@jbrowse/core 4.3.0 → 5.0.0-beta.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1140) hide show
  1. package/README.md +822 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -2
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +17 -0
  26. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
  27. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
  28. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  29. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
  30. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
  31. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
  32. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
  33. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
  34. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
  35. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
  36. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -10
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +62 -24
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +1 -1
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +18 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +50 -63
  71. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -59
  72. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
  73. package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
  74. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
  75. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
  76. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
  77. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
  78. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
  79. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
  80. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
  81. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
  82. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
  83. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
  84. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
  85. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
  86. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
  87. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
  88. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +1 -1
  89. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
  90. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
  91. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
  92. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
  93. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
  94. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
  95. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
  96. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
  97. package/esm/BaseFeatureWidget/configSchema.js +1 -1
  98. package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
  99. package/esm/BaseFeatureWidget/formatDetails.js +103 -0
  100. package/esm/BaseFeatureWidget/index.d.ts +3 -1
  101. package/esm/BaseFeatureWidget/index.js +2 -2
  102. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
  103. package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
  104. package/esm/BaseFeatureWidget/types.d.ts +4 -3
  105. package/esm/BaseFeatureWidget/util.d.ts +4 -29
  106. package/esm/BaseFeatureWidget/util.js +20 -84
  107. package/esm/CorePlugin.js +11 -6
  108. package/esm/PhasedScheduler.d.ts +4 -2
  109. package/esm/PhasedScheduler.js +18 -2
  110. package/esm/Plugin.d.ts +6 -1
  111. package/esm/Plugin.js +7 -0
  112. package/esm/PluginLoader.d.ts +41 -40
  113. package/esm/PluginLoader.js +206 -78
  114. package/esm/PluginManager.d.ts +421 -55
  115. package/esm/PluginManager.js +461 -89
  116. package/esm/ReExports/BaseFeatureDetails.js +7 -6
  117. package/esm/ReExports/MuiDataGridReExports.d.ts +2 -2
  118. package/esm/ReExports/MuiDataGridReExports.js +58 -130
  119. package/esm/ReExports/MuiReExports.d.ts +3 -134
  120. package/esm/ReExports/MuiReExports.js +43 -16
  121. package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
  122. package/esm/ReExports/MuiStylesReExports.js +55 -0
  123. package/esm/ReExports/index.js +1 -1
  124. package/esm/ReExports/lazify.d.ts +2 -2
  125. package/esm/ReExports/lazify.js +16 -3
  126. package/esm/ReExports/list.js +54 -229
  127. package/esm/ReExports/modules.js +62 -93
  128. package/esm/ReExports/muiComponentNames.d.ts +18 -0
  129. package/esm/ReExports/muiComponentNames.js +130 -0
  130. package/esm/ReExports/publicUtil.d.ts +1 -0
  131. package/esm/ReExports/publicUtil.js +28 -0
  132. package/esm/ReExports/registry.d.ts +2 -0
  133. package/esm/ReExports/registry.js +28 -0
  134. package/esm/ReExports/sharedModules.d.ts +96 -0
  135. package/esm/ReExports/sharedModules.js +59 -0
  136. package/esm/ReExports/uiStub.d.ts +1 -0
  137. package/esm/ReExports/uiStub.js +13 -0
  138. package/esm/ReExports/workerModules.d.ts +2 -0
  139. package/esm/ReExports/workerModules.js +10 -0
  140. package/esm/TextSearch/BaseResults.d.ts +20 -21
  141. package/esm/TextSearch/BaseResults.js +8 -33
  142. package/esm/TextSearch/TextSearchManager.d.ts +14 -34
  143. package/esm/TextSearch/TextSearchManager.js +87 -34
  144. package/esm/assemblyManager/assembly.d.ts +307 -34
  145. package/esm/assemblyManager/assembly.js +551 -262
  146. package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
  147. package/esm/assemblyManager/assemblyAdapters.js +18 -0
  148. package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
  149. package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
  150. package/esm/assemblyManager/assemblyManager.d.ts +711 -303
  151. package/esm/assemblyManager/assemblyManager.js +351 -46
  152. package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
  153. package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
  154. package/esm/assemblyManager/geneticCodes.d.ts +21 -0
  155. package/esm/assemblyManager/geneticCodes.js +47 -0
  156. package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
  157. package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
  158. package/esm/assemblyManager/index.d.ts +1 -1
  159. package/esm/assemblyManager/index.js +2 -2
  160. package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
  161. package/esm/assemblyManager/loadRefNameMap.js +80 -0
  162. package/esm/assemblyManager/refNameColors.d.ts +1 -0
  163. package/esm/assemblyManager/refNameColors.js +32 -0
  164. package/esm/assemblyManager/refNameMaps.d.ts +26 -0
  165. package/esm/assemblyManager/refNameMaps.js +87 -0
  166. package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
  167. package/esm/assemblyManager/refNameMismatch.js +66 -0
  168. package/esm/checkPlugins.d.ts +11 -0
  169. package/esm/checkPlugins.js +77 -0
  170. package/esm/configuration/configurationSchema.d.ts +122 -20
  171. package/esm/configuration/configurationSchema.js +374 -140
  172. package/esm/configuration/configurationSlot.d.ts +283 -30
  173. package/esm/configuration/configurationSlot.js +205 -226
  174. package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
  175. package/esm/configuration/formatAboutConfigSchema.js +58 -0
  176. package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
  177. package/esm/configuration/formatDetailsConfigSchema.js +90 -0
  178. package/esm/configuration/fullConfSnapshot.d.ts +28 -0
  179. package/esm/configuration/fullConfSnapshot.js +66 -0
  180. package/esm/configuration/getConf.d.ts +88 -0
  181. package/esm/configuration/getConf.js +74 -0
  182. package/esm/configuration/index.d.ts +19 -3
  183. package/esm/configuration/index.js +19 -2
  184. package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
  185. package/esm/configuration/mergeFormatCallbacks.js +24 -0
  186. package/esm/configuration/promotableDefaults.d.ts +199 -0
  187. package/esm/configuration/promotableDefaults.js +332 -0
  188. package/esm/configuration/promotablePin.d.ts +55 -0
  189. package/esm/configuration/promotableResolve.d.ts +108 -0
  190. package/esm/configuration/promotableResolve.js +117 -0
  191. package/esm/configuration/promotableSlots.d.ts +12 -0
  192. package/esm/configuration/promotableSlots.js +45 -0
  193. package/esm/configuration/readConfObject.d.ts +56 -0
  194. package/esm/configuration/readConfObject.js +161 -0
  195. package/esm/configuration/schemaRegistry.d.ts +35 -0
  196. package/esm/configuration/schemaRegistry.js +50 -0
  197. package/esm/configuration/schemaTypes.d.ts +23 -0
  198. package/esm/configuration/schemaTypes.js +94 -0
  199. package/esm/configuration/slotFacade.d.ts +82 -0
  200. package/esm/configuration/slotFacade.js +89 -0
  201. package/esm/configuration/slotShape.d.ts +12 -0
  202. package/esm/configuration/slotShape.js +84 -0
  203. package/esm/configuration/slotValueUtils.d.ts +17 -0
  204. package/esm/configuration/slotValueUtils.js +25 -0
  205. package/esm/configuration/tabixIndexFields.d.ts +44 -0
  206. package/esm/configuration/tabixIndexFields.js +45 -0
  207. package/esm/configuration/tabixShorthand.d.ts +34 -0
  208. package/esm/configuration/tabixShorthand.js +45 -0
  209. package/esm/configuration/types.d.ts +170 -7
  210. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
  211. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
  212. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +132 -7
  213. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +136 -25
  214. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
  215. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
  216. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
  217. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
  218. package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
  219. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
  220. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +29 -0
  221. package/esm/data_adapters/BaseAdapter/featureDensity.js +17 -0
  222. package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
  223. package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
  224. package/esm/data_adapters/BaseAdapter/index.d.ts +7 -4
  225. package/esm/data_adapters/BaseAdapter/index.js +6 -5
  226. package/esm/data_adapters/BaseAdapter/stats.d.ts +37 -5
  227. package/esm/data_adapters/BaseAdapter/stats.js +89 -24
  228. package/esm/data_adapters/BaseAdapter/types.d.ts +11 -8
  229. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  230. package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
  231. package/esm/data_adapters/BaseAdapter/util.js +14 -3
  232. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
  233. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
  234. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
  235. package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
  236. package/esm/data_adapters/CytobandAdapter/index.js +3 -3
  237. package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
  238. package/esm/data_adapters/adapterSessionRefcount.js +96 -0
  239. package/esm/data_adapters/dataAdapterCache.d.ts +35 -1
  240. package/esm/data_adapters/dataAdapterCache.js +62 -22
  241. package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
  242. package/esm/data_adapters/getFeatureAdapter.js +27 -0
  243. package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
  244. package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
  245. package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
  246. package/esm/pluggableElementTypes/AdapterType.js +44 -5
  247. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
  248. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
  249. package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
  250. package/esm/pluggableElementTypes/ConnectionType.js +1 -1
  251. package/esm/pluggableElementTypes/DisplayType.d.ts +19 -10
  252. package/esm/pluggableElementTypes/DisplayType.js +53 -5
  253. package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
  254. package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
  255. package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
  256. package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
  257. package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
  258. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -9
  259. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
  260. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
  261. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
  262. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
  263. package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
  264. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +3 -3
  265. package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
  266. package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
  267. package/esm/pluggableElementTypes/TrackType.js +1 -1
  268. package/esm/pluggableElementTypes/ViewType.d.ts +27 -3
  269. package/esm/pluggableElementTypes/ViewType.js +84 -4
  270. package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
  271. package/esm/pluggableElementTypes/WidgetType.js +1 -1
  272. package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
  273. package/esm/pluggableElementTypes/addMenuItems.js +82 -0
  274. package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
  275. package/esm/pluggableElementTypes/extendElementType.js +73 -0
  276. package/esm/pluggableElementTypes/index.d.ts +7 -7
  277. package/esm/pluggableElementTypes/index.js +24 -14
  278. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
  279. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
  280. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +646 -84
  281. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +241 -60
  282. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +216 -35
  283. package/esm/pluggableElementTypes/models/BaseTrackModel.js +365 -83
  284. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +216 -16
  285. package/esm/pluggableElementTypes/models/BaseViewModel.js +150 -16
  286. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
  287. package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
  288. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
  289. package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
  290. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +177 -0
  291. package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
  292. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
  293. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
  294. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
  295. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
  296. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
  297. package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
  298. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
  299. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
  300. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
  301. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
  302. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
  303. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
  304. package/esm/pluggableElementTypes/models/index.d.ts +6 -3
  305. package/esm/pluggableElementTypes/models/index.js +10 -8
  306. package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
  307. package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
  308. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
  309. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
  310. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
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  1022. package/esm/util/useMeasure.d.ts +11 -1
  1023. package/esm/util/useMeasure.js +20 -6
  1024. package/esm/util/usePanZoom.d.ts +75 -0
  1025. package/esm/util/usePanZoom.js +175 -0
  1026. package/esm/util/usePanelVirtualScroll.d.ts +37 -0
  1027. package/esm/util/usePanelVirtualScroll.js +42 -0
  1028. package/esm/util/usePointerDrag.d.ts +37 -0
  1029. package/esm/util/usePointerDrag.js +61 -0
  1030. package/esm/util/useRafCommit.d.ts +4 -0
  1031. package/esm/util/useRafCommit.js +50 -0
  1032. package/esm/util/useResizeDrag.d.ts +91 -0
  1033. package/esm/util/useResizeDrag.js +105 -0
  1034. package/esm/util/useRowVirtualScroll.d.ts +32 -0
  1035. package/esm/util/useRowVirtualScroll.js +63 -0
  1036. package/esm/util/useVirtualScrollWheel.d.ts +7 -0
  1037. package/esm/util/useVirtualScrollWheel.js +108 -0
  1038. package/esm/util/viewStatus.d.ts +81 -0
  1039. package/esm/util/viewStatus.js +37 -0
  1040. package/esm/util/virtualRange.d.ts +36 -0
  1041. package/esm/util/virtualRange.js +26 -0
  1042. package/esm/util/webStorage.d.ts +26 -0
  1043. package/esm/util/webStorage.js +92 -0
  1044. package/esm/util/wheelZoom.d.ts +59 -0
  1045. package/esm/util/wheelZoom.js +231 -0
  1046. package/esm/util/whenViewSettled.d.ts +40 -0
  1047. package/esm/util/whenViewSettled.js +41 -0
  1048. package/esm/util/withFeatureDetails.d.ts +34 -0
  1049. package/esm/util/withFeatureDetails.js +59 -0
  1050. package/esm/util/withLaunchInput.d.ts +123 -0
  1051. package/esm/util/withLaunchInput.js +228 -0
  1052. package/package.json +243 -820
  1053. package/esm/ReExports/DataGrid.d.ts +0 -1
  1054. package/esm/ReExports/DataGrid.js +0 -1
  1055. package/esm/configuration/util.d.ts +0 -10
  1056. package/esm/configuration/util.js +0 -123
  1057. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
  1058. package/esm/data_adapters/util.d.ts +0 -1
  1059. package/esm/data_adapters/util.js +0 -6
  1060. package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
  1061. package/esm/pluggableElementTypes/GlyphType.js +0 -18
  1062. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
  1063. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
  1064. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
  1065. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
  1066. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
  1067. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
  1068. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
  1069. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
  1070. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
  1071. package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
  1072. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
  1073. package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
  1074. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
  1075. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
  1076. package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
  1077. package/esm/pluggableElementTypes/renderers/index.js +0 -6
  1078. package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
  1079. package/esm/pluggableElementTypes/renderers/util.js +0 -14
  1080. package/esm/rpc/baseRpcConfig.d.ts +0 -8
  1081. package/esm/rpc/baseRpcConfig.js +0 -10
  1082. package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
  1083. package/esm/rpc/mainThreadRpcConfig.js +0 -8
  1084. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
  1085. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
  1086. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
  1087. package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
  1088. package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
  1089. package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
  1090. package/esm/rpc/methods/CoreRender.d.ts +0 -14
  1091. package/esm/rpc/methods/CoreRender.js +0 -40
  1092. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
  1093. package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
  1094. package/esm/rpc/methods/util.d.ts +0 -15
  1095. package/esm/rpc/methods/util.js +0 -7
  1096. package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
  1097. package/esm/rpc/webWorkerRpcConfig.js +0 -8
  1098. package/esm/ui/MenuButton.d.ts +0 -1
  1099. package/esm/ui/MenuButton.js +0 -1
  1100. package/esm/ui/MenuItems.d.ts +0 -15
  1101. package/esm/ui/MenuItems.js +0 -59
  1102. package/esm/ui/useEvent.d.ts +0 -1
  1103. package/esm/ui/useEvent.js +0 -10
  1104. package/esm/util/blobToDataURL.d.ts +0 -1
  1105. package/esm/util/blobToDataURL.js +0 -14
  1106. package/esm/util/compositeMap.d.ts +0 -11
  1107. package/esm/util/compositeMap.js +0 -59
  1108. package/esm/util/flatqueue/index.d.ts +0 -11
  1109. package/esm/util/flatqueue/index.js +0 -61
  1110. package/esm/util/layouts/BaseLayout.d.ts +0 -30
  1111. package/esm/util/layouts/MultiLayout.d.ts +0 -12
  1112. package/esm/util/layouts/MultiLayout.js +0 -40
  1113. package/esm/util/layouts/PileupLayout.d.ts +0 -41
  1114. package/esm/util/layouts/PileupLayout.js +0 -202
  1115. package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
  1116. package/esm/util/layouts/PrecomputedLayout.js +0 -71
  1117. package/esm/util/layouts/SceneGraph.d.ts +0 -31
  1118. package/esm/util/layouts/SceneGraph.js +0 -121
  1119. package/esm/util/makeAbortableReaction.d.ts +0 -3
  1120. package/esm/util/makeAbortableReaction.js +0 -47
  1121. package/esm/util/map-obj/index.d.ts +0 -13
  1122. package/esm/util/map-obj/index.js +0 -92
  1123. package/esm/util/nextTick.d.ts +0 -1
  1124. package/esm/util/nextTick.js +0 -3
  1125. package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
  1126. package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
  1127. package/esm/util/offscreenCanvasUtils.d.ts +0 -12
  1128. package/esm/util/offscreenCanvasUtils.js +0 -19
  1129. package/esm/util/renderToAbstractCanvas.d.ts +0 -17
  1130. package/esm/util/renderToAbstractCanvas.js +0 -53
  1131. package/esm/util/transferables.d.ts +0 -2
  1132. package/esm/util/transferables.js +0 -35
  1133. package/esm/util/tss-react/mui/index.d.ts +0 -1
  1134. package/esm/util/tss-react/mui/index.js +0 -1
  1135. package/esm/util/tss-react/mui/mui.d.ts +0 -10
  1136. package/esm/util/tss-react/mui/mui.js +0 -5
  1137. package/esm/util/when.d.ts +0 -1
  1138. package/esm/util/when.js +0 -1
  1139. /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
  1140. /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
@@ -1 +0,0 @@
1
- export { DataGrid as default } from '@mui/x-data-grid';
@@ -1 +0,0 @@
1
- export { DataGrid as default } from '@mui/x-data-grid';
@@ -1,10 +0,0 @@
1
- import type { AnyConfigurationModel, AnyConfigurationSchemaType, ConfigurationSchemaForModel, ConfigurationSlotName } from './types.ts';
2
- export declare function readConfObject<CONFMODEL extends AnyConfigurationModel>(confObject: CONFMODEL, slotPath?: ConfigurationSlotName<ConfigurationSchemaForModel<CONFMODEL>> | string[], args?: Record<string, unknown>): any;
3
- export declare function getConf<CONFMODEL extends AnyConfigurationModel>(model: {
4
- configuration: CONFMODEL;
5
- }, slotPath?: Parameters<typeof readConfObject<CONFMODEL>>[1], args?: Parameters<typeof readConfObject<CONFMODEL>>[2]): any;
6
- export declare function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType: unknown): string[];
7
- export declare function isBareConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
8
- export declare function isConfigurationSchemaType(thing: unknown): thing is AnyConfigurationSchemaType;
9
- export declare function isConfigurationModel(thing: unknown): thing is AnyConfigurationModel;
10
- export declare function isConfigurationSlotType(thing: unknown): thing is object & Record<"isJBrowseConfigurationSlot", unknown>;
@@ -1,123 +0,0 @@
1
- import { getSnapshot, getType, isArrayType, isLateType, isMapType, isModelType, isOptionalType, isStateTreeNode, isType, isUnionType, } from '@jbrowse/mobx-state-tree';
2
- function isConfigSlot(slot) {
3
- return typeof slot?.getValue === 'function';
4
- }
5
- import { getDefaultValue, getSubType, getUnionSubTypes, resolveLateType, } from "../util/mst-reflection.js";
6
- export function readConfObject(confObject, slotPath, args = {}) {
7
- if (!slotPath) {
8
- return isStateTreeNode(confObject)
9
- ? structuredClone(getSnapshot(confObject))
10
- : structuredClone(confObject);
11
- }
12
- else if (typeof slotPath === 'string') {
13
- let slot = confObject[slotPath];
14
- if (!slot) {
15
- if (isStateTreeNode(confObject) && isMapType(getType(confObject))) {
16
- slot = confObject.get(slotPath);
17
- }
18
- if (!slot) {
19
- return undefined;
20
- }
21
- }
22
- const val = isConfigSlot(slot) ? slot.getValue(args) : slot;
23
- if (val === null || typeof val !== 'object') {
24
- return val;
25
- }
26
- return isStateTreeNode(val) ? structuredClone(getSnapshot(val)) : val;
27
- }
28
- else if (Array.isArray(slotPath)) {
29
- const slotName = slotPath[0];
30
- if (slotPath.length > 1) {
31
- const newPath = slotPath.slice(1);
32
- let subConf = confObject[slotName];
33
- if (!subConf &&
34
- isStateTreeNode(confObject) &&
35
- isMapType(getType(confObject))) {
36
- subConf = confObject.get(slotName);
37
- }
38
- return subConf ? readConfObject(subConf, newPath, args) : undefined;
39
- }
40
- return readConfObject(confObject, slotName, args);
41
- }
42
- throw new TypeError('slotPath must be a string or array');
43
- }
44
- export function getConf(model, slotPath, args) {
45
- return readConfObject(model.configuration, slotPath, args);
46
- }
47
- export function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
48
- if (isType(maybeUnionType)) {
49
- maybeUnionType = resolveLateType(maybeUnionType);
50
- if (isUnionType(maybeUnionType)) {
51
- const typeNames = [];
52
- for (let type of getUnionSubTypes(maybeUnionType)) {
53
- type = resolveLateType(type);
54
- let typeName = getTypeNamesFromExplicitlyTypedUnion(type);
55
- if (!typeName.length) {
56
- const def = getDefaultValue(type);
57
- typeName = [def.type];
58
- }
59
- if (!typeName[0]) {
60
- throw new Error(`invalid config schema type ${type}`);
61
- }
62
- typeNames.push(...typeName);
63
- }
64
- return typeNames;
65
- }
66
- }
67
- return [];
68
- }
69
- export function isBareConfigurationSchemaType(thing) {
70
- if (isType(thing)) {
71
- if (isModelType(thing) &&
72
- ('isJBrowseConfigurationSchema' in thing ||
73
- thing.name.includes('ConfigurationSchema'))) {
74
- return true;
75
- }
76
- if (isLateType(thing)) {
77
- return true;
78
- }
79
- }
80
- return false;
81
- }
82
- export function isConfigurationSchemaType(thing) {
83
- if (!isType(thing)) {
84
- return false;
85
- }
86
- else if (isBareConfigurationSchemaType(thing)) {
87
- return true;
88
- }
89
- else if (isUnionType(thing)) {
90
- return getUnionSubTypes(thing).every(t => isConfigurationSchemaType(t) || t.name === 'undefined');
91
- }
92
- else if (isOptionalType(thing) &&
93
- isConfigurationSchemaType(getSubType(thing))) {
94
- return true;
95
- }
96
- else if (isArrayType(thing) &&
97
- isConfigurationSchemaType(getSubType(thing))) {
98
- return true;
99
- }
100
- else if (isMapType(thing) && isConfigurationSchemaType(getSubType(thing))) {
101
- return true;
102
- }
103
- else {
104
- return false;
105
- }
106
- }
107
- const configurationModelCache = new WeakMap();
108
- export function isConfigurationModel(thing) {
109
- if (!thing || typeof thing !== 'object') {
110
- return false;
111
- }
112
- let cached = configurationModelCache.get(thing);
113
- if (cached === undefined) {
114
- cached = isStateTreeNode(thing) && isConfigurationSchemaType(getType(thing));
115
- configurationModelCache.set(thing, cached);
116
- }
117
- return cached;
118
- }
119
- export function isConfigurationSlotType(thing) {
120
- return (typeof thing === 'object' &&
121
- thing !== null &&
122
- 'isJBrowseConfigurationSlot' in thing);
123
- }
@@ -1,18 +0,0 @@
1
- import type { StopToken } from '../../util/stopToken.ts';
2
- export interface BaseOptions {
3
- stopToken?: StopToken;
4
- bpPerPx?: number;
5
- sessionId?: string;
6
- trackInstanceId?: string;
7
- statusCallback?: (message: string) => void;
8
- headers?: Record<string, string>;
9
- statsEstimationMode?: boolean;
10
- }
11
- export type SearchType = 'full' | 'prefix' | 'exact';
12
- export interface BaseTextSearchArgs {
13
- queryString: string;
14
- searchType?: SearchType;
15
- stopToken?: StopToken;
16
- limit?: number;
17
- pageNumber?: number;
18
- }
@@ -1 +0,0 @@
1
- export declare function adapterConfigCacheKey(conf?: Record<string, unknown>): string;
@@ -1,6 +0,0 @@
1
- import idMaker from "../util/idMaker.js";
2
- export function adapterConfigCacheKey(conf = {}) {
3
- return conf.type && conf.adapterId
4
- ? `${conf.type}-${conf.adapterId}`
5
- : `${idMaker(conf)}`;
6
- }
@@ -1,43 +0,0 @@
1
- import PluggableElementBase from './PluggableElementBase.ts';
2
- import type { AnyConfigurationModel } from '../configuration/index.ts';
3
- import type { Feature, Region } from '../util/index.ts';
4
- import type { Theme } from '@mui/material';
5
- export interface GlyphRenderContext {
6
- ctx: CanvasRenderingContext2D;
7
- feature: Feature;
8
- featureLayout: GlyphFeatureLayout;
9
- region: Region;
10
- bpPerPx: number;
11
- config: AnyConfigurationModel;
12
- theme: Theme;
13
- reversed: boolean;
14
- topLevel: boolean;
15
- canvasWidth: number;
16
- }
17
- export interface GlyphFeatureLayout {
18
- feature: Feature;
19
- x: number;
20
- y: number;
21
- width: number;
22
- height: number;
23
- children: GlyphFeatureLayout[];
24
- }
25
- export interface GlyphArgs {
26
- name: string;
27
- displayName?: string;
28
- draw: (context: GlyphRenderContext) => void;
29
- getChildFeatures?: (feature: Feature, config: AnyConfigurationModel) => Feature[];
30
- getHeightMultiplier?: (feature: Feature, config: AnyConfigurationModel) => number;
31
- getSubfeatureMouseover?: (childFeature: Feature) => string | undefined;
32
- match?: (feature: Feature) => boolean;
33
- priority?: number;
34
- }
35
- export default class GlyphType extends PluggableElementBase {
36
- draw: (context: GlyphRenderContext) => void;
37
- getChildFeatures?: (feature: Feature, config: AnyConfigurationModel) => Feature[];
38
- getHeightMultiplier?: (feature: Feature, config: AnyConfigurationModel) => number;
39
- getSubfeatureMouseover?: (childFeature: Feature) => string | undefined;
40
- match?: (feature: Feature) => boolean;
41
- priority: number;
42
- constructor(args: GlyphArgs);
43
- }
@@ -1,18 +0,0 @@
1
- import PluggableElementBase from "./PluggableElementBase.js";
2
- export default class GlyphType extends PluggableElementBase {
3
- draw;
4
- getChildFeatures;
5
- getHeightMultiplier;
6
- getSubfeatureMouseover;
7
- match;
8
- priority;
9
- constructor(args) {
10
- super(args);
11
- this.draw = args.draw;
12
- this.getChildFeatures = args.getChildFeatures;
13
- this.getHeightMultiplier = args.getHeightMultiplier;
14
- this.getSubfeatureMouseover = args.getSubfeatureMouseover;
15
- this.match = args.match;
16
- this.priority = args.priority ?? 0;
17
- }
18
- }
@@ -1,5 +0,0 @@
1
- import type { AbstractSessionModel, Region } from '../../../util/index.ts';
2
- export declare function fetchSequence({ session, region, }: {
3
- session: AbstractSessionModel;
4
- region: Region;
5
- }): Promise<string | undefined>;
@@ -1,17 +0,0 @@
1
- import { getConf } from "../../../configuration/index.js";
2
- export async function fetchSequence({ session, region, }) {
3
- const { rpcManager, assemblyManager } = session;
4
- const assembly = assemblyManager.get(region.assemblyName);
5
- if (!assembly) {
6
- throw new Error(`assembly ${region.assemblyName} not found`);
7
- }
8
- const sessionId = 'getSequence';
9
- return rpcManager.call(sessionId, 'CoreGetSequence', {
10
- adapterConfig: getConf(assembly, ['sequence', 'adapter']),
11
- region: {
12
- ...region,
13
- refName: assembly.getCanonicalRefName(region.refName),
14
- },
15
- sessionId,
16
- });
17
- }
@@ -1,52 +0,0 @@
1
- import FeatureRendererType from './FeatureRendererType.ts';
2
- import PrecomputedLayout from '../../util/layouts/PrecomputedLayout.ts';
3
- import type { RenderArgs as FeatureRenderArgs, RenderArgsDeserialized as FeatureRenderArgsDeserialized, RenderArgsSerialized as FeatureRenderArgsSerialized, RenderResults as FeatureRenderResults, ResultsDeserialized as FeatureResultsDeserialized, ResultsSerialized as FeatureResultsSerialized } from './FeatureRendererType.ts';
4
- import type { LayoutSessionLike, LayoutSessionProps } from './LayoutSession.ts';
5
- import type { RenderReturn } from './RendererType.tsx';
6
- import type RpcManager from '../../rpc/RpcManager.ts';
7
- import type { Feature, Region } from '../../util/index.ts';
8
- import type { BaseLayout, SerializedLayout } from '../../util/layouts/BaseLayout.ts';
9
- export interface RenderArgs extends FeatureRenderArgs {
10
- bpPerPx: number;
11
- trackInstanceId: string;
12
- }
13
- export interface RenderArgsSerialized extends FeatureRenderArgsSerialized {
14
- bpPerPx: number;
15
- }
16
- export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
17
- statusCallback?: (arg: string) => void;
18
- bpPerPx: number;
19
- trackInstanceId: string;
20
- }
21
- export interface RenderResults extends FeatureRenderResults {
22
- layout?: BaseLayout<Feature> | SerializedLayout;
23
- }
24
- export interface ResultsSerialized extends FeatureResultsSerialized {
25
- maxHeightReached: boolean;
26
- layout: SerializedLayout;
27
- }
28
- export interface ResultsDeserialized extends FeatureResultsDeserialized {
29
- maxHeightReached: boolean;
30
- layout: PrecomputedLayout<string>;
31
- }
32
- export default class BoxRendererType extends FeatureRendererType {
33
- layoutSessions: Record<string, LayoutSessionLike>;
34
- createLayoutSession(props: LayoutSessionProps): LayoutSessionLike;
35
- getLayoutSession(props: {
36
- sessionId: string;
37
- trackInstanceId: string;
38
- }): LayoutSessionLike | undefined;
39
- getWorkerSession(props: LayoutSessionProps & {
40
- sessionId: string;
41
- trackInstanceId: string;
42
- }): LayoutSessionLike;
43
- getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): Region;
44
- freeResources(args: RenderArgs): void;
45
- freeResourcesInClient(rpcManager: RpcManager, args: RenderArgs): Promise<void>;
46
- deserializeLayoutInClient(json: SerializedLayout): PrecomputedLayout<unknown>;
47
- deserializeResultsInClient(result: ResultsSerialized, args: RenderArgs): ResultsDeserialized;
48
- createLayoutInWorker(args: RenderArgsDeserialized): BaseLayout<unknown>;
49
- serializeLayout(layout: BaseLayout<unknown>, args: RenderArgsDeserialized): SerializedLayout;
50
- render(renderArgs: RenderArgsDeserialized): Promise<RenderReturn>;
51
- serializeResultsInWorker(results: RenderResults, args: RenderArgsDeserialized): ResultsSerialized;
52
- }
@@ -1,78 +0,0 @@
1
- import FeatureRendererType from "./FeatureRendererType.js";
2
- import { LayoutSession } from "./LayoutSession.js";
3
- import { expandRegion } from "./util.js";
4
- import { readConfObject } from "../../configuration/index.js";
5
- import { getLayoutId } from "../../util/index.js";
6
- import PrecomputedLayout from "../../util/layouts/PrecomputedLayout.js";
7
- export default class BoxRendererType extends FeatureRendererType {
8
- layoutSessions = {};
9
- createLayoutSession(props) {
10
- return new LayoutSession(props);
11
- }
12
- getLayoutSession(props) {
13
- return this.layoutSessions[getLayoutId(props)];
14
- }
15
- getWorkerSession(props) {
16
- const key = getLayoutId(props);
17
- if (!this.layoutSessions[key]) {
18
- this.layoutSessions[key] = this.createLayoutSession(props);
19
- }
20
- return this.layoutSessions[key].update(props);
21
- }
22
- getExpandedRegion(region, renderArgs) {
23
- const { bpPerPx, config } = renderArgs;
24
- const maxFeatureGlyphExpansion = readConfObject(config, 'maxFeatureGlyphExpansion') || 0;
25
- const bpExpansion = Math.round(maxFeatureGlyphExpansion * bpPerPx);
26
- return expandRegion(region, bpExpansion);
27
- }
28
- freeResources(args) {
29
- const key = getLayoutId(args);
30
- const session = this.layoutSessions[key];
31
- if (session) {
32
- const region = args.regions[0];
33
- session.layout.discardRange(region.refName, region.start, region.end);
34
- }
35
- }
36
- async freeResourcesInClient(rpcManager, args) {
37
- this.freeResources(args);
38
- return super.freeResourcesInClient(rpcManager, args);
39
- }
40
- deserializeLayoutInClient(json) {
41
- return new PrecomputedLayout(json);
42
- }
43
- deserializeResultsInClient(result, args) {
44
- const layout = this.deserializeLayoutInClient(result.layout);
45
- return super.deserializeResultsInClient({
46
- ...result,
47
- layout,
48
- }, args);
49
- }
50
- createLayoutInWorker(args) {
51
- const { regions } = args;
52
- const { layout } = this.getWorkerSession(args);
53
- return layout.getSublayout(regions[0].refName);
54
- }
55
- serializeLayout(layout, args) {
56
- const region = args.regions[0];
57
- return layout.serializeRegion(this.getExpandedRegion(region, args));
58
- }
59
- async render(renderArgs) {
60
- const features = await this.getFeatures(renderArgs);
61
- const layout = this.createLayoutInWorker(renderArgs);
62
- return { features, layout };
63
- }
64
- serializeResultsInWorker(results, args) {
65
- const { features, ...rest } = super.serializeResultsInWorker(results, args);
66
- const region = args.regions[0];
67
- const resultLayout = results.layout;
68
- const layout = resultLayout && 'serializeRegion' in resultLayout
69
- ? resultLayout.serializeRegion(this.getExpandedRegion(region, args))
70
- : resultLayout;
71
- return {
72
- ...rest,
73
- layout,
74
- maxHeightReached: layout.maxHeightReached,
75
- features: features?.filter(f => !!layout.rectangles[f.uniqueId]),
76
- };
77
- }
78
- }
@@ -1,4 +0,0 @@
1
- import FeatureRenderer from './FeatureRendererType.ts';
2
- export default class CircularChordRendererType extends FeatureRenderer {
3
- supportsSVG: boolean;
4
- }
@@ -1,4 +0,0 @@
1
- import FeatureRenderer from "./FeatureRendererType.js";
2
- export default class CircularChordRendererType extends FeatureRenderer {
3
- supportsSVG = true;
4
- }
@@ -1,58 +0,0 @@
1
- import ServerSideRendererType from './ServerSideRendererType.ts';
2
- import type { RenderArgs as ServerSideRenderArgs, RenderArgsDeserialized as ServerSideRenderArgsDeserialized, RenderArgsSerialized as ServerSideRenderArgsSerialized, RenderResults as ServerSideRenderResults, RenderReturn, ResultsDeserialized as ServerSideResultsDeserialized, ResultsSerialized as ServerSideResultsSerialized } from './ServerSideRendererType.ts';
3
- import type { AnyConfigurationModel } from '../../configuration/index.ts';
4
- import type { Feature, SimpleFeatureSerialized } from '../../util/simpleFeature.ts';
5
- import type { AugmentedRegion as Region } from '../../util/types/index.ts';
6
- export interface RenderArgs extends ServerSideRenderArgs {
7
- displayModel?: {
8
- id: string;
9
- selectedFeatureId?: string;
10
- };
11
- regions: Region[];
12
- blockKey: string;
13
- }
14
- export interface RenderArgsSerialized extends ServerSideRenderArgsSerialized {
15
- displayModel?: {
16
- id: string;
17
- selectedFeatureId?: string;
18
- };
19
- regions: Region[];
20
- blockKey: string;
21
- }
22
- export interface RenderArgsDeserialized extends ServerSideRenderArgsDeserialized {
23
- displayModel: {
24
- id: string;
25
- selectedFeatureId?: string;
26
- };
27
- regions: Region[];
28
- blockKey: string;
29
- adapterConfig: AnyConfigurationModel;
30
- }
31
- export interface RenderResults extends ServerSideRenderResults {
32
- features?: Map<string, Feature>;
33
- }
34
- export interface ResultsSerialized extends ServerSideResultsSerialized {
35
- features?: SimpleFeatureSerialized[];
36
- }
37
- export interface ResultsDeserialized extends ServerSideResultsDeserialized {
38
- features: Map<string, Feature>;
39
- blockKey: string;
40
- }
41
- export default class FeatureRendererType extends ServerSideRendererType {
42
- renderDirect(args: RenderArgs): Promise<{
43
- blockKey: string;
44
- reactElement?: React.ReactElement;
45
- html?: string;
46
- } | {
47
- blockKey: string;
48
- reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
49
- html?: string;
50
- }>;
51
- serializeArgsInClient(args: RenderArgs): ServerSideRenderArgsSerialized;
52
- deserializeResultsInClient(result: ResultsSerialized, args: RenderArgs): ResultsDeserialized;
53
- serializeResultsInWorker(result: RenderResults, args: RenderArgsDeserialized): ResultsSerialized;
54
- getExpandedRegion(region: Region, _renderArgs: RenderArgsDeserialized): Region;
55
- getFeatures(renderArgs: RenderArgsDeserialized): Promise<Map<string, Feature>>;
56
- featurePassesFilters(renderArgs: RenderArgsDeserialized, feature: Feature): boolean;
57
- render(renderArgs: RenderArgsDeserialized): Promise<RenderReturn>;
58
- }
@@ -1,77 +0,0 @@
1
- import { firstValueFrom } from 'rxjs';
2
- import { toArray } from 'rxjs/operators';
3
- import ServerSideRendererType from "./ServerSideRendererType.js";
4
- import { normalizeRegion } from "./util.js";
5
- import { isFeatureAdapter } from "../../data_adapters/BaseAdapter/index.js";
6
- import { getAdapter } from "../../data_adapters/dataAdapterCache.js";
7
- import { iterMap } from "../../util/index.js";
8
- import SimpleFeature from "../../util/simpleFeature.js";
9
- export default class FeatureRendererType extends ServerSideRendererType {
10
- async renderDirect(args) {
11
- const result = await super.renderDirect(args);
12
- return {
13
- ...result,
14
- blockKey: args.blockKey,
15
- };
16
- }
17
- serializeArgsInClient(args) {
18
- return super.serializeArgsInClient({
19
- ...args,
20
- displayModel: undefined,
21
- regions: structuredClone(args.regions),
22
- });
23
- }
24
- deserializeResultsInClient(result, args) {
25
- const deserializedFeatures = new Map(result.features
26
- ?.map(f => SimpleFeature.fromJSON(f))
27
- .map(f => [f.id(), f]));
28
- const deserialized = super.deserializeResultsInClient({
29
- ...result,
30
- features: deserializedFeatures,
31
- }, args);
32
- return {
33
- ...deserialized,
34
- blockKey: args.blockKey,
35
- features: deserializedFeatures,
36
- };
37
- }
38
- serializeResultsInWorker(result, args) {
39
- const serialized = super.serializeResultsInWorker(result, args);
40
- const { features } = result;
41
- return {
42
- ...serialized,
43
- features: features instanceof Map
44
- ? iterMap(features.values(), f => f.toJSON(), features.size)
45
- : undefined,
46
- };
47
- }
48
- getExpandedRegion(region, _renderArgs) {
49
- return region;
50
- }
51
- async getFeatures(renderArgs) {
52
- const pm = this.pluginManager;
53
- const { regions, sessionId, adapterConfig } = renderArgs;
54
- const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
55
- if (!isFeatureAdapter(dataAdapter)) {
56
- throw new Error('Adapter does not support retrieving features');
57
- }
58
- const requestRegions = regions.map(r => normalizeRegion(r));
59
- const featureObservable = requestRegions.length === 1
60
- ? dataAdapter.getFeatures(this.getExpandedRegion(requestRegions[0], renderArgs), renderArgs)
61
- : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
62
- const feats = await firstValueFrom(featureObservable.pipe(toArray()));
63
- return new Map(feats
64
- .filter(feat => this.featurePassesFilters(renderArgs, feat))
65
- .map(feat => [feat.id(), feat]));
66
- }
67
- featurePassesFilters(renderArgs, feature) {
68
- return renderArgs.filters
69
- ? renderArgs.filters.passes(feature, renderArgs)
70
- : true;
71
- }
72
- async render(renderArgs) {
73
- const features = await this.getFeatures(renderArgs);
74
- const result = await super.render({ ...renderArgs, features });
75
- return { ...result, features };
76
- }
77
- }
@@ -1,31 +0,0 @@
1
- import GranularRectLayout from '../../util/layouts/GranularRectLayout.ts';
2
- import MultiLayout from '../../util/layouts/MultiLayout.ts';
3
- import type SerializableFilterChain from './util/serializableFilterChain.ts';
4
- import type { AnyConfigurationModel } from '../../configuration/index.ts';
5
- import type { Region } from '../../util/index.ts';
6
- import type { BaseLayout } from '../../util/layouts/index.ts';
7
- export interface LayoutSessionProps {
8
- regions: Region[];
9
- config: AnyConfigurationModel;
10
- bpPerPx: number;
11
- filters?: SerializableFilterChain;
12
- }
13
- export type BaseMultiLayout = MultiLayout<BaseLayout<unknown>, unknown>;
14
- export type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
15
- export interface CachedLayout {
16
- layout: BaseMultiLayout;
17
- props: LayoutSessionProps;
18
- }
19
- export interface LayoutSessionLike {
20
- layout: BaseMultiLayout;
21
- update(props: LayoutSessionProps): LayoutSessionLike;
22
- }
23
- export declare class LayoutSession implements LayoutSessionLike {
24
- props: LayoutSessionProps;
25
- cachedLayout: CachedLayout | undefined;
26
- constructor(props: LayoutSessionProps);
27
- update(props: LayoutSessionProps): this;
28
- makeLayout(): MultiLayout<GranularRectLayout<unknown>, unknown>;
29
- cachedLayoutIsValid(cachedLayout: CachedLayout): boolean;
30
- get layout(): BaseMultiLayout;
31
- }
@@ -1,40 +0,0 @@
1
- import deepEqual from 'fast-deep-equal';
2
- import { readConfObject } from "../../configuration/index.js";
3
- import GranularRectLayout from "../../util/layouts/GranularRectLayout.js";
4
- import MultiLayout from "../../util/layouts/MultiLayout.js";
5
- export class LayoutSession {
6
- props;
7
- cachedLayout;
8
- constructor(props) {
9
- this.props = props;
10
- }
11
- update(props) {
12
- this.props = props;
13
- return this;
14
- }
15
- makeLayout() {
16
- return new MultiLayout(GranularRectLayout, {
17
- maxHeight: readConfObject(this.props.config, 'maxHeight'),
18
- displayMode: readConfObject(this.props.config, 'displayMode'),
19
- pitchX: this.props.bpPerPx,
20
- pitchY: readConfObject(this.props.config, 'noSpacing') ? 1 : 3,
21
- });
22
- }
23
- cachedLayoutIsValid(cachedLayout) {
24
- const bpPerPxMatch = cachedLayout.props.bpPerPx === this.props.bpPerPx;
25
- const currentConfig = readConfObject(this.props.config);
26
- const cachedConfig = readConfObject(cachedLayout.props.config);
27
- const configMatch = deepEqual(currentConfig, cachedConfig);
28
- const filtersMatch = deepEqual(this.props.filters, cachedLayout.props.filters);
29
- return bpPerPxMatch && configMatch && filtersMatch;
30
- }
31
- get layout() {
32
- if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
33
- this.cachedLayout = {
34
- layout: this.makeLayout(),
35
- props: this.props,
36
- };
37
- }
38
- return this.cachedLayout.layout;
39
- }
40
- }
@@ -1,28 +0,0 @@
1
- import type React from 'react';
2
- import PluggableElementBase from '../PluggableElementBase.ts';
3
- import type PluginManager from '../../PluginManager.ts';
4
- import type { AnyConfigurationSchemaType } from '../../configuration/index.ts';
5
- import type { AnyReactComponentType } from '../../util/index.ts';
6
- import type { RpcResult } from '../../util/librpc.ts';
7
- export type RenderProps = Record<string, unknown>;
8
- export interface RenderResults {
9
- reactElement?: React.ReactElement;
10
- html?: string;
11
- [key: string]: unknown;
12
- }
13
- export type RenderReturn = RenderResults | RpcResult;
14
- export default class RendererType extends PluggableElementBase {
15
- ReactComponent: AnyReactComponentType;
16
- supportsSVG: boolean;
17
- configSchema: AnyConfigurationSchemaType;
18
- pluginManager: PluginManager;
19
- constructor(stuff: {
20
- name: string;
21
- ReactComponent: AnyReactComponentType;
22
- displayName?: string;
23
- configSchema: AnyConfigurationSchemaType;
24
- pluginManager: PluginManager;
25
- });
26
- render(props: RenderProps): Promise<RenderReturn>;
27
- freeResources(_args: any): void;
28
- }
@@ -1,20 +0,0 @@
1
- import { jsx as _jsx } from "react/jsx-runtime";
2
- import PluggableElementBase from "../PluggableElementBase.js";
3
- export default class RendererType extends PluggableElementBase {
4
- ReactComponent;
5
- supportsSVG = true;
6
- configSchema;
7
- pluginManager;
8
- constructor(stuff) {
9
- super(stuff);
10
- this.ReactComponent = stuff.ReactComponent;
11
- this.configSchema = stuff.configSchema;
12
- this.pluginManager = stuff.pluginManager;
13
- }
14
- async render(props) {
15
- return {
16
- reactElement: _jsx(this.ReactComponent, { ...props }),
17
- };
18
- }
19
- freeResources(_args) { }
20
- }