ -0,0 +1,2 @@
1
+ export declare function isObject(x: unknown): x is Record<string | symbol | number, unknown>;
2
+ export declare function isPlainObject(x: unknown): x is Record<string, unknown>;
@@ -0,0 +1,9 @@
1
+ // MIT https://github.com/inspect-js/is-object
2
+ export function isObject(x) {
3
+ return typeof x === 'object' && x !== null;
4
+ }
5
+ // `isObject` minus arrays: the branch `deepEqual` and `deepMerge` recurse into
6
+ // key by key, as opposed to the one they walk by index.
7
+ export function isPlainObject(x) {
8
+ return isObject(x) && !Array.isArray(x);
9
+ }
@@ -1,5 +1,6 @@
1
- export { collectTransferables, isDetachedBuffer } from './transferables.ts';
2
- export declare function isImageBitmap(value: unknown): value is ImageBitmap;
1
+ /**
2
+ * Paint a worker-produced image onto a 2d context: either a real
3
+ * ImageBitmap/canvas, or the serialized canvas-sequencer command list a worker
4
+ * without OffscreenCanvas sends instead.
5
+ */
3
6
  export declare function drawImageOntoCanvasContext(imageData: any, context: CanvasRenderingContext2D): void;
4
- export declare function createCanvas(width: number, height: number): any;
5
- export declare function createImageBitmap(canvas: any): Promise<unknown>;
@@ -1,9 +1,9 @@
1
1
  import { CanvasSequence } from 'canvas-sequencer-ts';
2
- import isNode from 'detect-node';
3
- export { collectTransferables, isDetachedBuffer } from "./transferables.js";
4
- export function isImageBitmap(value) {
5
- return typeof ImageBitmap !== 'undefined' && value instanceof ImageBitmap;
6
- }
2
+ /**
3
+ * Paint a worker-produced image onto a 2d context: either a real
4
+ * ImageBitmap/canvas, or the serialized canvas-sequencer command list a worker
5
+ * without OffscreenCanvas sends instead.
6
+ */
7
7
  export function drawImageOntoCanvasContext(imageData, context) {
8
8
  if (imageData.serializedCommands) {
9
9
  const seq = new CanvasSequence(imageData.serializedCommands);
@@ -13,45 +13,3 @@ export function drawImageOntoCanvasContext(imageData, context) {
13
13
  context.drawImage(imageData, 0, 0);
14
14
  }
15
15
  }
16
- export function createCanvas(width, height) {
17
- if (typeof OffscreenCanvas === 'function') {
18
- return new OffscreenCanvas(width, height);
19
- }
20
- else if (isNode) {
21
- return nodeCreateCanvas(width, height);
22
- }
23
- else {
24
- const context = new CanvasSequence();
25
- return {
26
- width,
27
- height,
28
- getContext() {
29
- return context;
30
- },
31
- };
32
- }
33
- }
34
- export async function createImageBitmap(canvas) {
35
- if (typeof OffscreenCanvas === 'function') {
36
- return canvas.transferToImageBitmap();
37
- }
38
- else if (isNode) {
39
- const dataUri = canvas.toDataURL();
40
- const img = new nodeImage();
41
- return new Promise((resolve, reject) => {
42
- img.onload = () => {
43
- resolve(img);
44
- };
45
- img.onerror = reject;
46
- img.src = dataUri;
47
- });
48
- }
49
- else {
50
- const ctx = canvas.getContext('2d');
51
- return {
52
- height: canvas.height,
53
- width: canvas.width,
54
- serializedCommands: ctx.toJSON(),
55
- };
56
- }
57
- }
@@ -0,0 +1,23 @@
1
+ import type { ResolvableDisplay } from '../configuration/promotableResolve.ts';
2
+ import type { AbstractSessionModel } from './types/index.ts';
3
+ /**
4
+ * #api core/util
5
+ * Every display on an open track, across all open views — the reach of anything
6
+ * that acts on "the tracks the user is looking at": a promoted default's "apply
7
+ * to open tracks", and the share/export bake. One walk so those can't drift
8
+ * apart.
9
+ *
10
+ * Recurses into composite views. A display nested in one resolves the cascade
11
+ * like any other but was invisible to both callers, so the share/export bake
12
+ * didn't bake its inherited values and a shared session containing a
13
+ * breakpoint-split or synteny view rendered differently for the recipient.
14
+ * `LGVSyntenyDisplay` is only ever reached through this branch, so don't flatten
15
+ * the recursion away. `hasChildViews` names the one composite shape it does not
16
+ * cover.
17
+ *
18
+ * A view holding neither (e.g. spreadsheet) drops out via the structural guards.
19
+ * A view whose displays declare no promotable slot (e.g. dotplot, which does
20
+ * hold tracks) is walked and contributes nothing — harmless, and cheaper than
21
+ * asking each display whether it has anything to promote.
22
+ */
23
+ export declare function openPromotableDisplays(session: AbstractSessionModel): ResolvableDisplay[];
@@ -0,0 +1,79 @@
1
+ /**
2
+ * @module
3
+ * One walk of "every display on an open track, across all open views".
4
+ *
5
+ * Lives here rather than in `configuration/promotableDefaults.ts`, where it grew:
6
+ * nothing about it is a cascade concern — it answers "the tracks the user is
7
+ * looking at", and its two callers want that for different reasons (the promoted
8
+ * default's "apply to open tracks", and `product-core`'s share/export bake). It
9
+ * cannot move next to either one: `product-core` imports `@jbrowse/core`, never
10
+ * the reverse.
11
+ *
12
+ * The displays are typed `ResolvableDisplay` because both callers immediately
13
+ * resolve config off them, and that shape (`IStateTreeNode` + `type` +
14
+ * `configuration`) is the smallest thing either needs.
15
+ */
16
+ import { isObject } from './objectUtils.js';
17
+ import { isViewContainer } from './types/index.js';
18
+ // A view whose open tracks we can enumerate. The generic view interface doesn't
19
+ // surface `tracks`, so narrow structurally — the declared display shape is the
20
+ // same ResolvableDisplay the cascade already operates on.
21
+ //
22
+ // Checks the elements, not just that `tracks` is an array: this narrowing is
23
+ // what every consumer downstream trusts, and an element without `displays`
24
+ // would put `undefined` in the walk and throw at the first `display.type` —
25
+ // inside a share/export bake, i.e. as far from the cause as it gets. Every
26
+ // `tracks`-bearing view today holds real track models, so this only ever
27
+ // confirms what is already true.
28
+ function hasOpenTracks(view) {
29
+ return ('tracks' in view &&
30
+ Array.isArray(view.tracks) &&
31
+ view.tracks.every(t => isObject(t) && Array.isArray(t.displays)));
32
+ }
33
+ // A composite view holding child views in a `views` array: breakpoint-split and
34
+ // the linear-comparative family incl. synteny. Not exclusive with
35
+ // `hasOpenTracks`: LinearComparativeView has both its own synteny tracks and two
36
+ // child LGVs.
37
+ //
38
+ // A view that holds its children under *named* props instead (SvInspectorView's
39
+ // `spreadsheetView`/`circularView`) is NOT reached. Enumerating a view's own
40
+ // properties to find them isn't an option — reading every key of an MST node
41
+ // invokes every computed view on it, several of which throw before the view is
42
+ // initialized. No display reachable that way declares a promotable slot today,
43
+ // so nothing is currently missed; if one ever does, give that view a `views`
44
+ // getter returning its children rather than duck-typing harder here.
45
+ function hasChildViews(view) {
46
+ return ('views' in view &&
47
+ Array.isArray(view.views) &&
48
+ view.views.every(v => typeof v === 'object' && v !== null));
49
+ }
50
+ function displaysInView(view) {
51
+ return [
52
+ ...(hasOpenTracks(view) ? view.tracks.flatMap(t => t.displays) : []),
53
+ ...(hasChildViews(view) ? view.views.flatMap(displaysInView) : []),
54
+ ];
55
+ }
56
+ /**
57
+ * #api core/util
58
+ * Every display on an open track, across all open views — the reach of anything
59
+ * that acts on "the tracks the user is looking at": a promoted default's "apply
60
+ * to open tracks", and the share/export bake. One walk so those can't drift
61
+ * apart.
62
+ *
63
+ * Recurses into composite views. A display nested in one resolves the cascade
64
+ * like any other but was invisible to both callers, so the share/export bake
65
+ * didn't bake its inherited values and a shared session containing a
66
+ * breakpoint-split or synteny view rendered differently for the recipient.
67
+ * `LGVSyntenyDisplay` is only ever reached through this branch, so don't flatten
68
+ * the recursion away. `hasChildViews` names the one composite shape it does not
69
+ * cover.
70
+ *
71
+ * A view holding neither (e.g. spreadsheet) drops out via the structural guards.
72
+ * A view whose displays declare no promotable slot (e.g. dotplot, which does
73
+ * hold tracks) is walked and contributes nothing — harmless, and cheaper than
74
+ * asking each display whether it has anything to promote.
75
+ */
76
+ export function openPromotableDisplays(session) {
77
+ const views = isViewContainer(session) ? session.views : [];
78
+ return views.flatMap(displaysInView);
79
+ }
@@ -0,0 +1,33 @@
1
+ import type { Feature, SimpleFeatureSerialized } from './simpleFeature.ts';
2
+ import type { Widget } from './types/index.ts';
3
+ import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
4
+ export interface FeatureWidgetTypeRef {
5
+ type: string;
6
+ id: string;
7
+ }
8
+ export declare function openFeatureWidget(node: IAnyStateTreeNode, featureData: SimpleFeatureSerialized, opts?: {
9
+ widget?: FeatureWidgetTypeRef;
10
+ extra?: Record<string, unknown>;
11
+ feature?: Feature;
12
+ }): Widget | undefined;
13
+ /**
14
+ * The other half of the flow above: the details lookup came back with nothing,
15
+ * so there is no widget to open.
16
+ *
17
+ * Every display paints from slim render arrays and re-fetches the whole feature
18
+ * on click, so a lookup can come back empty for reasons the user cannot see —
19
+ * the data was evicted under them, or the id does not compare in the tier that
20
+ * answered. **Silently doing nothing is the worst response to a click**, and it
21
+ * was what three canvas paths did.
22
+ *
23
+ * Here rather than per plugin because the sentence is one fact and the two
24
+ * families would otherwise word it differently for the same event. It is
25
+ * deliberately NOT what an *error* says: a throw already reaches `notifyError`
26
+ * with the reason, and a display that notifies both tells the user off twice for
27
+ * one click.
28
+ *
29
+ * A **speculative** lookup must not call this — alignments pre-warms the read
30
+ * behind a context menu, and the user asked for nothing there, so the menu just
31
+ * doesn't grow its feature items.
32
+ */
33
+ export declare function notifyFeatureDetailsMiss(node: IAnyStateTreeNode): void;
@@ -0,0 +1,64 @@
1
+ // straight from mstUtils rather than the barrel, which re-exports this module:
2
+ // a value import of './index.ts' from a module the barrel re-exports is the
3
+ // cycle shape that bites under Rollup (TDZ) and babel/CJS (getter before
4
+ // require) alike
5
+ import { getContainingTrack, getContainingView, getSession, } from './mstUtils.js';
6
+ import { getNotificationSink } from './sessionServices.js';
7
+ import SimpleFeature from './simpleFeature.js';
8
+ import { isSessionModelWithWidgets } from './types/index.js';
9
+ const DEFAULT_FEATURE_WIDGET = {
10
+ type: 'BaseFeatureWidget',
11
+ id: 'baseFeature',
12
+ };
13
+ // Open a feature widget for the given featureData and mark it as the
14
+ // session's selected feature. Node is any MST node in the display tree —
15
+ // used to resolve session + containing view + containing track. Returns
16
+ // the new widget, or undefined if the session can't host widgets (e.g.
17
+ // headless export contexts).
18
+ //
19
+ // This consolidates the addWidget/showWidget/setSelection/getContainingView/
20
+ // getContainingTrack/isSessionModelWithWidgets boilerplate that every
21
+ // "click a feature → open details" flow had to repeat. setSelection is
22
+ // always called so cross-view selection-sync features work uniformly —
23
+ // callers previously split on this, which was likely accidental (the
24
+ // non-BaseLinearDisplay-composers had hand-rolled selectFeature actions
25
+ // and just omitted it).
26
+ export function openFeatureWidget(node, featureData, opts = {}) {
27
+ const session = getSession(node);
28
+ if (!isSessionModelWithWidgets(session)) {
29
+ return undefined;
30
+ }
31
+ session.setSelection(opts.feature ?? new SimpleFeature(featureData));
32
+ const { type, id } = opts.widget ?? DEFAULT_FEATURE_WIDGET;
33
+ const widget = session.addWidget(type, id, {
34
+ featureData,
35
+ view: getContainingView(node),
36
+ track: getContainingTrack(node),
37
+ ...opts.extra,
38
+ });
39
+ session.showWidget(widget);
40
+ return widget;
41
+ }
42
+ /**
43
+ * The other half of the flow above: the details lookup came back with nothing,
44
+ * so there is no widget to open.
45
+ *
46
+ * Every display paints from slim render arrays and re-fetches the whole feature
47
+ * on click, so a lookup can come back empty for reasons the user cannot see —
48
+ * the data was evicted under them, or the id does not compare in the tier that
49
+ * answered. **Silently doing nothing is the worst response to a click**, and it
50
+ * was what three canvas paths did.
51
+ *
52
+ * Here rather than per plugin because the sentence is one fact and the two
53
+ * families would otherwise word it differently for the same event. It is
54
+ * deliberately NOT what an *error* says: a throw already reaches `notifyError`
55
+ * with the reason, and a display that notifies both tells the user off twice for
56
+ * one click.
57
+ *
58
+ * A **speculative** lookup must not call this — alignments pre-warms the read
59
+ * behind a context menu, and the user asked for nothing there, so the menu just
60
+ * doesn't grow its feature items.
61
+ */
62
+ export function notifyFeatureDetailsMiss(node) {
63
+ getNotificationSink(node).notify('Could not load details for this feature', 'warning');
64
+ }
@@ -0,0 +1,32 @@
1
+ import { SvgCanvas } from './SvgCanvas.ts';
2
+ import type { SvgRasterCanvasOpts } from './createSvgRasterCanvas.ts';
3
+ import type React from 'react';
4
+ export type Ctx2D = CanvasRenderingContext2D | SvgCanvas;
5
+ export type PaintLayerOpts = SvgRasterCanvasOpts & {
6
+ rasterizeLayers?: boolean;
7
+ };
8
+ /**
9
+ * Paint into either a 2× rasterize canvas (PNG-embedded as <image>) or an
10
+ * SvgCanvas (serialized into a <g>). Renders one element — callers don't
11
+ * branch on which mode was picked.
12
+ *
13
+ * Used by every renderSvg.tsx that has a heavy draw path: the same `paint`
14
+ * callback runs on both surfaces, with `paint(ctx)` doing whatever drawing
15
+ * the plugin needs in logical coordinates (the raster canvas is pre-scaled, so
16
+ * callbacks never deal with devicePixelRatio). Width 0 or height 0 falls
17
+ * through to the vector branch (canvas creation rejects 0×0).
18
+ *
19
+ * A vector layer whose `paint` drew nothing renders nothing — not an empty
20
+ * `<g>`. Layers are routinely conditional on data (a highlight pass with no
21
+ * highlighted feature, a legend-less track, a band that is switched off), and
22
+ * every such layer was leaving a stray group in the file for a reader to open
23
+ * and find empty. The raster branch has no cheap equivalent — asking whether a
24
+ * canvas is blank means reading its pixels back — and it does not need one: a
25
+ * fully transparent PNG is a couple of hundred bytes.
26
+ */
27
+ export declare function PaintLayer({ width, height, opts, paint, }: {
28
+ width: number;
29
+ height: number;
30
+ opts?: PaintLayerOpts;
31
+ paint: (ctx: Ctx2D) => void;
32
+ }): React.ReactNode;