@jbrowse/core 4.3.0 → 5.0.0-beta.10

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1265) hide show
  1. package/README.md +1994 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
  37. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
  38. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  39. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
  40. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -1
  41. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  97. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  98. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  99. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  100. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  101. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  102. package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
  103. package/esm/BaseFeatureWidget/formatDetails.js +82 -0
  104. package/esm/BaseFeatureWidget/index.d.ts +4 -1
  105. package/esm/BaseFeatureWidget/index.js +2 -2
  106. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
  107. package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
  108. package/esm/BaseFeatureWidget/types.d.ts +15 -8
  109. package/esm/BaseFeatureWidget/util.d.ts +2 -37
  110. package/esm/BaseFeatureWidget/util.js +4 -85
  111. package/esm/CorePlugin.js +12 -7
  112. package/esm/PhasedScheduler.d.ts +4 -2
  113. package/esm/PhasedScheduler.js +18 -2
  114. package/esm/Plugin.d.ts +6 -1
  115. package/esm/Plugin.js +7 -0
  116. package/esm/PluginLoader.d.ts +55 -44
  117. package/esm/PluginLoader.js +290 -90
  118. package/esm/PluginManager.d.ts +476 -57
  119. package/esm/PluginManager.js +480 -91
  120. package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
  121. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  122. package/esm/ReExports/MuiReExports.d.ts +3 -134
  123. package/esm/ReExports/MuiReExports.js +43 -16
  124. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  125. package/esm/ReExports/MuiStylesReExports.js +55 -0
  126. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  127. package/esm/ReExports/coreModules.generated.js +528 -0
  128. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  129. package/esm/ReExports/coreWorkerModules.generated.js +488 -0
  130. package/esm/ReExports/frameworkModules.d.ts +2 -0
  131. package/esm/ReExports/frameworkModules.js +68 -0
  132. package/esm/ReExports/frameworkShared.d.ts +12 -0
  133. package/esm/ReExports/frameworkShared.js +16 -0
  134. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  135. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  136. package/esm/ReExports/lazify.d.ts +2 -2
  137. package/esm/ReExports/lazify.js +16 -3
  138. package/esm/ReExports/list.js +433 -160
  139. package/esm/ReExports/modules.d.ts +1 -1
  140. package/esm/ReExports/modules.js +10 -146
  141. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  142. package/esm/ReExports/muiComponentNames.js +130 -0
  143. package/esm/ReExports/registry.d.ts +3 -0
  144. package/esm/ReExports/registry.js +46 -0
  145. package/esm/ReExports/uiStub.d.ts +3 -0
  146. package/esm/ReExports/uiStub.js +33 -0
  147. package/esm/ReExports/workerModules.d.ts +2 -0
  148. package/esm/ReExports/workerModules.js +11 -0
  149. package/esm/TextSearch/BaseResults.d.ts +20 -21
  150. package/esm/TextSearch/BaseResults.js +8 -33
  151. package/esm/TextSearch/TextSearchManager.d.ts +30 -36
  152. package/esm/TextSearch/TextSearchManager.js +138 -44
  153. package/esm/TextSearch/places.d.ts +12 -0
  154. package/esm/TextSearch/places.js +94 -0
  155. package/esm/assemblyManager/assembly.d.ts +310 -35
  156. package/esm/assemblyManager/assembly.js +554 -263
  157. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  158. package/esm/assemblyManager/assemblyAdapters.js +24 -0
  159. package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
  160. package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
  161. package/esm/assemblyManager/assemblyManager.d.ts +586 -323
  162. package/esm/assemblyManager/assemblyManager.js +352 -51
  163. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
  164. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
  165. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  166. package/esm/assemblyManager/geneticCodes.js +44 -0
  167. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
  168. package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
  169. package/esm/assemblyManager/index.d.ts +1 -1
  170. package/esm/assemblyManager/index.js +2 -2
  171. package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
  172. package/esm/assemblyManager/indexAssemblyNames.js +22 -0
  173. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  174. package/esm/assemblyManager/loadRefNameMap.js +75 -0
  175. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  176. package/esm/assemblyManager/refNameColors.js +32 -0
  177. package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
  178. package/esm/assemblyManager/refNameMapKey.js +12 -0
  179. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  180. package/esm/assemblyManager/refNameMaps.js +87 -0
  181. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  182. package/esm/assemblyManager/refNameMismatch.js +66 -0
  183. package/esm/checkPlugins.d.ts +13 -0
  184. package/esm/checkPlugins.js +98 -0
  185. package/esm/configuration/bamIndexFields.d.ts +49 -0
  186. package/esm/configuration/bamIndexFields.js +41 -0
  187. package/esm/configuration/configurationSchema.d.ts +194 -29
  188. package/esm/configuration/configurationSchema.js +439 -145
  189. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  190. package/esm/configuration/configurationSchemaUnion.js +56 -0
  191. package/esm/configuration/configurationSlot.d.ts +373 -30
  192. package/esm/configuration/configurationSlot.js +231 -224
  193. package/esm/configuration/fillLocations.d.ts +14 -0
  194. package/esm/configuration/fillLocations.js +14 -0
  195. package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
  196. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  197. package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
  198. package/esm/configuration/formatDetailsConfigSchema.js +87 -0
  199. package/esm/configuration/fullConfSnapshot.d.ts +13 -0
  200. package/esm/configuration/fullConfSnapshot.js +44 -0
  201. package/esm/configuration/getConf.d.ts +92 -0
  202. package/esm/configuration/getConf.js +141 -0
  203. package/esm/configuration/index.d.ts +32 -3
  204. package/esm/configuration/index.js +27 -2
  205. package/esm/configuration/indexType.d.ts +26 -0
  206. package/esm/configuration/indexType.js +38 -0
  207. package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
  208. package/esm/configuration/mergeFormatCallbacks.js +27 -0
  209. package/esm/configuration/readConfObject.d.ts +34 -0
  210. package/esm/configuration/readConfObject.js +118 -0
  211. package/esm/configuration/requirements.d.ts +37 -0
  212. package/esm/configuration/requirements.js +88 -0
  213. package/esm/configuration/schemaRegistry.d.ts +52 -0
  214. package/esm/configuration/schemaRegistry.js +48 -0
  215. package/esm/configuration/schemaTypes.d.ts +39 -0
  216. package/esm/configuration/schemaTypes.js +105 -0
  217. package/esm/configuration/slotFacade.d.ts +65 -0
  218. package/esm/configuration/slotFacade.js +110 -0
  219. package/esm/configuration/slotValueUtils.d.ts +17 -0
  220. package/esm/configuration/slotValueUtils.js +25 -0
  221. package/esm/configuration/snapshotPreprocess.d.ts +43 -0
  222. package/esm/configuration/snapshotPreprocess.js +161 -0
  223. package/esm/configuration/tabixIndexFields.d.ts +70 -0
  224. package/esm/configuration/tabixIndexFields.js +62 -0
  225. package/esm/configuration/tabixShorthand.d.ts +51 -0
  226. package/esm/configuration/tabixShorthand.js +72 -0
  227. package/esm/configuration/types.d.ts +315 -13
  228. package/esm/configuration/uriShorthand.d.ts +9 -0
  229. package/esm/configuration/uriShorthand.js +16 -0
  230. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
  231. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
  232. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
  233. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
  234. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  235. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  236. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  237. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  238. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  239. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  240. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
  241. package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
  242. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  243. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  244. package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
  245. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  246. package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
  247. package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
  248. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  249. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  250. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
  251. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  252. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  253. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  254. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  255. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  256. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
  257. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
  258. package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
  259. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  260. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  261. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  262. package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
  263. package/esm/data_adapters/dataAdapterCache.js +99 -25
  264. package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
  265. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  266. package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
  267. package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
  268. package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
  269. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  270. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  271. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  272. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  273. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  274. package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
  275. package/esm/pluggableElementTypes/DisplayType.js +30 -7
  276. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  277. package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
  278. package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
  279. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
  280. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  281. package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
  282. package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
  283. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
  284. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  285. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  286. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  287. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  288. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  289. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  290. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  291. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  292. package/esm/pluggableElementTypes/TrackType.js +1 -1
  293. package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
  294. package/esm/pluggableElementTypes/ViewType.js +40 -5
  295. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  296. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  297. package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
  298. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  299. package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
  300. package/esm/pluggableElementTypes/extendElementType.js +72 -0
  301. package/esm/pluggableElementTypes/index.d.ts +8 -7
  302. package/esm/pluggableElementTypes/index.js +24 -14
  303. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
  304. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  305. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
  306. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
  307. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
  308. package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
  309. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
  310. package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
  311. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
  312. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  313. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
  314. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
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  1021. package/esm/util/revlist.js +14 -0
  1022. package/esm/util/rowStackGeometry.d.ts +66 -0
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  1024. package/esm/util/rpc.d.ts +16 -1
  1025. package/esm/util/rpc.js +12 -1
  1026. package/esm/util/rxjs.d.ts +30 -2
  1027. package/esm/util/rxjs.js +85 -10
  1028. package/esm/util/sameStrings.d.ts +16 -0
  1029. package/esm/util/sameStrings.js +20 -0
  1030. package/esm/util/samplesTsv.d.ts +49 -0
  1031. package/esm/util/samplesTsv.js +86 -0
  1032. package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
  1033. package/esm/util/scheduleDetachedDestroy.js +24 -0
  1034. package/esm/util/scrollLatch.d.ts +5 -0
  1035. package/esm/util/scrollLatch.js +67 -0
  1036. package/esm/util/selectEncodedFeature.d.ts +16 -0
  1037. package/esm/util/selectEncodedFeature.js +34 -0
  1038. package/esm/util/selectNamedRegions.d.ts +136 -0
  1039. package/esm/util/selectNamedRegions.js +222 -0
  1040. package/esm/util/seqUtils.d.ts +17 -0
  1041. package/esm/util/seqUtils.js +80 -0
  1042. package/esm/util/sessionServices.d.ts +29 -0
  1043. package/esm/util/sessionServices.js +46 -0
  1044. package/esm/util/sessionSharing.d.ts +40 -0
  1045. package/esm/util/sessionSharing.js +154 -0
  1046. package/esm/util/sessionStorage.d.ts +1 -0
  1047. package/esm/util/sessionStorage.js +15 -0
  1048. package/esm/util/setStackTraceLimit.d.ts +6 -0
  1049. package/esm/util/setStackTraceLimit.js +20 -0
  1050. package/esm/util/shapeNameList.d.ts +2 -0
  1051. package/esm/util/shapeNameList.js +6 -0
  1052. package/esm/util/shapeNames.d.ts +7 -0
  1053. package/esm/util/shapeNames.js +11 -0
  1054. package/esm/util/simpleFeature.d.ts +111 -4
  1055. package/esm/util/simpleFeature.js +181 -29
  1056. package/esm/util/springAnimate.d.ts +20 -0
  1057. package/esm/util/springAnimate.js +80 -0
  1058. package/esm/util/starFusion.d.ts +26 -0
  1059. package/esm/util/starFusion.js +37 -0
  1060. package/esm/util/stats.d.ts +25 -2
  1061. package/esm/util/stats.js +39 -8
  1062. package/esm/util/stepTables.d.ts +82 -0
  1063. package/esm/util/stepTables.js +243 -0
  1064. package/esm/util/stringUtils.d.ts +5 -0
  1065. package/esm/util/stringUtils.js +34 -0
  1066. package/esm/util/svAlt.d.ts +145 -0
  1067. package/esm/util/svAlt.js +364 -0
  1068. package/esm/util/svgColorProps.d.ts +18 -0
  1069. package/esm/util/svgColorProps.js +55 -0
  1070. package/esm/util/systemColorScheme.d.ts +12 -0
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  1074. package/esm/util/tags.d.ts +2 -0
  1075. package/esm/util/tags.js +5 -0
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  1078. package/esm/util/thresholdScale.d.ts +91 -0
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  1080. package/esm/util/tickLabels.d.ts +36 -0
  1081. package/esm/util/tickLabels.js +45 -0
  1082. package/esm/util/timeGate.d.ts +25 -0
  1083. package/esm/util/timeGate.js +78 -0
  1084. package/esm/util/trackConfigDelta.d.ts +84 -0
  1085. package/esm/util/trackConfigDelta.js +206 -0
  1086. package/esm/util/tracks.d.ts +431 -30
  1087. package/esm/util/tracks.js +952 -185
  1088. package/esm/util/translateTranscript.d.ts +44 -0
  1089. package/esm/util/translateTranscript.js +102 -0
  1090. package/esm/util/tss-react/cssAndCx.js +11 -66
  1091. package/esm/util/tss-react/index.d.ts +11 -2
  1092. package/esm/util/tss-react/index.js +9 -2
  1093. package/esm/util/tss-react/makeStyles.js +7 -4
  1094. package/esm/util/tss-react/mergeClasses.js +1 -0
  1095. package/esm/util/tss-react/tools/classnames.d.ts +3 -0
  1096. package/esm/util/tss-react/tools/classnames.js +3 -0
  1097. package/esm/util/tss-react/tools/getDependencyArrayRef.d.ts +18 -0
  1098. package/esm/util/tss-react/tools/getDependencyArrayRef.js +19 -0
  1099. package/esm/util/tss-react/types.d.ts +1 -1
  1100. package/esm/util/tss-react/types.js +1 -6
  1101. package/esm/util/types/ElementId.js +1 -1
  1102. package/esm/util/types/data.d.ts +73 -0
  1103. package/esm/util/types/data.js +41 -0
  1104. package/esm/util/types/index.d.ts +459 -121
  1105. package/esm/util/types/index.js +96 -64
  1106. package/esm/util/types/isAny.d.ts +11 -0
  1107. package/esm/util/types/isAny.js +1 -0
  1108. package/esm/util/types/mst.d.ts +74 -47
  1109. package/esm/util/types/mst.js +31 -22
  1110. package/esm/util/types/predicate.d.ts +9 -0
  1111. package/esm/util/types/predicate.js +1 -0
  1112. package/esm/util/types/renameIds.d.ts +1 -0
  1113. package/esm/util/types/renameIds.js +29 -0
  1114. package/esm/util/types/renderingServices.d.ts +16 -0
  1115. package/esm/util/types/renderingServices.js +1 -0
  1116. package/esm/util/types/services.d.ts +55 -0
  1117. package/esm/util/types/services.js +10 -0
  1118. package/esm/util/types/util.d.ts +8 -2
  1119. package/esm/util/unknownSnapshotKeys.d.ts +51 -0
  1120. package/esm/util/unknownSnapshotKeys.js +82 -0
  1121. package/esm/util/unzip.d.ts +1 -0
  1122. package/esm/util/unzip.js +6 -0
  1123. package/esm/util/useEventCallback.d.ts +1 -0
  1124. package/esm/util/useEventCallback.js +16 -0
  1125. package/esm/util/useFeatureSequence.d.ts +13 -7
  1126. package/esm/util/useFeatureSequence.js +55 -77
  1127. package/esm/util/useFetch.d.ts +55 -0
  1128. package/esm/util/useFetch.js +197 -0
  1129. package/esm/util/useFetchPlugins.d.ts +16 -0
  1130. package/esm/util/useFetchPlugins.js +18 -0
  1131. package/esm/util/useMeasure.d.ts +11 -1
  1132. package/esm/util/useMeasure.js +20 -6
  1133. package/esm/util/usePanZoom.d.ts +75 -0
  1134. package/esm/util/usePanZoom.js +175 -0
  1135. package/esm/util/usePanelVirtualScroll.d.ts +9 -0
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  1137. package/esm/util/usePointerDrag.d.ts +37 -0
  1138. package/esm/util/usePointerDrag.js +61 -0
  1139. package/esm/util/useRafCommit.d.ts +4 -0
  1140. package/esm/util/useRafCommit.js +50 -0
  1141. package/esm/util/useResizeDrag.d.ts +91 -0
  1142. package/esm/util/useResizeDrag.js +105 -0
  1143. package/esm/util/useRowVirtualScroll.d.ts +9 -0
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  1145. package/esm/util/useVirtualScrollWheel.d.ts +23 -0
  1146. package/esm/util/useVirtualScrollWheel.js +74 -0
  1147. package/esm/util/viewHighlights.d.ts +3 -0
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  1151. package/esm/util/virtualRange.d.ts +36 -0
  1152. package/esm/util/virtualRange.js +26 -0
  1153. package/esm/util/webStorage.d.ts +26 -0
  1154. package/esm/util/webStorage.js +92 -0
  1155. package/esm/util/wheelZoom.d.ts +65 -0
  1156. package/esm/util/wheelZoom.js +297 -0
  1157. package/esm/util/whenViewSettled.d.ts +74 -0
  1158. package/esm/util/whenViewSettled.js +77 -0
  1159. package/esm/util/withFeatureDetails.d.ts +34 -0
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  1162. package/esm/util/withLaunchInput.js +274 -0
  1163. package/package.json +290 -820
  1164. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
  1165. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
  1166. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
  1167. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  1168. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  1169. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
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  1177. package/esm/configuration/util.d.ts +0 -10
  1178. package/esm/configuration/util.js +0 -123
  1179. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1180. package/esm/data_adapters/util.d.ts +0 -1
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  1264. /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
  1265. /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
@@ -0,0 +1,13 @@
1
+ /**
2
+ * The body of every view's `exportSvg` action: load the view's lazy
3
+ * `renderToSvg`, render, save unless `save: false`, and return the markup.
4
+ */
5
+ export async function exportViewSvg(view, opts, load) {
6
+ const { renderToSvg } = await load();
7
+ const html = await renderToSvg(view, opts);
8
+ if (opts.save !== false) {
9
+ const { saveSvgAsImage } = await import('./saveSvgAsImage.js');
10
+ await saveSvgAsImage(html, opts);
11
+ }
12
+ return html;
13
+ }
@@ -0,0 +1,7 @@
1
+ /**
2
+ * The markup rules an SVG file has to meet that a React render into an HTML
3
+ * container does not: XML entities only (HTML serialization writes U+00A0 as
4
+ * ` `, which XML does not define, so one no-break space in a feature label
5
+ * made the whole file unparsable), SVG 1.1 colors, and rounded numbers.
6
+ */
7
+ export declare function normalizeSvgMarkup(html: string): string;
@@ -0,0 +1,99 @@
1
+ import { splitPaintAlpha } from '../util/svgColorProps.js';
2
+ // Coordinates computed as bp/bpPerPx land in attributes as long floats
3
+ // (`-32.4816`) or floating-point noise (`242.23839999999998`), bloating exports
4
+ // with sub-pixel precision no renderer needs. Round numbers inside a fixed
5
+ // whitelist of numeric attributes, so a track label or id that happens to look
6
+ // numeric is never a candidate for rewriting. Geometry gets 2 decimals
7
+ // (sub-pixel); opacity keeps 3 so a faint 0.01 mark can't collapse to 0.
8
+ const COORD_ATTRS = [
9
+ 'x',
10
+ 'y',
11
+ 'x1',
12
+ 'y1',
13
+ 'x2',
14
+ 'y2',
15
+ 'cx',
16
+ 'cy',
17
+ 'r',
18
+ 'rx',
19
+ 'ry',
20
+ 'dx',
21
+ 'dy',
22
+ 'width',
23
+ 'height',
24
+ 'd',
25
+ 'points',
26
+ 'transform',
27
+ 'gradientTransform',
28
+ 'offset',
29
+ 'viewBox',
30
+ 'font-size',
31
+ 'stroke-width',
32
+ 'stroke-dashoffset',
33
+ 'stroke-dasharray',
34
+ ];
35
+ const OPACITY_ATTRS = [
36
+ 'opacity',
37
+ 'fill-opacity',
38
+ 'stroke-opacity',
39
+ 'stop-opacity',
40
+ 'flood-opacity',
41
+ ];
42
+ function makeRounder(attrs, digits) {
43
+ const re = new RegExp(`\\b(${attrs.join('|')})="([^"]*)"`, 'g');
44
+ return (svg) => svg.replaceAll(re, (_, name, value) => {
45
+ const rounded = value.replaceAll(/-?\d+\.\d{3,}(?:e-?\d+)?/gi, n => String(Number.parseFloat(Number(n).toFixed(digits))));
46
+ return `${name}="${rounded}"`;
47
+ });
48
+ }
49
+ const roundCoords = makeRounder(COORD_ATTRS, 2);
50
+ const roundOpacity = makeRounder(OPACITY_ATTRS, 3);
51
+ const OPACITY_OF = {
52
+ fill: 'fill-opacity',
53
+ stroke: 'stroke-opacity',
54
+ 'stop-color': 'stop-opacity',
55
+ 'flood-color': 'flood-opacity',
56
+ };
57
+ // a start tag, attribute by attribute, so a `>` inside a quoted value (which
58
+ // HTML serialization leaves unescaped) cannot end it early
59
+ const START_TAG = /<[a-zA-Z][^\s/>]*(?:\s+[^\s"'/=>]+="[^"]*")*\s*\/?>/g;
60
+ const PAINT_ATTR = /\s(fill|stroke|stop-color|flood-color)="([^"]*)"/g;
61
+ const MAY_NEED_SPLIT = /(?:fill|stroke|stop-color|flood-color)="(?:rgba|hsl|#[\da-f]{4}"|#[\da-f]{8}"|transparent)/i;
62
+ // A JSX color reaches the file as React wrote it, and theme palette entries are
63
+ // routinely `rgba()` (`divider`, `text.secondary`) — see `splitPaintAlpha` for
64
+ // why that can't stay. Scoped to one start tag so an alpha folds into an
65
+ // opacity attribute the element already carries instead of duplicating it,
66
+ // which would not parse as XML.
67
+ function splitTagPaintAlpha(tag) {
68
+ const alphas = [];
69
+ let out = tag.replaceAll(PAINT_ATTR, (whole, name, value) => {
70
+ const split = splitPaintAlpha(value);
71
+ if (!split) {
72
+ return whole;
73
+ }
74
+ if (split.opacity < 1) {
75
+ alphas.push([OPACITY_OF[name], split.opacity]);
76
+ }
77
+ return ` ${name}="${split.color}"`;
78
+ });
79
+ for (const [opacityName, alpha] of alphas) {
80
+ const existing = new RegExp(`\\s${opacityName}="([^"]*)"`);
81
+ out = existing.test(out)
82
+ ? out.replace(existing, (_, v) => ` ${opacityName}="${Number(v) * alpha}"`)
83
+ : out.replace(/\s*(\/?>)$/, ` ${opacityName}="${alpha}"$1`);
84
+ }
85
+ return out;
86
+ }
87
+ /**
88
+ * The markup rules an SVG file has to meet that a React render into an HTML
89
+ * container does not: XML entities only (HTML serialization writes U+00A0 as
90
+ * `&nbsp;`, which XML does not define, so one no-break space in a feature label
91
+ * made the whole file unparsable), SVG 1.1 colors, and rounded numbers.
92
+ */
93
+ export function normalizeSvgMarkup(html) {
94
+ const xml = html.replaceAll('&nbsp;', '&#160;');
95
+ const split = MAY_NEED_SPLIT.test(xml)
96
+ ? xml.replaceAll(START_TAG, splitTagPaintAlpha)
97
+ : xml;
98
+ return roundOpacity(roundCoords(split));
99
+ }
@@ -0,0 +1,6 @@
1
+ export interface SaveSvgAsImageOptions {
2
+ format?: string;
3
+ filename?: string;
4
+ }
5
+ export declare function svgHtmlToPngBlob(html: string, scale?: number): Promise<Blob>;
6
+ export declare function saveSvgAsImage(html: string, opts?: SaveSvgAsImageOptions): Promise<void>;
@@ -0,0 +1,90 @@
1
+ import { saveAs } from '../util/FileSaver/index.js';
2
+ // Supersample factor for PNG rasterization. The vector text/gridlines/rulers
3
+ // rasterize crisply at this scale, and the heavy track layers are already
4
+ // embedded as 2× rasters (see createSvgRasterCanvas), so a 1× output canvas
5
+ // would otherwise *downsample* them back to screen resolution. Kept at 2× to
6
+ // match that embedded DPR: a higher factor sharpens vector text further but
7
+ // upscales the 2× rasters (blur), and inflates the canvas toward browser size
8
+ // limits.
9
+ const PNG_SCALE = 2;
10
+ // Bump the root <svg> width/height by `scale` while leaving viewBox alone, so
11
+ // the browser re-rasterizes the *vector* content natively at the higher
12
+ // resolution. Drawing the unscaled <img> with drawImage(...,w*scale,h*scale)
13
+ // instead would only stretch the 1×-rasterized bitmap (blurry text, resample
14
+ // artifacts on the embedded rasters).
15
+ function scaleSvgMarkup(html, scale) {
16
+ return html.replace(/<svg\b[^>]*>/, tag => tag
17
+ .replace(/(\bwidth=")([\d.]+)(")/, (_m, p, n, s) => `${p}${+n * scale}${s}`)
18
+ .replace(/(\bheight=")([\d.]+)(")/, (_m, p, n, s) => `${p}${+n * scale}${s}`));
19
+ }
20
+ // Rasterizes an SVG string to a PNG Blob by routing through a hidden <img>
21
+ // + Canvas2D. Rejects with the actual underlying cause so bug reports
22
+ // distinguish "SVG failed to load" (usually malformed markup) from
23
+ // "canvas.toBlob returned null" (rasterized image exceeded browser limits).
24
+ export function svgHtmlToPngBlob(html, scale = PNG_SCALE) {
25
+ return new Promise((resolve, reject) => {
26
+ const img = new Image();
27
+ const svgBlob = new Blob([scaleSvgMarkup(html, scale)], {
28
+ type: 'image/svg+xml',
29
+ });
30
+ const url = URL.createObjectURL(svgBlob);
31
+ img.onload = () => {
32
+ // Everything here runs in an event handler, so a throw would escape the
33
+ // promise instead of rejecting it and leave the export dialog spinning
34
+ // forever with nothing said — the hang `awaitViewInitialized` cures on
35
+ // the other end of this pipeline. Reject explicitly instead.
36
+ try {
37
+ const canvas = document.createElement('canvas');
38
+ const w = img.width;
39
+ const h = img.height;
40
+ // stated once: both the context and the blob give out at this size,
41
+ // and both failures are silent (a null, not a throw)
42
+ const tooLarge = `The image may be too large (${w}x${h}). Try reducing the view size or use SVG format.`;
43
+ canvas.width = w;
44
+ canvas.height = h;
45
+ const ctx = canvas.getContext('2d');
46
+ if (!ctx) {
47
+ // browsers hand back a null 2d context rather than throwing once the
48
+ // canvas exceeds their area limit, which PNG_SCALE makes 4x easier to
49
+ // hit than the on-screen canvases
50
+ throw new Error(`Failed to create PNG rendering context. ${tooLarge}`);
51
+ }
52
+ ctx.imageSmoothingEnabled = true;
53
+ ctx.imageSmoothingQuality = 'high';
54
+ ctx.drawImage(img, 0, 0);
55
+ canvas.toBlob(blob => {
56
+ if (blob) {
57
+ resolve(blob);
58
+ }
59
+ else {
60
+ reject(new Error(`Failed to create PNG. ${tooLarge}`));
61
+ }
62
+ }, 'image/png');
63
+ }
64
+ catch (e) {
65
+ reject(e instanceof Error ? e : new Error(`${e}`));
66
+ }
67
+ finally {
68
+ URL.revokeObjectURL(url);
69
+ }
70
+ };
71
+ img.onerror = event => {
72
+ URL.revokeObjectURL(url);
73
+ const detail = typeof event === 'string' ? event : 'image load failed';
74
+ reject(new Error(`Failed to load SVG for PNG conversion: ${detail}`));
75
+ };
76
+ img.src = url;
77
+ });
78
+ }
79
+ // Shared "save the rendered SVG" sink used by every view's `exportSvg`
80
+ // action. `format: 'png'` rasterizes through svgHtmlToPngBlob; anything else
81
+ // (default) saves the raw SVG markup.
82
+ export async function saveSvgAsImage(html, opts = {}) {
83
+ if (opts.format === 'png') {
84
+ const blob = await svgHtmlToPngBlob(html);
85
+ saveAs(blob, opts.filename ?? 'image.png');
86
+ }
87
+ else {
88
+ saveAs(new Blob([html], { type: 'image/svg+xml' }), opts.filename ?? 'image.svg');
89
+ }
90
+ }
@@ -0,0 +1,7 @@
1
+ import type React from 'react';
2
+ export { normalizeSvgMarkup } from './normalizeSvgMarkup.ts';
3
+ /**
4
+ * Serialize one standalone SVG document: its own clip-id numbering run (see
5
+ * `withFreshSvgClipIds`) and the file rules in `normalizeSvgMarkup`.
6
+ */
7
+ export declare function serializeSvg(node: React.ReactElement): string;
@@ -0,0 +1,11 @@
1
+ import { withFreshSvgClipIds } from '../util/SvgCanvas.js';
2
+ import { renderToStaticMarkup } from '../util/renderToStaticMarkup.js';
3
+ import { normalizeSvgMarkup } from './normalizeSvgMarkup.js';
4
+ export { normalizeSvgMarkup } from './normalizeSvgMarkup.js';
5
+ /**
6
+ * Serialize one standalone SVG document: its own clip-id numbering run (see
7
+ * `withFreshSvgClipIds`) and the file rules in `normalizeSvgMarkup`.
8
+ */
9
+ export function serializeSvg(node) {
10
+ return normalizeSvgMarkup(withFreshSvgClipIds(() => renderToStaticMarkup(node)));
11
+ }
@@ -0,0 +1,42 @@
1
+ /**
2
+ * Make an SVG id safe to both carry in an `id` attribute and point at with
3
+ * `url(#...)`.
4
+ *
5
+ * Injective but NOT idempotent — escaping the marker is what buys injectivity,
6
+ * so a second pass re-escapes the `~`s the first one wrote. Apply it exactly
7
+ * once, at the place that emits both the id and the reference to it
8
+ * (`SvgClipRect` and `SvgColorLegend` already do; a hand-rolled `<clipPath>`
9
+ * must). Double-applying is harmless to correctness — the id and its `url()`
10
+ * still agree, since both are derived from one call — but it produces noisy ids
11
+ * for no reason.
12
+ */
13
+ export declare function svgSafeId(id: string): string;
14
+ /**
15
+ * The id to build a view's or display's SVG ids out of. It has to be two things
16
+ * at once, and each rules out the obvious answer to the other.
17
+ *
18
+ * **Unique within the document.** The configured `displayId` is not: a synteny
19
+ * or breakpoint split view exports several LGVs into one file, and a track
20
+ * shown in more than one of them instantiates a display from the *same* config
21
+ * in each, so both emitted the identical
22
+ * `alignments-clip-volvox_inv_indels-LGVSyntenyDisplay`. A duplicate id is
23
+ * silent — `url(#id)` resolves to the first match, so the second display simply
24
+ * renders unclipped and paints over its neighbours. `assertNoDuplicateSvgIds`
25
+ * in the web tests catches it.
26
+ *
27
+ * **Stable across session loads.** `model.id` is not: it is a `nanoid(10)`
28
+ * minted when the MST node is created, so two exports of the same unchanged
29
+ * view differ in every clip-path id. That is why the checked-in export
30
+ * snapshots churned on `wiggle-clip-5GfQp_z8Ji` → `-FePoZy7IhS` without a
31
+ * pixel moving, and why diffing two saved SVGs shows changes that aren't real.
32
+ *
33
+ * The state tree path is both. It is unique by construction — two nodes cannot
34
+ * occupy one path — and it is a function of where the node sits in the session
35
+ * rather than of when it was created, so the same session exports to the same
36
+ * bytes. Only the numeric indices are kept (`/views/0/tracks/2/displays/0` →
37
+ * `0-2-0`), since the property names in between are fixed by the schema and
38
+ * just make the id long.
39
+ */
40
+ export declare function svgNodeId(model: {
41
+ id: string;
42
+ }): string;
@@ -0,0 +1,84 @@
1
+ import { getPath, isStateTreeNode } from '@jbrowse/mobx-state-tree';
2
+ /**
3
+ * SVG ids in an export are routinely built out of config data — a `trackId`, a
4
+ * `displayId`, a block key carrying a refName. All three are arbitrary strings
5
+ * from a config file or a FASTA header, and an id is not just an attribute: it
6
+ * is pointed at by `clip-path="url(#id)"` / `fill="url(#id)"`, which is a CSS
7
+ * `url()` token. An unquoted `url()` cannot hold whitespace, parentheses or
8
+ * quotes, so a track named `Genes (curated)` or a refName like
9
+ * `gi|123|ref|NC_000001|` silently produced an unresolvable reference: the clip
10
+ * never applied and the track painted over its neighbours, or the gradient fill
11
+ * came out transparent.
12
+ *
13
+ * Percent-encoding is the wrong tool here even though the characters line up —
14
+ * a fragment reference is percent-*decoded* before it is matched against an id,
15
+ * so `url(#a%20b)` looks for the id `a b`, not `a%20b`, and encoding both ends
16
+ * just moves the mismatch.
17
+ *
18
+ * So: escape to a safe alphabet instead. `~` is the marker because it is legal
19
+ * in both an id and a `url()`, and essentially never appears in a real trackId
20
+ * — which means ordinary ids pass through byte-for-byte and no existing export
21
+ * changes.
22
+ */
23
+ // Everything outside this set is escaped. `\w` is [A-Za-z0-9_]; `.`, `-` and
24
+ // `:` are added because existing ids (block keys are `refName:start:end:idx`)
25
+ // are full of them and all three are safe in an id and in a `url()`. `~` is
26
+ // deliberately NOT in the set, so it escapes itself and the mapping stays
27
+ // injective — two ids that differ only in an unsafe character must not collide
28
+ // into one, or the second element silently steals the first's clip.
29
+ const UNSAFE_ID_CHAR = /[^\w.:-]/g;
30
+ /**
31
+ * Make an SVG id safe to both carry in an `id` attribute and point at with
32
+ * `url(#...)`.
33
+ *
34
+ * Injective but NOT idempotent — escaping the marker is what buys injectivity,
35
+ * so a second pass re-escapes the `~`s the first one wrote. Apply it exactly
36
+ * once, at the place that emits both the id and the reference to it
37
+ * (`SvgClipRect` and `SvgColorLegend` already do; a hand-rolled `<clipPath>`
38
+ * must). Double-applying is harmless to correctness — the id and its `url()`
39
+ * still agree, since both are derived from one call — but it produces noisy ids
40
+ * for no reason.
41
+ */
42
+ export function svgSafeId(id) {
43
+ return id.replaceAll(UNSAFE_ID_CHAR, c => `~${c.codePointAt(0).toString(16)}~`);
44
+ }
45
+ /**
46
+ * The id to build a view's or display's SVG ids out of. It has to be two things
47
+ * at once, and each rules out the obvious answer to the other.
48
+ *
49
+ * **Unique within the document.** The configured `displayId` is not: a synteny
50
+ * or breakpoint split view exports several LGVs into one file, and a track
51
+ * shown in more than one of them instantiates a display from the *same* config
52
+ * in each, so both emitted the identical
53
+ * `alignments-clip-volvox_inv_indels-LGVSyntenyDisplay`. A duplicate id is
54
+ * silent — `url(#id)` resolves to the first match, so the second display simply
55
+ * renders unclipped and paints over its neighbours. `assertNoDuplicateSvgIds`
56
+ * in the web tests catches it.
57
+ *
58
+ * **Stable across session loads.** `model.id` is not: it is a `nanoid(10)`
59
+ * minted when the MST node is created, so two exports of the same unchanged
60
+ * view differ in every clip-path id. That is why the checked-in export
61
+ * snapshots churned on `wiggle-clip-5GfQp_z8Ji` → `-FePoZy7IhS` without a
62
+ * pixel moving, and why diffing two saved SVGs shows changes that aren't real.
63
+ *
64
+ * The state tree path is both. It is unique by construction — two nodes cannot
65
+ * occupy one path — and it is a function of where the node sits in the session
66
+ * rather than of when it was created, so the same session exports to the same
67
+ * bytes. Only the numeric indices are kept (`/views/0/tracks/2/displays/0` →
68
+ * `0-2-0`), since the property names in between are fixed by the schema and
69
+ * just make the id long.
70
+ */
71
+ export function svgNodeId(model) {
72
+ // getPath throws on anything that is not a live MST node, and unit tests
73
+ // render these components against plain object stand-ins. Their own id is
74
+ // unique, which is the half that matters when there is no tree to place them
75
+ // in — a detached node is not in a document with anything to collide with.
76
+ // Narrowed through a widened alias so that the guard doesn't also narrow
77
+ // `model` itself, whose `id` the fallback still needs.
78
+ const node = model;
79
+ if (!isStateTreeNode(node)) {
80
+ return model.id;
81
+ }
82
+ const indices = getPath(node).match(/\d+/g);
83
+ return indices ? indices.join('-') : model.id;
84
+ }
@@ -0,0 +1,138 @@
1
+ /**
2
+ * The contract every GPU display's `renderSvg` relies on: a `svgReady` gate
3
+ * (the per-display terminal-state getter — see MultiRegionDisplayMixin /
4
+ * GlobalFetchMixin) and the `error` it fails the export on.
5
+ * Duck-typed `renderSvg` model interfaces extend this so the compiler catches a
6
+ * missing field instead of it surfacing as a runtime hang or a silent blank.
7
+ */
8
+ export interface SvgExportable {
9
+ svgReady: boolean;
10
+ error: unknown;
11
+ regionTooLarge: boolean;
12
+ fetchCanceled?: boolean;
13
+ }
14
+ /**
15
+ * The terminal states that let an export proceed with no current data. Mirrors
16
+ * `DisplayPhaseInputs`: named fields, all required, so adding a state is a
17
+ * compile error at every call site rather than a silently missing branch.
18
+ *
19
+ * `extraTerminal` is the display-specific escape hatch — sequence sets it when
20
+ * zoomed past base resolution, where it renders a static "zoom in" message and
21
+ * fetches nothing, so a data-only gate would never resolve.
22
+ *
23
+ * `fetchCanceled` is the user's own resting state: a standing cancel holds the
24
+ * fetch gate shut until Retry or a viewport change, and an export causes
25
+ * neither, so without this terminal `awaitSvgReady` waits out its whole bound
26
+ * with the dialog up and nothing said, then fails. A display family with no
27
+ * cancel affordance answers it `false`.
28
+ */
29
+ export interface SvgReadyTerminals {
30
+ error: unknown;
31
+ regionTooLarge: boolean;
32
+ extraTerminal: boolean;
33
+ fetchCanceled: boolean;
34
+ }
35
+ /**
36
+ * Whether an off-screen (SVG) export can read this display's data now: the held
37
+ * data is current for what is on screen, or the fetch reached a terminal state.
38
+ *
39
+ * Single-sourced for the same reason as `computeDisplayPhase`: every display
40
+ * family expresses freshness differently — spatial coverage (per-region), a
41
+ * signature compare (global, dotplot, synteny) — but the *policy* wrapping it
42
+ * is identical, and each of the five
43
+ * hand-written copies this replaced was one place to forget a terminal and hang
44
+ * the export, or to forget freshness and capture a stale viewport (both have
45
+ * shipped; see agent-docs/reference/SVG_EXPORT.md).
46
+ *
47
+ * `dataCurrent` is a **thunk**, evaluated only after the terminals are ruled
48
+ * out, for the same MobX reason `computeDisplayPhase`'s `loading` is: freshness
49
+ * typically reads the containing view's `visibleRegions` / `loadedRegions`, and
50
+ * the `when()` in `awaitSvgReady` shouldn't subscribe to that churn while a
51
+ * banner is up.
52
+ */
53
+ export declare function computeSvgReady({ error, regionTooLarge, extraTerminal, fetchCanceled }: SvgReadyTerminals, dataCurrent: () => boolean): boolean;
54
+ /**
55
+ * Off-screen renderers (SVG export, headless jbrowse-img) must wait until the
56
+ * display reaches a terminal state before reading its data. That whole policy
57
+ * lives in `svgReady`; this is the one shared way to await it, so renderers
58
+ * never re-inline `data != null || error || …`. `svgReady` is a terminal state
59
+ * (data loaded, or error / too-large / canceled), so it resolves once the fetch
60
+ * it observes settles; the half-hour `timeoutMs` is only a backstop for a gate
61
+ * that cannot converge. If a throwing `svgReady` getter rejects the wait, that
62
+ * error propagates faithfully rather than being masked.
63
+ *
64
+ * It then fails the export if the terminal it settled on was the error
65
+ * (`throwOnExportErrors`, below, for why that is fatal), making this the exact
66
+ * display-level twin of `awaitViewInitialized`: both wait for `settled || error`
67
+ * and both refuse to continue on the error, so the postcondition of each is
68
+ * "there is something to draw". Folded in rather than left to the caller because
69
+ * `svgReady` is *true* on error, so a caller that awaits and stops there gets a
70
+ * display with nothing to draw and no sign of why.
71
+ *
72
+ * Every display uses this one, including the ones with nowhere to draw an error
73
+ * (dotplot, synteny) — a display never has to know whether it owns the surface
74
+ * it paints, because the thing that made that distinction matter, reporting all
75
+ * the failures rather than one, is `awaitSvgRenders`'s job.
76
+ *
77
+ * A standing user cancel fails the export the same way an error does, and for
78
+ * the same reason the error is folded in rather than left to the caller: the
79
+ * cancel terminal makes `svgReady` *true* over a display with nothing to draw,
80
+ * so a caller that awaits and stops there exports that track blank in silence.
81
+ * On screen the same state shows "Loading canceled / Retry", so the loud
82
+ * failure matches what the user is looking at.
83
+ */
84
+ export declare function awaitSvgReady(model: Pick<SvgExportable, 'svgReady' | 'error' | 'fetchCanceled'>, timeoutMs?: number): Promise<void>;
85
+ /**
86
+ * The view-level counterpart, for the wait every `renderToSvg` opens with:
87
+ * `whenViewSettled` in the export's own vocabulary. Why the bare
88
+ * `when(() => view.initialized)` it replaced could not fail — only hang — is
89
+ * documented there.
90
+ *
91
+ * Only a view that never initialized is fatal *here*. A track error on an
92
+ * initialized view is fatal too, but it is the displays' readiness waits that
93
+ * report it (`throwOnExportErrors`), after this one has let the export start.
94
+ */
95
+ export declare function awaitViewInitialized(view: {
96
+ initialized: boolean;
97
+ error: unknown;
98
+ pendingLaunch?: unknown;
99
+ }): Promise<void>;
100
+ /**
101
+ * How the export answers "a track failed": by failing. A track whose data won't
102
+ * load has its error caught by the fetch layer and stored on the display, so the
103
+ * render itself still returns — with that track blank.
104
+ *
105
+ * An export is a standalone artifact, so a failed track is fatal: the dialog
106
+ * shows its error banner and saves nothing, and a headless caller (jbrowse-img)
107
+ * exits nonzero instead of writing a broken image. Drawing the error into the
108
+ * figure instead costs more than the red rect it leaves in the picture: on a
109
+ * shared surface (dotplot plot rect, synteny band) the box covers the tracks
110
+ * that *did* render, and a snapshot regenerated while a display is broken
111
+ * absorbs the stack trace as expected output — which is how a real crash sat
112
+ * inside two committed goldens without turning anything red.
113
+ *
114
+ * `regionTooLarge` is deliberately not routed here — see `SvgChrome`.
115
+ *
116
+ * The failures are kept on the thrown error so that nesting one `awaitSvgRenders`
117
+ * inside another (synteny: rows of tracks *and* levels of ribbons) still reports
118
+ * every leaf rather than one per group.
119
+ */
120
+ export declare function throwOnExportErrors(errors: unknown[]): void;
121
+ /**
122
+ * `Promise.all` for the renders a view fans out, differing in the one way an
123
+ * export needs: it fails with **every** failure instead of whichever rejected
124
+ * first. Exporting a session with three broken tracks should not mean finding
125
+ * the second one by fixing the first and exporting again. Nest it freely — an
126
+ * inner fan-out's failures are flattened into the outer one's report.
127
+ *
128
+ * That is also what lets every display await through the plain `awaitSvgReady`.
129
+ * A display on a shared surface (the dotplot's plot rect, a synteny level's
130
+ * band) has nowhere to draw an error and nothing complete to say alone; the
131
+ * alternative is for it to stay silent and let its view read the combined error
132
+ * back *after* the waits, which nothing enforces and every new shared-surface
133
+ * view has to rediscover. Here the display just throws, and being complete is
134
+ * the fan-out's job rather than the display's.
135
+ */
136
+ export declare function awaitSvgRenders<T extends readonly unknown[] | []>(renders: T): Promise<{
137
+ -readonly [K in keyof T]: Awaited<T[K]>;
138
+ }>;