@jbrowse/core 3.6.5 → 4.0.0

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 (940) hide show
  1. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +32 -0
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +13 -0
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +43 -0
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +8 -0
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +7 -0
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +2 -0
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +17 -0
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +2 -0
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +7 -0
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +20 -0
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +2 -0
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +24 -0
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +57 -0
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +11 -0
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +42 -0
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +24 -0
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +2 -0
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +14 -0
  19. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +14 -0
  20. package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +22 -0
  21. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -0
  22. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +24 -0
  23. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +7 -0
  24. package/esm/BaseFeatureWidget/BaseFeatureDetail/types.js +1 -0
  25. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +26 -0
  26. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +10 -0
  27. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +41 -0
  28. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +7 -0
  29. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +44 -0
  30. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +7 -0
  31. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +34 -0
  32. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +8 -0
  33. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +26 -0
  34. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +3 -0
  35. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +29 -0
  36. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +6 -0
  37. package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +6 -0
  38. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +11 -0
  39. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +8 -0
  40. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +40 -0
  41. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +8 -0
  42. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +105 -0
  43. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +5 -0
  44. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +64 -0
  45. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +6 -0
  46. package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +48 -0
  47. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.d.ts +1 -0
  48. package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -0
  49. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +31 -0
  50. package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +83 -0
  51. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +16 -0
  52. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +83 -0
  53. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +8 -0
  54. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +16 -0
  55. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +10 -0
  56. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +52 -0
  57. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +9 -0
  58. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +21 -0
  59. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +10 -0
  60. package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +22 -0
  61. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +80 -0
  62. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +583 -0
  63. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +141 -0
  64. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +1116 -0
  65. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -0
  66. package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.js +1 -0
  67. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +13 -0
  68. package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +73 -0
  69. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +10 -0
  70. package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +42 -0
  71. package/esm/BaseFeatureWidget/configSchema.d.ts +2 -0
  72. package/esm/BaseFeatureWidget/configSchema.js +3 -0
  73. package/esm/BaseFeatureWidget/index.d.ts +2 -0
  74. package/esm/BaseFeatureWidget/index.js +2 -0
  75. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +101 -0
  76. package/esm/BaseFeatureWidget/stateModelFactory.js +96 -0
  77. package/esm/BaseFeatureWidget/types.d.ts +22 -0
  78. package/esm/BaseFeatureWidget/types.js +1 -0
  79. package/esm/BaseFeatureWidget/util.d.ts +51 -0
  80. package/esm/BaseFeatureWidget/util.js +95 -0
  81. package/esm/CorePlugin.d.ts +6 -0
  82. package/esm/CorePlugin.js +24 -0
  83. package/esm/PhasedScheduler.js +25 -0
  84. package/esm/Plugin.d.ts +13 -0
  85. package/esm/Plugin.js +9 -0
  86. package/esm/PluginLoader.d.ts +64 -0
  87. package/esm/PluginLoader.js +164 -0
  88. package/esm/PluginManager.d.ts +125 -0
  89. package/esm/PluginManager.js +414 -0
  90. package/esm/ReExports/BaseFeatureDetails.js +9 -0
  91. package/esm/ReExports/DataGrid.js +1 -0
  92. package/esm/ReExports/MuiDataGridReExports.js +131 -0
  93. package/esm/ReExports/MuiReExports.d.ts +134 -0
  94. package/esm/ReExports/MuiReExports.js +115 -0
  95. package/esm/ReExports/index.d.ts +1 -0
  96. package/esm/ReExports/index.js +1 -0
  97. package/esm/ReExports/lazify.js +10 -0
  98. package/esm/ReExports/list.js +275 -0
  99. package/esm/ReExports/modules.js +149 -0
  100. package/esm/TextSearch/BaseResults.d.ts +46 -0
  101. package/esm/TextSearch/BaseResults.js +67 -0
  102. package/esm/TextSearch/TextSearchManager.d.ts +48 -0
  103. package/esm/TextSearch/TextSearchManager.js +77 -0
  104. package/esm/assemblyManager/assembly.d.ts +75 -0
  105. package/esm/assemblyManager/assembly.js +328 -0
  106. package/esm/assemblyManager/assemblyConfigSchema.d.ts +27 -0
  107. package/esm/assemblyManager/assemblyConfigSchema.js +51 -0
  108. package/esm/assemblyManager/assemblyManager.d.ts +528 -0
  109. package/esm/assemblyManager/assemblyManager.js +131 -0
  110. package/esm/assemblyManager/index.d.ts +3 -0
  111. package/esm/assemblyManager/index.js +2 -0
  112. package/esm/configuration/configurationSchema.d.ts +37 -0
  113. package/esm/configuration/configurationSchema.js +230 -0
  114. package/esm/configuration/configurationSlot.d.ts +33 -0
  115. package/esm/configuration/configurationSlot.js +239 -0
  116. package/esm/configuration/index.d.ts +3 -0
  117. package/esm/configuration/index.js +2 -0
  118. package/esm/configuration/types.d.ts +14 -0
  119. package/esm/configuration/types.js +1 -0
  120. package/esm/configuration/util.d.ts +10 -0
  121. package/esm/configuration/util.js +123 -0
  122. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +16 -0
  123. package/esm/data_adapters/BaseAdapter/BaseAdapter.js +31 -0
  124. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +24 -0
  125. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +68 -0
  126. package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +18 -0
  127. package/esm/data_adapters/BaseAdapter/BaseOptions.js +1 -0
  128. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +10 -0
  129. package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.js +1 -0
  130. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +11 -0
  131. package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +12 -0
  132. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +6 -0
  133. package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.js +1 -0
  134. package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +6 -0
  135. package/esm/data_adapters/BaseAdapter/RegionsAdapter.js +1 -0
  136. package/esm/data_adapters/BaseAdapter/index.d.ts +13 -0
  137. package/esm/data_adapters/BaseAdapter/index.js +5 -0
  138. package/esm/data_adapters/BaseAdapter/stats.d.ts +10 -0
  139. package/esm/data_adapters/BaseAdapter/stats.js +48 -0
  140. package/esm/data_adapters/BaseAdapter/types.d.ts +23 -0
  141. package/esm/data_adapters/BaseAdapter/types.js +1 -0
  142. package/esm/data_adapters/BaseAdapter/util.d.ts +12 -0
  143. package/esm/data_adapters/BaseAdapter/util.js +15 -0
  144. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +6 -0
  145. package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +28 -0
  146. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +9 -0
  147. package/esm/data_adapters/CytobandAdapter/configSchema.js +24 -0
  148. package/esm/data_adapters/CytobandAdapter/index.d.ts +2 -0
  149. package/esm/data_adapters/CytobandAdapter/index.js +12 -0
  150. package/esm/data_adapters/dataAdapterCache.d.ts +14 -0
  151. package/esm/data_adapters/dataAdapterCache.js +54 -0
  152. package/esm/data_adapters/util.js +4 -0
  153. package/esm/pluggableElementTypes/AdapterType.d.ts +25 -0
  154. package/esm/pluggableElementTypes/AdapterType.js +17 -0
  155. package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
  156. package/esm/pluggableElementTypes/AddTrackWorkflowType.js +10 -0
  157. package/esm/pluggableElementTypes/ConnectionType.d.ts +20 -0
  158. package/esm/pluggableElementTypes/ConnectionType.js +16 -0
  159. package/esm/pluggableElementTypes/DisplayType.d.ts +30 -0
  160. package/esm/pluggableElementTypes/DisplayType.js +20 -0
  161. package/esm/pluggableElementTypes/GlyphType.d.ts +43 -0
  162. package/esm/pluggableElementTypes/GlyphType.js +18 -0
  163. package/esm/pluggableElementTypes/InternetAccountType.d.ts +12 -0
  164. package/esm/pluggableElementTypes/InternetAccountType.js +10 -0
  165. package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
  166. package/esm/pluggableElementTypes/RpcMethodType.d.ts +19 -0
  167. package/esm/pluggableElementTypes/RpcMethodType.js +88 -0
  168. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +11 -0
  169. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +28 -0
  170. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +18 -0
  171. package/esm/pluggableElementTypes/TextSearchAdapterType.js +15 -0
  172. package/esm/pluggableElementTypes/TrackType.d.ts +16 -0
  173. package/esm/pluggableElementTypes/TrackType.js +14 -0
  174. package/esm/pluggableElementTypes/ViewType.d.ts +29 -0
  175. package/esm/pluggableElementTypes/ViewType.js +18 -0
  176. package/esm/pluggableElementTypes/WidgetType.d.ts +27 -0
  177. package/esm/pluggableElementTypes/WidgetType.js +18 -0
  178. package/esm/pluggableElementTypes/index.d.ts +27 -0
  179. package/esm/pluggableElementTypes/index.js +14 -0
  180. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +29 -0
  181. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +35 -0
  182. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +180 -0
  183. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +104 -0
  184. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +74 -0
  185. package/esm/pluggableElementTypes/models/BaseTrackModel.js +203 -0
  186. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +52 -0
  187. package/esm/pluggableElementTypes/models/BaseViewModel.js +42 -0
  188. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +86 -0
  189. package/esm/pluggableElementTypes/models/InternetAccountModel.js +151 -0
  190. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +16 -0
  191. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -0
  192. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +27 -0
  193. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +32 -0
  194. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +87 -0
  195. package/esm/pluggableElementTypes/models/baseTrackConfig.js +134 -0
  196. package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +11 -0
  197. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +158 -0
  198. package/esm/pluggableElementTypes/models/index.d.ts +14 -0
  199. package/esm/pluggableElementTypes/models/index.js +8 -0
  200. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.d.ts +4 -0
  201. package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +9 -0
  202. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +5 -0
  203. package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +17 -0
  204. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +7 -0
  205. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +108 -0
  206. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +5 -0
  207. package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +91 -0
  208. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +11 -0
  209. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.js +1 -0
  210. package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +52 -0
  211. package/esm/pluggableElementTypes/renderers/BoxRendererType.js +78 -0
  212. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +4 -0
  213. package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +4 -0
  214. package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +58 -0
  215. package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +77 -0
  216. package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +31 -0
  217. package/esm/pluggableElementTypes/renderers/LayoutSession.js +37 -0
  218. package/esm/pluggableElementTypes/renderers/RendererType.d.ts +28 -0
  219. package/esm/pluggableElementTypes/renderers/RendererType.js +20 -0
  220. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +57 -0
  221. package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +113 -0
  222. package/esm/pluggableElementTypes/renderers/index.d.ts +6 -0
  223. package/esm/pluggableElementTypes/renderers/index.js +6 -0
  224. package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +30 -0
  225. package/esm/pluggableElementTypes/renderers/util.d.ts +3 -0
  226. package/esm/pluggableElementTypes/renderers/util.js +14 -0
  227. package/esm/rpc/BaseRpcDriver.d.ts +40 -0
  228. package/esm/rpc/BaseRpcDriver.js +116 -0
  229. package/esm/rpc/MainThreadRpcDriver.d.ts +14 -0
  230. package/esm/rpc/MainThreadRpcDriver.js +33 -0
  231. package/esm/rpc/RpcManager.d.ts +35 -0
  232. package/esm/rpc/RpcManager.js +63 -0
  233. package/esm/rpc/WebWorkerRpcDriver.d.ts +31 -0
  234. package/esm/rpc/WebWorkerRpcDriver.js +77 -0
  235. package/esm/rpc/baseRpcConfig.d.ts +8 -0
  236. package/esm/rpc/baseRpcConfig.js +10 -0
  237. package/esm/rpc/configSchema.d.ts +9 -0
  238. package/esm/rpc/configSchema.js +22 -0
  239. package/esm/rpc/coreRpcMethods.d.ts +12 -0
  240. package/esm/rpc/coreRpcMethods.js +12 -0
  241. package/esm/rpc/mainThreadRpcConfig.d.ts +8 -0
  242. package/esm/rpc/mainThreadRpcConfig.js +8 -0
  243. package/esm/rpc/methods/CoreFreeResources.d.ts +6 -0
  244. package/esm/rpc/methods/CoreFreeResources.js +14 -0
  245. package/esm/rpc/methods/CoreGetExportData.d.ts +19 -0
  246. package/esm/rpc/methods/CoreGetExportData.js +18 -0
  247. package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +17 -0
  248. package/esm/rpc/methods/CoreGetFeatureDensityStats.js +25 -0
  249. package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +11 -0
  250. package/esm/rpc/methods/CoreGetFeatureDetails.js +24 -0
  251. package/esm/rpc/methods/CoreGetFeatures.d.ts +18 -0
  252. package/esm/rpc/methods/CoreGetFeatures.js +31 -0
  253. package/esm/rpc/methods/CoreGetFileInfo.d.ts +9 -0
  254. package/esm/rpc/methods/CoreGetFileInfo.js +15 -0
  255. package/esm/rpc/methods/CoreGetMetadata.d.ts +9 -0
  256. package/esm/rpc/methods/CoreGetMetadata.js +15 -0
  257. package/esm/rpc/methods/CoreGetRefNames.d.ts +10 -0
  258. package/esm/rpc/methods/CoreGetRefNames.js +19 -0
  259. package/esm/rpc/methods/CoreGetRegions.d.ts +8 -0
  260. package/esm/rpc/methods/CoreGetRegions.js +15 -0
  261. package/esm/rpc/methods/CoreGetSequence.d.ts +13 -0
  262. package/esm/rpc/methods/CoreGetSequence.js +17 -0
  263. package/esm/rpc/methods/CoreRender.d.ts +14 -0
  264. package/esm/rpc/methods/CoreRender.js +35 -0
  265. package/esm/rpc/methods/CoreSaveFeatureData.d.ts +16 -0
  266. package/esm/rpc/methods/CoreSaveFeatureData.js +32 -0
  267. package/esm/rpc/methods/util.d.ts +15 -0
  268. package/esm/rpc/methods/util.js +7 -0
  269. package/esm/rpc/webWorkerRpcConfig.d.ts +8 -0
  270. package/esm/rpc/webWorkerRpcConfig.js +8 -0
  271. package/esm/ui/AppLogo.d.ts +7 -0
  272. package/esm/ui/AppLogo.js +10 -0
  273. package/esm/ui/AssemblySelector.d.ts +13 -0
  274. package/esm/ui/AssemblySelector.js +39 -0
  275. package/esm/ui/BaseTooltip.d.ts +8 -0
  276. package/esm/ui/BaseTooltip.js +42 -0
  277. package/esm/ui/CascadingMenu.d.ts +30 -0
  278. package/esm/ui/CascadingMenu.js +48 -0
  279. package/esm/ui/CascadingMenuButton.d.ts +26 -0
  280. package/esm/ui/CascadingMenuButton.js +24 -0
  281. package/esm/ui/CascadingMenuHelpDialog.d.ts +5 -0
  282. package/esm/ui/CascadingMenuHelpDialog.js +10 -0
  283. package/esm/ui/CascadingMenuHelpIconButton.d.ts +5 -0
  284. package/esm/ui/CascadingMenuHelpIconButton.js +15 -0
  285. package/esm/ui/ColorPicker.js +62 -0
  286. package/esm/ui/ConfirmDialog.d.ts +10 -0
  287. package/esm/ui/ConfirmDialog.js +13 -0
  288. package/esm/ui/DataGridFlexContainer.d.ts +5 -0
  289. package/esm/ui/DataGridFlexContainer.js +12 -0
  290. package/esm/ui/Dialog.d.ts +7 -0
  291. package/esm/ui/Dialog.js +45 -0
  292. package/esm/ui/DraggableDialog.js +27 -0
  293. package/esm/ui/DropDownMenu.d.ts +6 -0
  294. package/esm/ui/DropDownMenu.js +24 -0
  295. package/esm/ui/EditableTypography.js +60 -0
  296. package/esm/ui/ErrorBoundary.d.ts +17 -0
  297. package/esm/ui/ErrorBoundary.js +16 -0
  298. package/esm/ui/ErrorMessage.js +56 -0
  299. package/esm/ui/ErrorMessageStackTraceContents.d.ts +4 -0
  300. package/esm/ui/ErrorMessageStackTraceContents.js +25 -0
  301. package/esm/ui/ErrorMessageStackTraceDialog.js +108 -0
  302. package/esm/ui/ExternalLink.js +7 -0
  303. package/esm/ui/FactoryResetDialog.js +18 -0
  304. package/esm/ui/FatalErrorDialog.js +18 -0
  305. package/esm/ui/FileSelector/FileSelector.d.ts +11 -0
  306. package/esm/ui/FileSelector/FileSelector.js +52 -0
  307. package/esm/ui/FileSelector/LocalFileChooser.d.ts +6 -0
  308. package/esm/ui/FileSelector/LocalFileChooser.js +39 -0
  309. package/esm/ui/FileSelector/LocationInput.d.ts +9 -0
  310. package/esm/ui/FileSelector/LocationInput.js +15 -0
  311. package/esm/ui/FileSelector/SourceTypeSelector.d.ts +9 -0
  312. package/esm/ui/FileSelector/SourceTypeSelector.js +38 -0
  313. package/esm/ui/FileSelector/UrlChooser.d.ts +8 -0
  314. package/esm/ui/FileSelector/UrlChooser.js +17 -0
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  671. package/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +0 -27
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  687. package/pluggableElementTypes/renderers/RendererType.d.ts +0 -25
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  689. package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.d.ts +0 -9
  690. package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.js +0 -9
  691. package/pluggableElementTypes/renderers/ServerSideRenderedContent.d.ts +0 -6
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  695. package/pluggableElementTypes/renderers/index.d.ts +0 -7
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  698. package/rpc/BaseRpcDriver.d.ts +0 -43
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  700. package/rpc/MainThreadRpcDriver.d.ts +0 -14
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  712. package/rpc/mainThreadRpcConfig.d.ts +0 -8
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  714. package/rpc/methods/CoreFreeResources.d.ts +0 -6
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  716. package/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
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  724. package/rpc/methods/CoreGetMetadata.d.ts +0 -9
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  726. package/rpc/methods/CoreGetRefNames.d.ts +0 -9
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  731. package/rpc/methods/util.js +0 -9
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  734. package/stories/JBrowseCore.stories.d.ts +0 -5
  735. package/stories/JBrowseCore.stories.js +0 -10
  736. package/stories/examples/WithSequencePanel.d.ts +0 -6
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  738. package/stories/examples/index.d.ts +0 -1
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  742. package/tsconfig.build.tsbuildinfo +0 -1
  743. package/ui/AppLogo.d.ts +0 -7
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  759. package/ui/DropDownMenu.d.ts +0 -8
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  766. package/ui/ExternalLink.js +0 -13
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  769. package/ui/FileSelector/FileSelector.d.ts +0 -11
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  779. package/ui/LoadingEllipses.d.ts +0 -6
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  781. package/ui/Logo.js +0 -46
  782. package/ui/Menu.d.ts +0 -53
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  784. package/ui/MenuButton.d.ts +0 -10
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  786. package/ui/PrerenderedCanvas.d.ts +0 -10
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  788. package/ui/RedErrorMessageBox.js +0 -19
  789. package/ui/ResizeHandle.js +0 -72
  790. package/ui/ReturnToImportFormDialog.js +0 -18
  791. package/ui/SanitizedHTML.js +0 -64
  792. package/ui/Snackbar.d.ts +0 -10
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  799. package/ui/hooks.d.ts +0 -66
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  810. package/util/Base1DViewModel.d.ts +0 -61
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  817. package/util/analytics.js +0 -86
  818. package/util/blobToDataURL.js +0 -17
  819. package/util/blockTypes.d.ts +0 -58
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  827. package/util/color/cssColorsLevel4.js +0 -160
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  836. package/util/idMaker.js +0 -24
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  890. package/util/when.js +0 -5
  891. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/ArrayValue.d.ts +0 -0
  892. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/BasicValue.d.ts +0 -0
  893. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/DataGridDetails.d.ts +0 -0
  894. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/FieldName.d.ts +0 -0
  895. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/SimpleField.d.ts +0 -0
  896. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/UriField.d.ts +0 -0
  897. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/util.d.ts +0 -0
  898. /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +0 -0
  899. /package/{PhasedScheduler.d.ts → esm/PhasedScheduler.d.ts} +0 -0
  900. /package/{ReExports → esm/ReExports}/BaseFeatureDetails.d.ts +0 -0
  901. /package/{ReExports → esm/ReExports}/DataGrid.d.ts +0 -0
  902. /package/{ReExports → esm/ReExports}/MuiDataGridReExports.d.ts +0 -0
  903. /package/{ReExports → esm/ReExports}/lazify.d.ts +0 -0
  904. /package/{ReExports → esm/ReExports}/list.d.ts +0 -0
  905. /package/{ReExports → esm/ReExports}/modules.d.ts +0 -0
  906. /package/{data_adapters → esm/data_adapters}/util.d.ts +0 -0
  907. /package/{pluggableElementTypes → esm/pluggableElementTypes}/PluggableElementBase.d.ts +0 -0
  908. /package/{pluggableElementTypes → esm/pluggableElementTypes}/renderers/util/serializableFilterChain.d.ts +0 -0
  909. /package/{ui → esm/ui}/ColorPicker.d.ts +0 -0
  910. /package/{ui → esm/ui}/DraggableDialog.d.ts +0 -0
  911. /package/{ui → esm/ui}/EditableTypography.d.ts +0 -0
  912. /package/{ui → esm/ui}/ErrorMessage.d.ts +0 -0
  913. /package/{ui → esm/ui}/ErrorMessageStackTraceDialog.d.ts +0 -0
  914. /package/{ui → esm/ui}/ExternalLink.d.ts +0 -0
  915. /package/{ui → esm/ui}/FactoryResetDialog.d.ts +0 -0
  916. /package/{ui → esm/ui}/FatalErrorDialog.d.ts +0 -0
  917. /package/{ui → esm/ui}/HoverMenu.d.ts +0 -0
  918. /package/{ui → esm/ui}/Icons.d.ts +0 -0
  919. /package/{ui → esm/ui}/Logo.d.ts +0 -0
  920. /package/{ui → esm/ui}/RedErrorMessageBox.d.ts +0 -0
  921. /package/{ui → esm/ui}/ResizeHandle.d.ts +0 -0
  922. /package/{ui → esm/ui}/ReturnToImportFormDialog.d.ts +0 -0
  923. /package/{ui → esm/ui}/SanitizedHTML.d.ts +0 -0
  924. /package/{ui → esm/ui}/colors.d.ts +0 -0
  925. /package/{ui → esm/ui}/useEvent.d.ts +0 -0
  926. /package/{util → esm/util}/aborting.d.ts +0 -0
  927. /package/{util → esm/util}/analytics.d.ts +0 -0
  928. /package/{util → esm/util}/blobToDataURL.d.ts +0 -0
  929. /package/{util → esm/util}/color/cssColorsLevel4.d.ts +0 -0
  930. /package/{util → esm/util}/dedupe.d.ts +0 -0
  931. /package/{util → esm/util}/formatFastaStrings.d.ts +0 -0
  932. /package/{util → esm/util}/idMaker.d.ts +0 -0
  933. /package/{util → esm/util}/io/RemoteFileWithRangeCache.d.ts +0 -0
  934. /package/{util → esm/util}/jexlStrings.d.ts +0 -0
  935. /package/{util → esm/util}/layouts/SceneGraph.d.ts +0 -0
  936. /package/{util → esm/util}/nextTick.d.ts +0 -0
  937. /package/{util → esm/util}/parseLineByLine.d.ts +0 -0
  938. /package/{util → esm/util}/range.d.ts +0 -0
  939. /package/{util → esm/util}/useMeasure.d.ts +0 -0
  940. /package/{util → esm/util}/when.d.ts +0 -0
@@ -1,8 +0,0 @@
1
- import type { SequenceFeatureDetailsModel } from './model';
2
- import type { SimpleFeatureSerialized } from '../../util';
3
- import type { SeqState } from '../util';
4
- export interface SequencePanelProps {
5
- sequence: SeqState;
6
- feature: SimpleFeatureSerialized;
7
- model: SequenceFeatureDetailsModel;
8
- }
@@ -1,2 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
@@ -1,17 +0,0 @@
1
- export declare const intronColor: undefined;
2
- export declare const utrColor = "rgb(200,240,240)";
3
- export declare const proteinColor = "rgb(220,160,220)";
4
- export declare const cdsColor = "rgb(220,220,180)";
5
- export declare const updownstreamColor = "rgba(250,200,200)";
6
- export declare const genomeColor = "rgb(200,280,200)";
7
- export declare function splitString({ str, charactersPerRow, showCoordinates, currRemainder, splitSize, }: {
8
- str: string;
9
- charactersPerRow: number;
10
- showCoordinates: boolean;
11
- currRemainder?: number;
12
- splitStart?: number;
13
- splitSize?: number;
14
- }): {
15
- segments: any[];
16
- remainder: number;
17
- };
@@ -1,49 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
4
- exports.splitString = splitString;
5
- exports.intronColor = undefined;
6
- exports.utrColor = 'rgb(200,240,240)';
7
- exports.proteinColor = 'rgb(220,160,220)';
8
- exports.cdsColor = 'rgb(220,220,180)';
9
- exports.updownstreamColor = 'rgba(250,200,200)';
10
- exports.genomeColor = 'rgb(200,280,200)';
11
- function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0, splitSize = 10, }) {
12
- var _a;
13
- const numChunks = Math.ceil(str.length / charactersPerRow);
14
- const chunks = new Array(numChunks);
15
- let splitStart = currRemainder % 10;
16
- let iter = 0;
17
- let offset = 0;
18
- for (; iter < numChunks + 1; ++iter) {
19
- const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow;
20
- const r = str.slice(offset, offset + inc);
21
- if (!r) {
22
- break;
23
- }
24
- if (showCoordinates) {
25
- let res = '';
26
- for (let i = 0, j = splitStart; i < r.length; i++, j++) {
27
- if (j % splitSize === 0) {
28
- res += ' ';
29
- j = 0;
30
- }
31
- res += r[i];
32
- }
33
- if (res) {
34
- chunks[iter] = res;
35
- }
36
- }
37
- else {
38
- chunks[iter] = r;
39
- }
40
- splitStart = 0;
41
- offset += inc;
42
- }
43
- return {
44
- segments: chunks,
45
- remainder: ((((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
46
- (iter < 2 ? currRemainder : 0)) %
47
- charactersPerRow,
48
- };
49
- }
@@ -1,2 +0,0 @@
1
- declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
2
- export { configSchema };
@@ -1,6 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.configSchema = void 0;
4
- const configuration_1 = require("../configuration");
5
- const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
6
- exports.configSchema = configSchema;
@@ -1,2 +0,0 @@
1
- export { configSchema } from './configSchema';
2
- export { stateModelFactory } from './stateModelFactory';
@@ -1,7 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.stateModelFactory = exports.configSchema = void 0;
4
- var configSchema_1 = require("./configSchema");
5
- Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return configSchema_1.configSchema; } });
6
- var stateModelFactory_1 = require("./stateModelFactory");
7
- Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return stateModelFactory_1.stateModelFactory; } });
@@ -1,101 +0,0 @@
1
- import type PluginManager from '../PluginManager';
2
- import type { SimpleFeatureSerialized } from '../util';
3
- import type { MaybeSerializedFeat } from './types';
4
- import type { Instance } from 'mobx-state-tree';
5
- export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
6
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
7
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
8
- featureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
9
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
10
- unformattedFeatureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
11
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
12
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
13
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
14
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
15
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
16
- sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
17
- showCoordinatesSetting: string;
18
- intronBp: number;
19
- upDownBp: number;
20
- upperCaseCDS: boolean;
21
- charactersPerRow: number;
22
- feature: SimpleFeatureSerialized | undefined;
23
- mode: string;
24
- } & {
25
- setFeature(f: SimpleFeatureSerialized): void;
26
- setUpDownBp(f: number): void;
27
- setIntronBp(f: number): void;
28
- setUpperCaseCDS(f: boolean): void;
29
- setShowCoordinates(f: "none" | "relative" | "genomic"): void;
30
- setMode(mode: string): void;
31
- } & {
32
- readonly showCoordinates: boolean;
33
- readonly showGenomicCoordsOption: boolean;
34
- readonly hasCDS: boolean | undefined;
35
- readonly hasExon: boolean | undefined;
36
- readonly hasExonOrCDS: boolean | undefined;
37
- } & {
38
- afterAttach(): void;
39
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
40
- descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
41
- }, {
42
- error: unknown;
43
- } & {
44
- setFeatureData(featureData: SimpleFeatureSerialized): void;
45
- clearFeatureData(): void;
46
- setFormattedData(feat: SimpleFeatureSerialized): void;
47
- setExtra(type?: string, trackId?: string, maxDepth?: number): void;
48
- setError(e: unknown): void;
49
- } & {
50
- afterCreate(): void;
51
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
52
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
53
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
54
- featureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
55
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
56
- unformattedFeatureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
57
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
58
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
59
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
60
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
61
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
62
- sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
63
- showCoordinatesSetting: string;
64
- intronBp: number;
65
- upDownBp: number;
66
- upperCaseCDS: boolean;
67
- charactersPerRow: number;
68
- feature: SimpleFeatureSerialized | undefined;
69
- mode: string;
70
- } & {
71
- setFeature(f: SimpleFeatureSerialized): void;
72
- setUpDownBp(f: number): void;
73
- setIntronBp(f: number): void;
74
- setUpperCaseCDS(f: boolean): void;
75
- setShowCoordinates(f: "none" | "relative" | "genomic"): void;
76
- setMode(mode: string): void;
77
- } & {
78
- readonly showCoordinates: boolean;
79
- readonly showGenomicCoordsOption: boolean;
80
- readonly hasCDS: boolean | undefined;
81
- readonly hasExon: boolean | undefined;
82
- readonly hasExonOrCDS: boolean | undefined;
83
- } & {
84
- afterAttach(): void;
85
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
86
- descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
87
- }>>, {
88
- type: "BaseFeatureWidget";
89
- id: string;
90
- track: import("mobx-state-tree").ReferenceIdentifier | undefined;
91
- view: import("mobx-state-tree").ReferenceIdentifier | undefined;
92
- trackId: string | undefined;
93
- trackType: string | undefined;
94
- maxDepth: number | undefined;
95
- sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
96
- formattedFields: any;
97
- descriptions: Record<string, unknown> | undefined;
98
- finalizedFeatureData: any;
99
- }>;
100
- export type BaseFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
101
- export type BaseFeatureWidgetModel = Instance<BaseFeatureWidgetStateModel>;
@@ -1,99 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.stateModelFactory = stateModelFactory;
4
- const mobx_1 = require("mobx");
5
- const mobx_state_tree_1 = require("mobx-state-tree");
6
- const configuration_1 = require("../configuration");
7
- const util_1 = require("../util");
8
- const model_1 = require("./SequenceFeatureDetails/model");
9
- const util_2 = require("./util");
10
- const mst_1 = require("../util/types/mst");
11
- function stateModelFactory(pluginManager) {
12
- return mobx_state_tree_1.types
13
- .model('BaseFeatureWidget', {
14
- id: mst_1.ElementId,
15
- type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
16
- featureData: mobx_state_tree_1.types.frozen(),
17
- formattedFields: mobx_state_tree_1.types.frozen(),
18
- unformattedFeatureData: mobx_state_tree_1.types.frozen(),
19
- view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
20
- track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
21
- trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
22
- trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
23
- maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
24
- sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
25
- descriptions: mobx_state_tree_1.types.frozen(),
26
- })
27
- .volatile(() => ({
28
- error: undefined,
29
- }))
30
- .actions(self => ({
31
- setFeatureData(featureData) {
32
- self.unformattedFeatureData = featureData;
33
- },
34
- clearFeatureData() {
35
- self.featureData = undefined;
36
- },
37
- setFormattedData(feat) {
38
- self.featureData = feat;
39
- },
40
- setExtra(type, trackId, maxDepth) {
41
- self.trackId = trackId;
42
- self.trackType = type;
43
- self.maxDepth = maxDepth;
44
- },
45
- setError(e) {
46
- self.error = e;
47
- },
48
- }))
49
- .actions(self => ({
50
- afterCreate() {
51
- (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
52
- try {
53
- const { unformattedFeatureData, track } = self;
54
- const session = (0, util_1.getSession)(self);
55
- if (track) {
56
- self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
57
- }
58
- if (unformattedFeatureData) {
59
- const feature = structuredClone(unformattedFeatureData);
60
- const combine = (arg2, feature) => ({
61
- ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
62
- ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
63
- });
64
- if (track) {
65
- feature.__jbrowsefmt = combine('feature', feature);
66
- (0, util_2.formatSubfeatures)(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
67
- sub.__jbrowsefmt = combine('subfeatures', sub);
68
- });
69
- }
70
- self.setFormattedData(feature);
71
- }
72
- }
73
- catch (e) {
74
- console.error(e);
75
- self.setError(e);
76
- }
77
- }));
78
- },
79
- }))
80
- .preProcessSnapshot(snap => {
81
- const { featureData, finalizedFeatureData, ...rest } = snap;
82
- return {
83
- unformattedFeatureData: featureData,
84
- featureData: finalizedFeatureData,
85
- ...rest,
86
- };
87
- })
88
- .postProcessSnapshot(snap => {
89
- const { unformattedFeatureData, featureData, ...rest } = snap;
90
- const s2 = JSON.stringify(featureData, (_, v) => v === undefined ? null : v);
91
- const featureTooLargeToBeSerialized = !s2 || s2.length > 2000000;
92
- return {
93
- finalizedFeatureData: featureTooLargeToBeSerialized
94
- ? undefined
95
- : JSON.parse(s2),
96
- ...rest,
97
- };
98
- });
99
- }
@@ -1,22 +0,0 @@
1
- import type React from 'react';
2
- import type { BaseFeatureWidgetModel } from './stateModelFactory';
3
- import type { SimpleFeatureSerialized } from '../util/simpleFeature';
4
- export interface Descriptors {
5
- [key: string]: React.ReactNode | Descriptors;
6
- }
7
- export interface BaseProps extends BaseCardProps {
8
- feature: SimpleFeatureSerialized;
9
- formatter?: (val: unknown, key: string) => React.ReactNode;
10
- descriptions?: Descriptors;
11
- model?: BaseFeatureWidgetModel;
12
- }
13
- export interface BaseCardProps {
14
- title?: string;
15
- defaultExpanded?: boolean;
16
- children?: React.ReactNode;
17
- }
18
- export interface SerializedFeat {
19
- [key: string]: unknown;
20
- subfeatures?: Record<string, unknown>[];
21
- }
22
- export type MaybeSerializedFeat = SimpleFeatureSerialized | undefined;
@@ -1,2 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
@@ -1,48 +0,0 @@
1
- import type { SimpleFeatureSerialized } from '../util';
2
- import type { SerializedFeat } from './types';
3
- export interface Feat {
4
- start: number;
5
- end: number;
6
- type?: string;
7
- name?: string;
8
- id?: string;
9
- }
10
- export interface ParentFeat extends Feat {
11
- uniqueId: string;
12
- strand?: number;
13
- refName: string;
14
- subfeatures?: Feat[];
15
- parentId?: string;
16
- }
17
- export interface SeqState {
18
- seq: string;
19
- upstream?: string;
20
- downstream?: string;
21
- }
22
- export interface ErrorState {
23
- error: string;
24
- }
25
- export declare function stitch(subfeats: Feat[], sequence: string): string;
26
- export declare function dedupe(list: Feat[]): Feat[];
27
- export declare function revlist(list: Feat[], seqlen: number): {
28
- start: number;
29
- end: number;
30
- type?: string;
31
- name?: string;
32
- id?: string;
33
- }[];
34
- export declare function calculateUTRs(cds: Feat[], exons: Feat[]): {
35
- type: string;
36
- start: number;
37
- end: number;
38
- name?: string;
39
- id?: string;
40
- }[];
41
- export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
42
- type: string;
43
- start: number;
44
- end: number;
45
- }[];
46
- export declare function ellipses(slug: string): string;
47
- export declare function replaceUndefinedWithNull(obj: SimpleFeatureSerialized): any;
48
- export declare function formatSubfeatures(obj: SerializedFeat, depth: number, parse: (obj: Record<string, unknown>) => void, currentDepth?: number, returnObj?: Record<string, unknown>): void;
@@ -1,77 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.stitch = stitch;
4
- exports.dedupe = dedupe;
5
- exports.revlist = revlist;
6
- exports.calculateUTRs = calculateUTRs;
7
- exports.calculateUTRs2 = calculateUTRs2;
8
- exports.ellipses = ellipses;
9
- exports.replaceUndefinedWithNull = replaceUndefinedWithNull;
10
- exports.formatSubfeatures = formatSubfeatures;
11
- function stitch(subfeats, sequence) {
12
- return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
13
- }
14
- function getItemId(feat) {
15
- return `${feat.start}-${feat.end}`;
16
- }
17
- function dedupe(list) {
18
- return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
19
- }
20
- function revlist(list, seqlen) {
21
- return list
22
- .map(sub => ({
23
- ...sub,
24
- start: seqlen - sub.end,
25
- end: seqlen - sub.start,
26
- }))
27
- .sort((a, b) => a.start - b.start);
28
- }
29
- function calculateUTRs(cds, exons) {
30
- if (!cds.length) {
31
- return [];
32
- }
33
- const firstCds = cds.at(0);
34
- const lastCds = cds.at(-1);
35
- const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
36
- const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
37
- const lastCdsExon = exons[lastCdsIdx];
38
- const firstCdsExon = exons[firstCdsIdx];
39
- const fiveUTRs = [
40
- ...exons.slice(0, firstCdsIdx),
41
- { start: firstCdsExon.start, end: firstCds.start },
42
- ].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
43
- const threeUTRs = [
44
- { start: lastCds.end, end: lastCdsExon.end },
45
- ...exons.slice(lastCdsIdx + 1),
46
- ].map(elt => ({ ...elt, type: 'three_prime_UTR' }));
47
- return [...fiveUTRs, ...threeUTRs];
48
- }
49
- function calculateUTRs2(cds, parentFeat) {
50
- if (!cds.length) {
51
- return [];
52
- }
53
- const firstCds = cds.at(0);
54
- const lastCds = cds.at(-1);
55
- const fiveUTRs = [{ start: parentFeat.start, end: firstCds.start }].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
56
- const threeUTRs = [{ start: lastCds.end, end: parentFeat.end }].map(elt => ({
57
- ...elt,
58
- type: 'three_prime_UTR',
59
- }));
60
- return [...fiveUTRs, ...threeUTRs];
61
- }
62
- function ellipses(slug) {
63
- return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
64
- }
65
- function replaceUndefinedWithNull(obj) {
66
- return JSON.parse(JSON.stringify(obj, (_, v) => (v === undefined ? null : v)));
67
- }
68
- function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
69
- var _a;
70
- if (depth <= currentDepth) {
71
- return;
72
- }
73
- (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
74
- formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
75
- parse(sub);
76
- });
77
- }
package/CorePlugin.d.ts DELETED
@@ -1,6 +0,0 @@
1
- import Plugin from './Plugin';
2
- import type PluginManager from './PluginManager';
3
- export default class CorePlugin extends Plugin {
4
- name: string;
5
- install(pluginManager: PluginManager): void;
6
- }
package/CorePlugin.js DELETED
@@ -1,66 +0,0 @@
1
- "use strict";
2
- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
3
- if (k2 === undefined) k2 = k;
4
- var desc = Object.getOwnPropertyDescriptor(m, k);
5
- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
6
- desc = { enumerable: true, get: function() { return m[k]; } };
7
- }
8
- Object.defineProperty(o, k2, desc);
9
- }) : (function(o, m, k, k2) {
10
- if (k2 === undefined) k2 = k;
11
- o[k2] = m[k];
12
- }));
13
- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
14
- Object.defineProperty(o, "default", { enumerable: true, value: v });
15
- }) : function(o, v) {
16
- o["default"] = v;
17
- });
18
- var __importStar = (this && this.__importStar) || (function () {
19
- var ownKeys = function(o) {
20
- ownKeys = Object.getOwnPropertyNames || function (o) {
21
- var ar = [];
22
- for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
23
- return ar;
24
- };
25
- return ownKeys(o);
26
- };
27
- return function (mod) {
28
- if (mod && mod.__esModule) return mod;
29
- var result = {};
30
- if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
31
- __setModuleDefault(result, mod);
32
- return result;
33
- };
34
- })();
35
- var __importDefault = (this && this.__importDefault) || function (mod) {
36
- return (mod && mod.__esModule) ? mod : { "default": mod };
37
- };
38
- Object.defineProperty(exports, "__esModule", { value: true });
39
- const react_1 = require("react");
40
- const BaseFeatureWidget_1 = require("./BaseFeatureWidget");
41
- const Plugin_1 = __importDefault(require("./Plugin"));
42
- const CytobandAdapter_1 = __importDefault(require("./data_adapters/CytobandAdapter"));
43
- const WidgetType_1 = __importDefault(require("./pluggableElementTypes/WidgetType"));
44
- const coreRpcMethods = __importStar(require("./rpc/coreRpcMethods"));
45
- class CorePlugin extends Plugin_1.default {
46
- constructor() {
47
- super(...arguments);
48
- this.name = 'CorePlugin';
49
- }
50
- install(pluginManager) {
51
- for (const RpcMethod of Object.values(coreRpcMethods)) {
52
- pluginManager.addRpcMethod(() => new RpcMethod(pluginManager));
53
- }
54
- (0, CytobandAdapter_1.default)(pluginManager);
55
- pluginManager.addWidgetType(() => {
56
- return new WidgetType_1.default({
57
- name: 'BaseFeatureWidget',
58
- heading: 'Feature details',
59
- configSchema: BaseFeatureWidget_1.configSchema,
60
- stateModel: (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager),
61
- ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BaseFeatureWidget/BaseFeatureDetail')))),
62
- });
63
- });
64
- }
65
- }
66
- exports.default = CorePlugin;
@@ -1,28 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- class PhasedScheduler {
4
- constructor(...phaseOrder) {
5
- this.phaseCallbacks = new Map();
6
- this.phaseOrder = [];
7
- this.phaseOrder = phaseOrder;
8
- }
9
- add(phase, callback) {
10
- if (!this.phaseOrder.includes(phase)) {
11
- throw new Error(`unknown phase ${phase}`);
12
- }
13
- let phaseCallbacks = this.phaseCallbacks.get(phase);
14
- if (!phaseCallbacks) {
15
- phaseCallbacks = [];
16
- this.phaseCallbacks.set(phase, phaseCallbacks);
17
- }
18
- phaseCallbacks.push(callback);
19
- }
20
- run() {
21
- for (const phaseName of this.phaseOrder) {
22
- for (const callback of this.phaseCallbacks.get(phaseName) || []) {
23
- callback();
24
- }
25
- }
26
- }
27
- }
28
- exports.default = PhasedScheduler;
package/Plugin.d.ts DELETED
@@ -1,13 +0,0 @@
1
- import type PluginManager from './PluginManager';
2
- import type { AnyConfigurationSchemaType } from './configuration';
3
- export default abstract class Plugin {
4
- abstract name: string;
5
- url?: string;
6
- version?: string;
7
- install(_pluginManager: PluginManager): void;
8
- configure(_pluginManager: PluginManager): void;
9
- configurationSchema?: AnyConfigurationSchemaType;
10
- configurationSchemaUnnamespaced?: AnyConfigurationSchemaType;
11
- rootConfigurationSchema?: (arg: PluginManager) => Record<string, AnyConfigurationSchemaType>;
12
- }
13
- export type PluginConstructor = new (...args: unknown[]) => Plugin;
package/Plugin.js DELETED
@@ -1,7 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- class Plugin {
4
- install(_pluginManager) { }
5
- configure(_pluginManager) { }
6
- }
7
- exports.default = Plugin;
package/PluginLoader.d.ts DELETED
@@ -1,64 +0,0 @@
1
- import type { PluginConstructor } from './Plugin';
2
- export interface UMDLocPluginDefinition {
3
- umdLoc: {
4
- uri: string;
5
- baseUri?: string;
6
- };
7
- name: string;
8
- }
9
- export interface UMDUrlPluginDefinition {
10
- umdUrl: string;
11
- name: string;
12
- }
13
- export interface LegacyUMDPluginDefinition {
14
- url: string;
15
- name: string;
16
- }
17
- type UMDPluginDefinition = UMDLocPluginDefinition | UMDUrlPluginDefinition;
18
- export declare function isUMDPluginDefinition(def: PluginDefinition): def is UMDPluginDefinition | LegacyUMDPluginDefinition;
19
- export interface ESMLocPluginDefinition {
20
- esmLoc: {
21
- uri: string;
22
- baseUri?: string;
23
- };
24
- }
25
- export interface ESMUrlPluginDefinition {
26
- esmUrl: string;
27
- }
28
- export type ESMPluginDefinition = ESMLocPluginDefinition | ESMUrlPluginDefinition;
29
- export declare function isESMPluginDefinition(def: PluginDefinition): def is ESMPluginDefinition;
30
- export interface CJSPluginDefinition {
31
- cjsUrl: string;
32
- }
33
- export declare function isCJSPluginDefinition(def: PluginDefinition): def is CJSPluginDefinition;
34
- export type PluginDefinition = UMDUrlPluginDefinition | UMDLocPluginDefinition | LegacyUMDPluginDefinition | ESMLocPluginDefinition | ESMUrlPluginDefinition | CJSPluginDefinition;
35
- export interface PluginRecord {
36
- plugin: PluginConstructor;
37
- definition: PluginDefinition;
38
- }
39
- export interface LoadedPlugin {
40
- default: PluginConstructor;
41
- }
42
- export declare function pluginDescriptionString(d: PluginDefinition): string;
43
- export declare function pluginUrl(d: PluginDefinition): any;
44
- export default class PluginLoader {
45
- definitions: PluginDefinition[];
46
- fetchESM?: (url: string) => Promise<LoadedPlugin>;
47
- fetchCJS?: (url: string) => Promise<LoadedPlugin>;
48
- constructor(defs?: PluginDefinition[], args?: {
49
- fetchESM?: (url: string) => Promise<LoadedPlugin>;
50
- fetchCJS?: (url: string) => Promise<LoadedPlugin>;
51
- });
52
- loadCJSPlugin(def: CJSPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
53
- loadESMPlugin(def: ESMPluginDefinition, baseUri?: string): Promise<LoadedPlugin>;
54
- loadUMDPlugin(def: UMDPluginDefinition | LegacyUMDPluginDefinition, baseUri?: string): Promise<{
55
- default: PluginConstructor;
56
- }>;
57
- loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
58
- installGlobalReExports(target: WindowOrWorkerGlobalScope): this;
59
- load(baseUri?: string): Promise<{
60
- plugin: PluginConstructor;
61
- definition: PluginDefinition;
62
- }[]>;
63
- }
64
- export {};