@jbrowse/core 5.0.0-beta.7 → 5.0.0-beta.9

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 (379) hide show
  1. package/README.md +427 -130
  2. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +3 -2
  3. package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +5 -3
  4. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +3 -5
  5. package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +8 -9
  6. package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +8 -13
  7. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +2 -1
  8. package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +3 -3
  9. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
  10. package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
  11. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
  12. package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +5 -3
  13. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +1 -0
  14. package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +1 -4
  15. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
  16. package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +53 -0
  17. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -8
  18. package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +0 -16
  19. package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +7 -34
  20. package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
  21. package/esm/BaseFeatureWidget/formatDetails.d.ts +13 -29
  22. package/esm/BaseFeatureWidget/formatDetails.js +46 -79
  23. package/esm/BaseFeatureWidget/index.d.ts +1 -0
  24. package/esm/BaseFeatureWidget/stateModelFactory.d.ts +35 -28
  25. package/esm/BaseFeatureWidget/stateModelFactory.js +94 -102
  26. package/esm/BaseFeatureWidget/types.d.ts +3 -0
  27. package/esm/BaseFeatureWidget/util.d.ts +0 -3
  28. package/esm/BaseFeatureWidget/util.js +0 -17
  29. package/esm/PluginLoader.d.ts +14 -9
  30. package/esm/PluginLoader.js +34 -26
  31. package/esm/PluginManager.d.ts +4 -4
  32. package/esm/PluginManager.js +1 -1
  33. package/esm/ReExports/coreModules.generated.d.ts +2 -0
  34. package/esm/ReExports/coreModules.generated.js +492 -0
  35. package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
  36. package/esm/ReExports/coreWorkerModules.generated.js +453 -0
  37. package/esm/ReExports/frameworkModules.d.ts +2 -0
  38. package/esm/ReExports/frameworkModules.js +67 -0
  39. package/esm/ReExports/frameworkShared.d.ts +12 -0
  40. package/esm/ReExports/frameworkShared.js +16 -0
  41. package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
  42. package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
  43. package/esm/ReExports/list.js +493 -79
  44. package/esm/ReExports/modules.d.ts +1 -1
  45. package/esm/ReExports/modules.js +10 -87
  46. package/esm/ReExports/registry.d.ts +1 -0
  47. package/esm/ReExports/registry.js +23 -5
  48. package/esm/ReExports/uiStub.d.ts +2 -1
  49. package/esm/ReExports/uiStub.js +24 -2
  50. package/esm/ReExports/workerModules.js +8 -12
  51. package/esm/TextSearch/TextSearchManager.d.ts +3 -12
  52. package/esm/TextSearch/TextSearchManager.js +22 -10
  53. package/esm/assemblyManager/assembly.d.ts +10 -14
  54. package/esm/assemblyManager/assembly.js +10 -14
  55. package/esm/assemblyManager/assemblyConfigSchema.d.ts +23 -81
  56. package/esm/assemblyManager/assemblyManager.d.ts +10 -16
  57. package/esm/assemblyManager/assemblyManager.js +7 -10
  58. package/esm/assemblyManager/loadRefNameMap.js +3 -3
  59. package/esm/configuration/configurationSchema.d.ts +75 -31
  60. package/esm/configuration/configurationSchema.js +74 -40
  61. package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
  62. package/esm/configuration/configurationSchemaUnion.js +59 -0
  63. package/esm/configuration/configurationSlot.d.ts +37 -12
  64. package/esm/configuration/configurationSlot.js +83 -22
  65. package/esm/configuration/formatAboutConfigSchema.d.ts +7 -21
  66. package/esm/configuration/formatDetailsConfigSchema.d.ts +11 -37
  67. package/esm/configuration/formatDetailsConfigSchema.js +10 -13
  68. package/esm/configuration/getConf.d.ts +17 -9
  69. package/esm/configuration/getConf.js +52 -7
  70. package/esm/configuration/index.d.ts +11 -4
  71. package/esm/configuration/index.js +7 -4
  72. package/esm/configuration/mergeFormatCallbacks.d.ts +6 -7
  73. package/esm/configuration/mergeFormatCallbacks.js +13 -10
  74. package/esm/configuration/readConfObject.d.ts +2 -22
  75. package/esm/configuration/readConfObject.js +15 -49
  76. package/esm/configuration/requirements.d.ts +37 -0
  77. package/esm/configuration/requirements.js +88 -0
  78. package/esm/configuration/schemaRegistry.d.ts +21 -1
  79. package/esm/configuration/schemaRegistry.js +11 -0
  80. package/esm/configuration/schemaTypes.d.ts +3 -0
  81. package/esm/configuration/schemaTypes.js +10 -0
  82. package/esm/configuration/slotFacade.d.ts +35 -4
  83. package/esm/configuration/slotFacade.js +96 -9
  84. package/esm/configuration/snapshotPreprocess.d.ts +27 -0
  85. package/esm/configuration/snapshotPreprocess.js +102 -0
  86. package/esm/configuration/types.d.ts +161 -22
  87. package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +2 -2
  88. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +11 -2
  89. package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +12 -1
  90. package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +2 -3
  91. package/esm/data_adapters/BaseAdapter/featureDensity.js +2 -3
  92. package/esm/data_adapters/BaseAdapter/index.d.ts +22 -3
  93. package/esm/data_adapters/BaseAdapter/types.d.ts +3 -4
  94. package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
  95. package/esm/data_adapters/BaseAdapter/zoomRange.js +1 -0
  96. package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +9 -11
  97. package/esm/data_adapters/getSequenceSubAdapter.d.ts +1 -3
  98. package/esm/data_adapters/getSequenceSubAdapter.js +1 -3
  99. package/esm/pluggableElementTypes/AdapterType.d.ts +7 -7
  100. package/esm/pluggableElementTypes/RpcMethodType.d.ts +1 -1
  101. package/esm/pluggableElementTypes/RpcMethodType.js +3 -8
  102. package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +1 -2
  103. package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
  104. package/esm/pluggableElementTypes/index.d.ts +1 -1
  105. package/esm/pluggableElementTypes/index.js +1 -1
  106. package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +17 -7
  107. package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +45 -48
  108. package/esm/pluggableElementTypes/models/BaseDisplayModel.js +40 -36
  109. package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +10 -13
  110. package/esm/pluggableElementTypes/models/BaseTrackModel.js +6 -6
  111. package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +37 -17
  112. package/esm/pluggableElementTypes/models/BaseViewModel.js +25 -10
  113. package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +26 -16
  114. package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +1 -1
  115. package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -18
  116. package/esm/pluggableElementTypes/models/baseConnectionConfig.js +5 -5
  117. package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +26 -31
  118. package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +57 -141
  119. package/esm/pluggableElementTypes/models/baseTrackConfig.js +22 -26
  120. package/esm/pluggableElementTypes/models/components/SaveTrackData.js +2 -2
  121. package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +3 -4
  122. package/esm/pluggableElementTypes/models/components/fetchTrackData.js +3 -3
  123. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +15 -7
  124. package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +38 -29
  125. package/esm/pluggableElementTypes/models/index.d.ts +1 -2
  126. package/esm/pluggableElementTypes/models/index.js +1 -2
  127. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +3 -3
  128. package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +4 -4
  129. package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +3 -3
  130. package/esm/rpc/BaseRpcDriver.d.ts +1 -2
  131. package/esm/rpc/BaseRpcDriver.js +23 -30
  132. package/esm/rpc/MainThreadRpcDriver.d.ts +2 -2
  133. package/esm/rpc/MainThreadRpcDriver.js +13 -8
  134. package/esm/rpc/RpcClient.d.ts +17 -6
  135. package/esm/rpc/RpcClient.js +42 -12
  136. package/esm/rpc/RpcManager.d.ts +8 -10
  137. package/esm/rpc/RpcManager.js +1 -1
  138. package/esm/rpc/RpcRegistry.d.ts +8 -2
  139. package/esm/rpc/RpcServer.d.ts +3 -1
  140. package/esm/rpc/RpcServer.js +19 -12
  141. package/esm/rpc/WebWorkerRpcDriver.d.ts +3 -3
  142. package/esm/rpc/WebWorkerRpcDriver.js +9 -47
  143. package/esm/rpc/byteBudget.d.ts +3 -5
  144. package/esm/rpc/byteBudget.js +4 -4
  145. package/esm/rpc/configSchema.d.ts +7 -21
  146. package/esm/rpc/coreRpcMethods.d.ts +1 -0
  147. package/esm/rpc/coreRpcMethods.js +1 -0
  148. package/esm/rpc/methods/CoreEncodeFeatures.d.ts +6 -5
  149. package/esm/rpc/methods/CoreEncodeFeatures.js +26 -31
  150. package/esm/rpc/methods/CoreGetEncodedFeature.d.ts +13 -0
  151. package/esm/rpc/methods/CoreGetEncodedFeature.js +31 -0
  152. package/esm/rpc/methods/CoreGetExportData.js +2 -2
  153. package/esm/rpc/methods/CoreGetFeatureDensity.js +2 -2
  154. package/esm/rpc/methods/CoreGetFeatures.js +2 -2
  155. package/esm/rpc/methods/CoreGetSequence.js +2 -2
  156. package/esm/rpc/methods/layerFeatures.d.ts +26 -0
  157. package/esm/rpc/methods/layerFeatures.js +40 -0
  158. package/esm/svg/SvgExport.js +3 -4
  159. package/esm/svg/SvgThemeProviders.d.ts +12 -0
  160. package/esm/svg/SvgThemeProviders.js +15 -0
  161. package/esm/svg/exportViewSvg.d.ts +32 -0
  162. package/esm/svg/exportViewSvg.js +13 -0
  163. package/esm/svg/normalizeSvgMarkup.d.ts +7 -0
  164. package/esm/svg/normalizeSvgMarkup.js +99 -0
  165. package/esm/svg/serializeSvg.d.ts +7 -0
  166. package/esm/svg/serializeSvg.js +11 -0
  167. package/esm/svg/svgReady.d.ts +8 -7
  168. package/esm/svg/svgReady.js +8 -7
  169. package/esm/svg/trackNames.d.ts +5 -5
  170. package/esm/svg/trackNames.js +6 -6
  171. package/esm/svg/wrapSvgExport.js +6 -74
  172. package/esm/ui/CascadingMenu.js +83 -86
  173. package/esm/ui/ErrorMessageStackTraceDialog.js +0 -5
  174. package/esm/ui/FileSelector/useInternetAccounts.d.ts +156 -96
  175. package/esm/ui/HoverMenu.d.ts +1 -2
  176. package/esm/ui/HoverMenu.js +6 -3
  177. package/esm/ui/JexlFilterDialog.d.ts +13 -10
  178. package/esm/ui/JexlFilterDialog.js +122 -49
  179. package/esm/ui/JexlFilterRowEditors.d.ts +15 -0
  180. package/esm/ui/JexlFilterRowEditors.js +90 -0
  181. package/esm/ui/LazyBaseTooltip.d.ts +4 -0
  182. package/esm/ui/LazyBaseTooltip.js +9 -0
  183. package/esm/ui/LoadingOverlay.js +3 -1
  184. package/esm/ui/MonospaceTextField.d.ts +2 -1
  185. package/esm/ui/MonospaceTextField.js +21 -19
  186. package/esm/ui/PaletteContext.d.ts +7 -9
  187. package/esm/ui/PaletteContext.js +24 -10
  188. package/esm/ui/RefNameAutocomplete/index.d.ts +1 -2
  189. package/esm/ui/RefNameAutocomplete/index.js +1 -1
  190. package/esm/ui/ScrollChrome.d.ts +6 -9
  191. package/esm/ui/ScrollChrome.js +5 -6
  192. package/esm/ui/ScrollEdgeShadow.d.ts +6 -9
  193. package/esm/ui/ScrollEdgeShadow.js +9 -24
  194. package/esm/ui/SettingsChangesTable.js +3 -3
  195. package/esm/ui/VerticalScrollbar.d.ts +13 -34
  196. package/esm/ui/VerticalScrollbar.js +29 -83
  197. package/esm/ui/ViewLoadingScreen.d.ts +2 -2
  198. package/esm/ui/ViewLoadingScreen.js +3 -3
  199. package/esm/ui/colorScale.d.ts +26 -1
  200. package/esm/ui/colorScale.js +28 -5
  201. package/esm/ui/colors.d.ts +49 -1
  202. package/esm/ui/colors.js +139 -4
  203. package/esm/ui/hoverBoxStyle.d.ts +14 -2
  204. package/esm/ui/hoverBoxStyle.js +17 -2
  205. package/esm/ui/index.d.ts +5 -3
  206. package/esm/ui/index.js +9 -7
  207. package/esm/ui/launchViewMenu.js +3 -3
  208. package/esm/ui/legendSpec.d.ts +2 -0
  209. package/esm/ui/legendSpec.js +3 -0
  210. package/esm/ui/palette.d.ts +0 -1
  211. package/esm/ui/palette.js +3 -27
  212. package/esm/ui/replaceViewAction.d.ts +1 -1
  213. package/esm/ui/replaceViewAction.js +1 -1
  214. package/esm/ui/theme.d.ts +1 -1
  215. package/esm/ui/theme.js +6 -40
  216. package/esm/ui/viewHeaderHeight.d.ts +1 -0
  217. package/esm/ui/viewHeaderHeight.js +1 -0
  218. package/esm/util/Base1DUtils.d.ts +1 -1
  219. package/esm/util/Base1DUtils.js +2 -2
  220. package/esm/util/SvgCanvas.d.ts +15 -13
  221. package/esm/util/SvgCanvas.js +72 -53
  222. package/esm/util/aborting.d.ts +39 -0
  223. package/esm/util/aborting.js +84 -0
  224. package/esm/util/adapterMetadata.d.ts +1 -1
  225. package/esm/util/adapterMetadata.js +6 -6
  226. package/esm/util/addAndShowTrack.d.ts +1 -4
  227. package/esm/util/addRelativeUris.d.ts +10 -2
  228. package/esm/util/addRelativeUris.js +22 -7
  229. package/esm/util/addTrackFromWidget.d.ts +2 -5
  230. package/esm/util/animationAllowed.d.ts +9 -0
  231. package/esm/util/animationAllowed.js +13 -0
  232. package/esm/util/applyRowResizeWheel.d.ts +10 -5
  233. package/esm/util/applyRowResizeWheel.js +10 -21
  234. package/esm/util/bandLayout.d.ts +4 -4
  235. package/esm/util/bandLayout.js +4 -4
  236. package/esm/util/bezierConnector.js +5 -4
  237. package/esm/util/bgzfWorkerPool.d.ts +20 -74
  238. package/esm/util/bgzfWorkerPool.js +20 -74
  239. package/esm/util/cachedSetup.d.ts +1 -1
  240. package/esm/util/cachedSetup.js +2 -2
  241. package/esm/util/categoricalField.d.ts +37 -0
  242. package/esm/util/categoricalField.js +52 -0
  243. package/esm/util/color/cssColorsLevel4.d.ts +1 -0
  244. package/esm/util/color/cssColorsLevel4.js +1 -0
  245. package/esm/util/color/index.d.ts +5 -3
  246. package/esm/util/color/index.js +7 -4
  247. package/esm/util/colorBits.d.ts +1 -2
  248. package/esm/util/colorBits.js +17 -39
  249. package/esm/util/colorRamp.d.ts +27 -1
  250. package/esm/util/colorRamp.js +56 -2
  251. package/esm/util/colorSchemes.d.ts +9 -0
  252. package/esm/util/colorSchemes.js +7 -0
  253. package/esm/util/{createStopTokenRotation.d.ts → createAbortRotation.d.ts} +11 -14
  254. package/esm/util/{createStopTokenRotation.js → createAbortRotation.js} +14 -26
  255. package/esm/util/cssColorParse.d.ts +15 -0
  256. package/esm/util/cssColorParse.js +53 -0
  257. package/esm/util/diagonalizeRegions.d.ts +2 -3
  258. package/esm/util/diagonalizeRegions.js +7 -12
  259. package/esm/util/expandLooseSearchIndex.d.ts +7 -0
  260. package/esm/util/expandLooseSearchIndex.js +25 -0
  261. package/esm/util/featureTransforms.d.ts +30 -3
  262. package/esm/util/featureTransforms.js +233 -36
  263. package/esm/util/fetchAndMaybeUnzip.js +5 -6
  264. package/esm/util/fetchContext.d.ts +5 -6
  265. package/esm/util/fetchContext.js +1 -1
  266. package/esm/util/fetchHub.d.ts +3 -1
  267. package/esm/util/fetchHub.js +2 -2
  268. package/esm/util/fetchSeq.d.ts +2 -3
  269. package/esm/util/fetchSeq.js +2 -2
  270. package/esm/util/fieldReader.d.ts +17 -0
  271. package/esm/util/fieldReader.js +62 -0
  272. package/esm/util/groupKeys.d.ts +75 -0
  273. package/esm/util/groupKeys.js +152 -0
  274. package/esm/util/highlights.d.ts +6 -4
  275. package/esm/util/highlights.js +12 -25
  276. package/esm/util/hooks.d.ts +1 -2
  277. package/esm/util/hooks.js +1 -2
  278. package/esm/util/index.d.ts +3 -3
  279. package/esm/util/index.js +4 -3
  280. package/esm/util/indexCandidates.js +1 -1
  281. package/esm/util/installFetch.d.ts +13 -10
  282. package/esm/util/installFetch.js +11 -10
  283. package/esm/util/installPrerequisiteFetch.d.ts +5 -3
  284. package/esm/util/installPrerequisiteFetch.js +3 -4
  285. package/esm/util/io/index.js +12 -12
  286. package/esm/util/isDataCurrent.d.ts +7 -5
  287. package/esm/util/isDataCurrent.js +9 -6
  288. package/esm/util/jexl.js +24 -21
  289. package/esm/util/jexlFilterRows.d.ts +89 -0
  290. package/esm/util/jexlFilterRows.js +252 -0
  291. package/esm/util/jexlFilters.d.ts +7 -5
  292. package/esm/util/jexlStrings.d.ts +3 -4
  293. package/esm/util/jexlStrings.js +2 -3
  294. package/esm/util/legendCandidates.d.ts +31 -27
  295. package/esm/util/legendCandidates.js +79 -53
  296. package/esm/util/localStorage.js +4 -4
  297. package/esm/util/markEncoding.d.ts +32 -16
  298. package/esm/util/markEncoding.js +177 -150
  299. package/esm/util/markEncodingTypes.d.ts +137 -66
  300. package/esm/util/mstUtils.d.ts +19 -22
  301. package/esm/util/mstUtils.js +19 -22
  302. package/esm/util/numericUtils.d.ts +7 -0
  303. package/esm/util/numericUtils.js +16 -0
  304. package/esm/util/numericValue.d.ts +14 -0
  305. package/esm/util/numericValue.js +34 -0
  306. package/esm/util/openFeatureWidget.js +1 -2
  307. package/esm/util/openViews.d.ts +1 -0
  308. package/esm/util/openViews.js +3 -3
  309. package/esm/util/parseLineByLine.d.ts +3 -4
  310. package/esm/util/parseLineByLine.js +7 -13
  311. package/esm/util/progress.d.ts +21 -21
  312. package/esm/util/progress.js +27 -26
  313. package/esm/util/renameRegions.d.ts +1 -2
  314. package/esm/util/renderToStaticMarkup.js +16 -16
  315. package/esm/util/rxjs.d.ts +7 -8
  316. package/esm/util/rxjs.js +12 -15
  317. package/esm/util/simpleFeature.d.ts +0 -1
  318. package/esm/util/svgColorProps.d.ts +11 -0
  319. package/esm/util/svgColorProps.js +28 -1
  320. package/esm/util/tabix.d.ts +3 -4
  321. package/esm/util/tabix.js +6 -7
  322. package/esm/util/thresholdScale.d.ts +54 -0
  323. package/esm/util/thresholdScale.js +112 -0
  324. package/esm/util/timeGate.d.ts +4 -5
  325. package/esm/util/timeGate.js +4 -5
  326. package/esm/util/trackConfigDelta.d.ts +22 -18
  327. package/esm/util/trackConfigDelta.js +40 -38
  328. package/esm/util/tracks.d.ts +27 -4
  329. package/esm/util/tracks.js +116 -43
  330. package/esm/util/translateTranscript.d.ts +44 -0
  331. package/esm/util/translateTranscript.js +102 -0
  332. package/esm/util/types/index.d.ts +19 -7
  333. package/esm/util/types/services.d.ts +1 -1
  334. package/esm/util/unknownSnapshotKeys.d.ts +15 -0
  335. package/esm/util/unknownSnapshotKeys.js +13 -0
  336. package/esm/util/useFeatureSequence.js +4 -4
  337. package/esm/util/useFetch.d.ts +3 -4
  338. package/esm/util/useFetch.js +5 -6
  339. package/esm/util/usePanelVirtualScroll.d.ts +7 -39
  340. package/esm/util/usePanelVirtualScroll.js +9 -40
  341. package/esm/util/useRowVirtualScroll.d.ts +6 -29
  342. package/esm/util/useRowVirtualScroll.js +8 -49
  343. package/esm/util/useVirtualScrollWheel.d.ts +20 -4
  344. package/esm/util/useVirtualScrollWheel.js +40 -84
  345. package/esm/util/viewHighlights.d.ts +3 -0
  346. package/esm/util/viewHighlights.js +5 -0
  347. package/esm/util/viewStatus.d.ts +24 -15
  348. package/esm/util/viewStatus.js +17 -0
  349. package/esm/util/withLaunchInput.d.ts +1 -1
  350. package/esm/util/withLaunchInput.js +0 -4
  351. package/package.json +26 -12
  352. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
  353. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
  354. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
  355. package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
  356. package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
  357. package/esm/ReExports/BaseFeatureDetails.js +0 -10
  358. package/esm/ReExports/barrelOnlyNames.d.ts +0 -5
  359. package/esm/ReExports/barrelOnlyNames.js +0 -63
  360. package/esm/ReExports/index.d.ts +0 -1
  361. package/esm/ReExports/index.js +0 -1
  362. package/esm/ReExports/publicTracks.d.ts +0 -1
  363. package/esm/ReExports/publicTracks.js +0 -14
  364. package/esm/ReExports/publicUi.d.ts +0 -4
  365. package/esm/ReExports/publicUi.js +0 -33
  366. package/esm/ReExports/publicUtil.d.ts +0 -1
  367. package/esm/ReExports/publicUtil.js +0 -32
  368. package/esm/ReExports/sharedModules.d.ts +0 -96
  369. package/esm/ReExports/sharedModules.js +0 -66
  370. package/esm/ReExports/workerNamespaceNames.d.ts +0 -11
  371. package/esm/ReExports/workerNamespaceNames.js +0 -275
  372. package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +0 -51
  373. package/esm/pluggableElementTypes/models/HighlightsMixin.js +0 -78
  374. package/esm/ui/highlightChipReveal.d.ts +0 -32
  375. package/esm/ui/highlightChipReveal.js +0 -39
  376. package/esm/util/adapterConfigKey.d.ts +0 -12
  377. package/esm/util/adapterConfigKey.js +0 -14
  378. package/esm/util/stopToken.d.ts +0 -212
  379. package/esm/util/stopToken.js +0 -438
package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js DELETED
@@ -1,583 +0,0 @@
1
- export default {
2
- source: 'BestRefSeq',
3
- type: 'gene',
4
- start: 35331036,
5
- end: 35395251,
6
- strand: -1,
7
- phase: 0,
8
- refName: 'NC_000001.10',
9
- id: 'gene625',
10
- dbxref: ['GeneID:58512', 'HGNC:HGNC:30368', 'MIM:611413'],
11
- name: 'DLGAP3',
12
- description: 'DLG associated protein 3',
13
- gbkey: 'Gene',
14
- gene: 'DLGAP3',
15
- gene_biotype: 'protein_coding',
16
- gene_synonym: ['DAP3', 'SAPAP3'],
17
- subfeatures: [
18
- {
19
- source: 'BestRefSeq',
20
- type: 'mRNA',
21
- start: 35331036,
22
- end: 35395251,
23
- strand: -1,
24
- phase: 0,
25
- refName: 'NC_000001.10',
26
- id: 'mRNA1315',
27
- parent: 'gene625',
28
- dbxref: [
29
- 'GeneID:58512',
30
- 'Genbank:NM_001080418.3',
31
- 'HGNC:HGNC:30368',
32
- 'MIM:611413',
33
- ],
34
- name: 'NM_001080418.3',
35
- gbkey: 'mRNA',
36
- gene: 'DLGAP3',
37
- product: 'DLG associated protein 3',
38
- tag: 'RefSeq Select',
39
- transcript_id: 'NM_001080418.3',
40
- subfeatures: [
41
- {
42
- source: 'BestRefSeq',
43
- type: 'exon',
44
- start: 35331036,
45
- end: 35331902,
46
- strand: -1,
47
- phase: 0,
48
- refName: 'NC_000001.10',
49
- parent: 'mRNA1315',
50
- dbxref: [
51
- 'GeneID:58512',
52
- 'Genbank:NM_001080418.3',
53
- 'HGNC:HGNC:30368',
54
- 'MIM:611413',
55
- ],
56
- gbkey: 'mRNA',
57
- gene: 'DLGAP3',
58
- product: 'DLG associated protein 3',
59
- tag: 'RefSeq Select',
60
- transcript_id: 'NM_001080418.3',
61
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-0',
62
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
63
- },
64
- {
65
- source: 'BestRefSeq',
66
- type: 'CDS',
67
- start: 35331683,
68
- end: 35331902,
69
- strand: -1,
70
- phase: 0,
71
- refName: 'NC_000001.10',
72
- id: 'CDS1270',
73
- parent: 'mRNA1315',
74
- dbxref: [
75
- 'CCDS:CCDS30670.1',
76
- 'GeneID:58512',
77
- 'Genbank:NP_001073887.1',
78
- 'HGNC:HGNC:30368',
79
- 'MIM:611413',
80
- ],
81
- name: 'NP_001073887.1',
82
- gbkey: 'CDS',
83
- gene: 'DLGAP3',
84
- product: 'disks large-associated protein 3',
85
- protein_id: 'NP_001073887.1',
86
- tag: 'RefSeq Select',
87
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-1',
88
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
89
- },
90
- {
91
- source: 'BestRefSeq',
92
- type: 'CDS',
93
- start: 35332648,
94
- end: 35332792,
95
- strand: -1,
96
- phase: 0,
97
- refName: 'NC_000001.10',
98
- id: 'CDS1270',
99
- parent: 'mRNA1315',
100
- dbxref: [
101
- 'CCDS:CCDS30670.1',
102
- 'GeneID:58512',
103
- 'Genbank:NP_001073887.1',
104
- 'HGNC:HGNC:30368',
105
- 'MIM:611413',
106
- ],
107
- name: 'NP_001073887.1',
108
- gbkey: 'CDS',
109
- gene: 'DLGAP3',
110
- product: 'disks large-associated protein 3',
111
- protein_id: 'NP_001073887.1',
112
- tag: 'RefSeq Select',
113
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-2',
114
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
115
- },
116
- {
117
- source: 'BestRefSeq',
118
- type: 'CDS',
119
- start: 35333136,
120
- end: 35333228,
121
- strand: -1,
122
- phase: 2,
123
- refName: 'NC_000001.10',
124
- id: 'CDS1270',
125
- parent: 'mRNA1315',
126
- dbxref: [
127
- 'CCDS:CCDS30670.1',
128
- 'GeneID:58512',
129
- 'Genbank:NP_001073887.1',
130
- 'HGNC:HGNC:30368',
131
- 'MIM:611413',
132
- ],
133
- name: 'NP_001073887.1',
134
- gbkey: 'CDS',
135
- gene: 'DLGAP3',
136
- product: 'disks large-associated protein 3',
137
- protein_id: 'NP_001073887.1',
138
- tag: 'RefSeq Select',
139
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-3',
140
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
141
- },
142
- {
143
- source: 'BestRefSeq',
144
- type: 'CDS',
145
- start: 35334205,
146
- end: 35334690,
147
- strand: -1,
148
- phase: 1,
149
- refName: 'NC_000001.10',
150
- id: 'CDS1270',
151
- parent: 'mRNA1315',
152
- dbxref: [
153
- 'CCDS:CCDS30670.1',
154
- 'GeneID:58512',
155
- 'Genbank:NP_001073887.1',
156
- 'HGNC:HGNC:30368',
157
- 'MIM:611413',
158
- ],
159
- name: 'NP_001073887.1',
160
- gbkey: 'CDS',
161
- gene: 'DLGAP3',
162
- product: 'disks large-associated protein 3',
163
- protein_id: 'NP_001073887.1',
164
- tag: 'RefSeq Select',
165
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-4',
166
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
167
- },
168
- {
169
- source: 'BestRefSeq',
170
- type: 'CDS',
171
- start: 35350578,
172
- end: 35350664,
173
- strand: -1,
174
- phase: 0,
175
- refName: 'NC_000001.10',
176
- id: 'CDS1270',
177
- parent: 'mRNA1315',
178
- dbxref: [
179
- 'CCDS:CCDS30670.1',
180
- 'GeneID:58512',
181
- 'Genbank:NP_001073887.1',
182
- 'HGNC:HGNC:30368',
183
- 'MIM:611413',
184
- ],
185
- name: 'NP_001073887.1',
186
- gbkey: 'CDS',
187
- gene: 'DLGAP3',
188
- product: 'disks large-associated protein 3',
189
- protein_id: 'NP_001073887.1',
190
- tag: 'RefSeq Select',
191
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-5',
192
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
193
- },
194
- {
195
- source: 'BestRefSeq',
196
- type: 'CDS',
197
- start: 35351078,
198
- end: 35351392,
199
- strand: -1,
200
- phase: 2,
201
- refName: 'NC_000001.10',
202
- id: 'CDS1270',
203
- parent: 'mRNA1315',
204
- dbxref: [
205
- 'CCDS:CCDS30670.1',
206
- 'GeneID:58512',
207
- 'Genbank:NP_001073887.1',
208
- 'HGNC:HGNC:30368',
209
- 'MIM:611413',
210
- ],
211
- name: 'NP_001073887.1',
212
- gbkey: 'CDS',
213
- gene: 'DLGAP3',
214
- product: 'disks large-associated protein 3',
215
- protein_id: 'NP_001073887.1',
216
- tag: 'RefSeq Select',
217
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-6',
218
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
219
- },
220
- {
221
- source: 'BestRefSeq',
222
- type: 'CDS',
223
- start: 35351672,
224
- end: 35351886,
225
- strand: -1,
226
- phase: 0,
227
- refName: 'NC_000001.10',
228
- id: 'CDS1270',
229
- parent: 'mRNA1315',
230
- dbxref: [
231
- 'CCDS:CCDS30670.1',
232
- 'GeneID:58512',
233
- 'Genbank:NP_001073887.1',
234
- 'HGNC:HGNC:30368',
235
- 'MIM:611413',
236
- ],
237
- name: 'NP_001073887.1',
238
- gbkey: 'CDS',
239
- gene: 'DLGAP3',
240
- product: 'disks large-associated protein 3',
241
- protein_id: 'NP_001073887.1',
242
- tag: 'RefSeq Select',
243
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-7',
244
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
245
- },
246
- {
247
- source: 'BestRefSeq',
248
- type: 'CDS',
249
- start: 35365269,
250
- end: 35365342,
251
- strand: -1,
252
- phase: 1,
253
- refName: 'NC_000001.10',
254
- id: 'CDS1270',
255
- parent: 'mRNA1315',
256
- dbxref: [
257
- 'CCDS:CCDS30670.1',
258
- 'GeneID:58512',
259
- 'Genbank:NP_001073887.1',
260
- 'HGNC:HGNC:30368',
261
- 'MIM:611413',
262
- ],
263
- name: 'NP_001073887.1',
264
- gbkey: 'CDS',
265
- gene: 'DLGAP3',
266
- product: 'disks large-associated protein 3',
267
- protein_id: 'NP_001073887.1',
268
- tag: 'RefSeq Select',
269
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-8',
270
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
271
- },
272
- {
273
- source: 'BestRefSeq',
274
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275
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276
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277
- strand: -1,
278
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279
- refName: 'NC_000001.10',
280
- id: 'CDS1270',
281
- parent: 'mRNA1315',
282
- dbxref: [
283
- 'CCDS:CCDS30670.1',
284
- 'GeneID:58512',
285
- 'Genbank:NP_001073887.1',
286
- 'HGNC:HGNC:30368',
287
- 'MIM:611413',
288
- ],
289
- name: 'NP_001073887.1',
290
- gbkey: 'CDS',
291
- gene: 'DLGAP3',
292
- product: 'disks large-associated protein 3',
293
- protein_id: 'NP_001073887.1',
294
- tag: 'RefSeq Select',
295
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-9',
296
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
297
- },
298
- {
299
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300
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301
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305
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306
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307
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308
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- 'CCDS:CCDS30670.1',
310
- 'GeneID:58512',
311
- 'Genbank:NP_001073887.1',
312
- 'HGNC:HGNC:30368',
313
- 'MIM:611413',
314
- ],
315
- name: 'NP_001073887.1',
316
- gbkey: 'CDS',
317
- gene: 'DLGAP3',
318
- product: 'disks large-associated protein 3',
319
- protein_id: 'NP_001073887.1',
320
- tag: 'RefSeq Select',
321
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-10',
322
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
323
- },
324
- {
325
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326
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327
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328
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330
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331
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332
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333
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334
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335
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336
- 'HGNC:HGNC:30368',
337
- 'MIM:611413',
338
- ],
339
- gbkey: 'mRNA',
340
- gene: 'DLGAP3',
341
- product: 'DLG associated protein 3',
342
- tag: 'RefSeq Select',
343
- transcript_id: 'NM_001080418.3',
344
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-11',
345
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
346
- },
347
- {
348
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349
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350
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- 'GeneID:58512',
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- 'Genbank:NM_001080418.3',
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- 'HGNC:HGNC:30368',
360
- 'MIM:611413',
361
- ],
362
- gbkey: 'mRNA',
363
- gene: 'DLGAP3',
364
- product: 'DLG associated protein 3',
365
- tag: 'RefSeq Select',
366
- transcript_id: 'NM_001080418.3',
367
- uniqueId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0-12',
368
- parentId: 'type-Gff3TabixAdapter;type-Gff3TabixAdapter;uri-https://s3.amazonaws.com/jbrowse.org/genomes/hg19/nc-offset-162597949-0',
369
- },
370
- {
371
- source: 'BestRefSeq',
372
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373
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376
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377
- refName: 'NC_000001.10',
378
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379
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380
- 'GeneID:58512',
381
- 'Genbank:NM_001080418.3',
382
- 'HGNC:HGNC:30368',
383
- 'MIM:611413',
384
- ],
385
- gbkey: 'mRNA',
386
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387
- product: 'DLG associated protein 3',
388
- tag: 'RefSeq Select',
389
- transcript_id: 'NM_001080418.3',
390
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391
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392
- },
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405
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- ],
408
- gbkey: 'mRNA',
409
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410
- product: 'DLG associated protein 3',
411
- tag: 'RefSeq Select',
412
- transcript_id: 'NM_001080418.3',
413
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414
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- },
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417
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- ],
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432
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433
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434
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435
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436
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437
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438
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439
- {
440
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441
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442
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443
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445
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447
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449
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450
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451
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452
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453
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454
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455
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456
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457
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458
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459
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460
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461
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464
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470
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473
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474
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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486
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487
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489
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491
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498
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499
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500
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502
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503
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504
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505
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506
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507
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509
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510
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511
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515
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516
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519
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520
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521
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522
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524
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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537
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539
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543
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545
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546
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547
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548
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549
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550
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551
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552
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553
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556
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570
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571
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572
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573
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574
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575
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576
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577
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578
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582
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- };