@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.
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +32 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +13 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +43 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +8 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +7 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +2 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +17 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +2 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +7 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +20 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +2 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +57 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +42 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +2 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +14 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +14 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +22 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +7 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.js +1 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +26 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +41 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +7 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +44 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +7 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +34 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +26 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +3 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +29 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +11 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +40 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +105 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +5 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +64 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +48 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.d.ts +1 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +31 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +83 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +16 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +83 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +16 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +52 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +9 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +21 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +22 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +80 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +583 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +141 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +1116 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.js +1 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +13 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +73 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +42 -0
- package/esm/BaseFeatureWidget/configSchema.d.ts +2 -0
- package/esm/BaseFeatureWidget/configSchema.js +3 -0
- package/esm/BaseFeatureWidget/index.d.ts +2 -0
- package/esm/BaseFeatureWidget/index.js +2 -0
- package/esm/BaseFeatureWidget/stateModelFactory.d.ts +101 -0
- package/esm/BaseFeatureWidget/stateModelFactory.js +96 -0
- package/esm/BaseFeatureWidget/types.d.ts +22 -0
- package/esm/BaseFeatureWidget/types.js +1 -0
- package/esm/BaseFeatureWidget/util.d.ts +51 -0
- package/esm/BaseFeatureWidget/util.js +95 -0
- package/esm/CorePlugin.d.ts +6 -0
- package/esm/CorePlugin.js +24 -0
- package/esm/PhasedScheduler.js +25 -0
- package/esm/Plugin.d.ts +13 -0
- package/esm/Plugin.js +9 -0
- package/esm/PluginLoader.d.ts +64 -0
- package/esm/PluginLoader.js +164 -0
- package/esm/PluginManager.d.ts +125 -0
- package/esm/PluginManager.js +414 -0
- package/esm/ReExports/BaseFeatureDetails.js +9 -0
- package/esm/ReExports/DataGrid.js +1 -0
- package/esm/ReExports/MuiDataGridReExports.js +131 -0
- package/esm/ReExports/MuiReExports.d.ts +134 -0
- package/esm/ReExports/MuiReExports.js +115 -0
- package/esm/ReExports/index.d.ts +1 -0
- package/esm/ReExports/index.js +1 -0
- package/esm/ReExports/lazify.js +10 -0
- package/esm/ReExports/list.js +275 -0
- package/esm/ReExports/modules.js +149 -0
- package/esm/TextSearch/BaseResults.d.ts +46 -0
- package/esm/TextSearch/BaseResults.js +67 -0
- package/esm/TextSearch/TextSearchManager.d.ts +48 -0
- package/esm/TextSearch/TextSearchManager.js +77 -0
- package/esm/assemblyManager/assembly.d.ts +75 -0
- package/esm/assemblyManager/assembly.js +328 -0
- package/esm/assemblyManager/assemblyConfigSchema.d.ts +27 -0
- package/esm/assemblyManager/assemblyConfigSchema.js +51 -0
- package/esm/assemblyManager/assemblyManager.d.ts +528 -0
- package/esm/assemblyManager/assemblyManager.js +131 -0
- package/esm/assemblyManager/index.d.ts +3 -0
- package/esm/assemblyManager/index.js +2 -0
- package/esm/configuration/configurationSchema.d.ts +37 -0
- package/esm/configuration/configurationSchema.js +230 -0
- package/esm/configuration/configurationSlot.d.ts +33 -0
- package/esm/configuration/configurationSlot.js +239 -0
- package/esm/configuration/index.d.ts +3 -0
- package/esm/configuration/index.js +2 -0
- package/esm/configuration/types.d.ts +14 -0
- package/esm/configuration/types.js +1 -0
- package/esm/configuration/util.d.ts +10 -0
- package/esm/configuration/util.js +123 -0
- package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +16 -0
- package/esm/data_adapters/BaseAdapter/BaseAdapter.js +31 -0
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +24 -0
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +68 -0
- package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +18 -0
- package/esm/data_adapters/BaseAdapter/BaseOptions.js +1 -0
- package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +10 -0
- package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.js +1 -0
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +11 -0
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +12 -0
- package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +6 -0
- package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.js +1 -0
- package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +6 -0
- package/esm/data_adapters/BaseAdapter/RegionsAdapter.js +1 -0
- package/esm/data_adapters/BaseAdapter/index.d.ts +13 -0
- package/esm/data_adapters/BaseAdapter/index.js +5 -0
- package/esm/data_adapters/BaseAdapter/stats.d.ts +10 -0
- package/esm/data_adapters/BaseAdapter/stats.js +48 -0
- package/esm/data_adapters/BaseAdapter/types.d.ts +23 -0
- package/esm/data_adapters/BaseAdapter/types.js +1 -0
- package/esm/data_adapters/BaseAdapter/util.d.ts +12 -0
- package/esm/data_adapters/BaseAdapter/util.js +15 -0
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +6 -0
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +28 -0
- package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +9 -0
- package/esm/data_adapters/CytobandAdapter/configSchema.js +24 -0
- package/esm/data_adapters/CytobandAdapter/index.d.ts +2 -0
- package/esm/data_adapters/CytobandAdapter/index.js +12 -0
- package/esm/data_adapters/dataAdapterCache.d.ts +14 -0
- package/esm/data_adapters/dataAdapterCache.js +54 -0
- package/esm/data_adapters/util.js +4 -0
- package/esm/pluggableElementTypes/AdapterType.d.ts +25 -0
- package/esm/pluggableElementTypes/AdapterType.js +17 -0
- package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +17 -0
- package/esm/pluggableElementTypes/AddTrackWorkflowType.js +10 -0
- package/esm/pluggableElementTypes/ConnectionType.d.ts +20 -0
- package/esm/pluggableElementTypes/ConnectionType.js +16 -0
- package/esm/pluggableElementTypes/DisplayType.d.ts +30 -0
- package/esm/pluggableElementTypes/DisplayType.js +20 -0
- package/esm/pluggableElementTypes/GlyphType.d.ts +43 -0
- package/esm/pluggableElementTypes/GlyphType.js +18 -0
- package/esm/pluggableElementTypes/InternetAccountType.d.ts +12 -0
- package/esm/pluggableElementTypes/InternetAccountType.js +10 -0
- package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
- package/esm/pluggableElementTypes/RpcMethodType.d.ts +19 -0
- package/esm/pluggableElementTypes/RpcMethodType.js +88 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +11 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +28 -0
- package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +18 -0
- package/esm/pluggableElementTypes/TextSearchAdapterType.js +15 -0
- package/esm/pluggableElementTypes/TrackType.d.ts +16 -0
- package/esm/pluggableElementTypes/TrackType.js +14 -0
- package/esm/pluggableElementTypes/ViewType.d.ts +29 -0
- package/esm/pluggableElementTypes/ViewType.js +18 -0
- package/esm/pluggableElementTypes/WidgetType.d.ts +27 -0
- package/esm/pluggableElementTypes/WidgetType.js +18 -0
- package/esm/pluggableElementTypes/index.d.ts +27 -0
- package/esm/pluggableElementTypes/index.js +14 -0
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +29 -0
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +35 -0
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +180 -0
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +104 -0
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +74 -0
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +203 -0
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +52 -0
- package/esm/pluggableElementTypes/models/BaseViewModel.js +42 -0
- package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +86 -0
- package/esm/pluggableElementTypes/models/InternetAccountModel.js +151 -0
- package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +16 -0
- package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -0
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +27 -0
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +32 -0
- package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +87 -0
- package/esm/pluggableElementTypes/models/baseTrackConfig.js +134 -0
- package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +11 -0
- package/esm/pluggableElementTypes/models/components/SaveTrackData.js +158 -0
- package/esm/pluggableElementTypes/models/index.d.ts +14 -0
- package/esm/pluggableElementTypes/models/index.js +8 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.d.ts +4 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +9 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +5 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +17 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +7 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +108 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +5 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +91 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +11 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.js +1 -0
- package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +52 -0
- package/esm/pluggableElementTypes/renderers/BoxRendererType.js +78 -0
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +4 -0
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +4 -0
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +58 -0
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +77 -0
- package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +31 -0
- package/esm/pluggableElementTypes/renderers/LayoutSession.js +37 -0
- package/esm/pluggableElementTypes/renderers/RendererType.d.ts +28 -0
- package/esm/pluggableElementTypes/renderers/RendererType.js +20 -0
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +57 -0
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +113 -0
- package/esm/pluggableElementTypes/renderers/index.d.ts +6 -0
- package/esm/pluggableElementTypes/renderers/index.js +6 -0
- package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +30 -0
- package/esm/pluggableElementTypes/renderers/util.d.ts +3 -0
- package/esm/pluggableElementTypes/renderers/util.js +14 -0
- package/esm/rpc/BaseRpcDriver.d.ts +40 -0
- package/esm/rpc/BaseRpcDriver.js +116 -0
- package/esm/rpc/MainThreadRpcDriver.d.ts +14 -0
- package/esm/rpc/MainThreadRpcDriver.js +33 -0
- package/esm/rpc/RpcManager.d.ts +35 -0
- package/esm/rpc/RpcManager.js +63 -0
- package/esm/rpc/WebWorkerRpcDriver.d.ts +31 -0
- package/esm/rpc/WebWorkerRpcDriver.js +77 -0
- package/esm/rpc/baseRpcConfig.d.ts +8 -0
- package/esm/rpc/baseRpcConfig.js +10 -0
- package/esm/rpc/configSchema.d.ts +9 -0
- package/esm/rpc/configSchema.js +22 -0
- package/esm/rpc/coreRpcMethods.d.ts +12 -0
- package/esm/rpc/coreRpcMethods.js +12 -0
- package/esm/rpc/mainThreadRpcConfig.d.ts +8 -0
- package/esm/rpc/mainThreadRpcConfig.js +8 -0
- package/esm/rpc/methods/CoreFreeResources.d.ts +6 -0
- package/esm/rpc/methods/CoreFreeResources.js +14 -0
- package/esm/rpc/methods/CoreGetExportData.d.ts +19 -0
- package/esm/rpc/methods/CoreGetExportData.js +18 -0
- package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +17 -0
- package/esm/rpc/methods/CoreGetFeatureDensityStats.js +25 -0
- package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +11 -0
- package/esm/rpc/methods/CoreGetFeatureDetails.js +24 -0
- package/esm/rpc/methods/CoreGetFeatures.d.ts +18 -0
- package/esm/rpc/methods/CoreGetFeatures.js +31 -0
- package/esm/rpc/methods/CoreGetFileInfo.d.ts +9 -0
- package/esm/rpc/methods/CoreGetFileInfo.js +15 -0
- package/esm/rpc/methods/CoreGetMetadata.d.ts +9 -0
- package/esm/rpc/methods/CoreGetMetadata.js +15 -0
- package/esm/rpc/methods/CoreGetRefNames.d.ts +10 -0
- package/esm/rpc/methods/CoreGetRefNames.js +19 -0
- package/esm/rpc/methods/CoreGetRegions.d.ts +8 -0
- package/esm/rpc/methods/CoreGetRegions.js +15 -0
- package/esm/rpc/methods/CoreGetSequence.d.ts +13 -0
- package/esm/rpc/methods/CoreGetSequence.js +17 -0
- package/esm/rpc/methods/CoreRender.d.ts +14 -0
- package/esm/rpc/methods/CoreRender.js +35 -0
- package/esm/rpc/methods/CoreSaveFeatureData.d.ts +16 -0
- package/esm/rpc/methods/CoreSaveFeatureData.js +32 -0
- package/esm/rpc/methods/util.d.ts +15 -0
- package/esm/rpc/methods/util.js +7 -0
- package/esm/rpc/webWorkerRpcConfig.d.ts +8 -0
- package/esm/rpc/webWorkerRpcConfig.js +8 -0
- package/esm/ui/AppLogo.d.ts +7 -0
- package/esm/ui/AppLogo.js +10 -0
- package/esm/ui/AssemblySelector.d.ts +13 -0
- package/esm/ui/AssemblySelector.js +39 -0
- package/esm/ui/BaseTooltip.d.ts +8 -0
- package/esm/ui/BaseTooltip.js +42 -0
- package/esm/ui/CascadingMenu.d.ts +30 -0
- package/esm/ui/CascadingMenu.js +48 -0
- package/esm/ui/CascadingMenuButton.d.ts +26 -0
- package/esm/ui/CascadingMenuButton.js +24 -0
- package/esm/ui/CascadingMenuHelpDialog.d.ts +5 -0
- package/esm/ui/CascadingMenuHelpDialog.js +10 -0
- package/esm/ui/CascadingMenuHelpIconButton.d.ts +5 -0
- package/esm/ui/CascadingMenuHelpIconButton.js +15 -0
- package/esm/ui/ColorPicker.js +62 -0
- package/esm/ui/ConfirmDialog.d.ts +10 -0
- package/esm/ui/ConfirmDialog.js +13 -0
- package/esm/ui/DataGridFlexContainer.d.ts +5 -0
- package/esm/ui/DataGridFlexContainer.js +12 -0
- package/esm/ui/Dialog.d.ts +7 -0
- package/esm/ui/Dialog.js +45 -0
- package/esm/ui/DraggableDialog.js +27 -0
- package/esm/ui/DropDownMenu.d.ts +6 -0
- package/esm/ui/DropDownMenu.js +24 -0
- package/esm/ui/EditableTypography.js +60 -0
- package/esm/ui/ErrorBoundary.d.ts +17 -0
- package/esm/ui/ErrorBoundary.js +16 -0
- package/esm/ui/ErrorMessage.js +56 -0
- package/esm/ui/ErrorMessageStackTraceContents.d.ts +4 -0
- package/esm/ui/ErrorMessageStackTraceContents.js +25 -0
- package/esm/ui/ErrorMessageStackTraceDialog.js +108 -0
- package/esm/ui/ExternalLink.js +7 -0
- package/esm/ui/FactoryResetDialog.js +18 -0
- package/esm/ui/FatalErrorDialog.js +18 -0
- package/esm/ui/FileSelector/FileSelector.d.ts +11 -0
- package/esm/ui/FileSelector/FileSelector.js +52 -0
- package/esm/ui/FileSelector/LocalFileChooser.d.ts +6 -0
- package/esm/ui/FileSelector/LocalFileChooser.js +39 -0
- package/esm/ui/FileSelector/LocationInput.d.ts +9 -0
- package/esm/ui/FileSelector/LocationInput.js +15 -0
- package/esm/ui/FileSelector/SourceTypeSelector.d.ts +9 -0
- package/esm/ui/FileSelector/SourceTypeSelector.js +38 -0
- package/esm/ui/FileSelector/UrlChooser.d.ts +8 -0
- package/esm/ui/FileSelector/UrlChooser.js +17 -0
- package/esm/ui/FileSelector/index.d.ts +1 -0
- package/esm/ui/FileSelector/index.js +1 -0
- package/esm/ui/FileSelector/useInternetAccounts.d.ts +178 -0
- package/esm/ui/FileSelector/useInternetAccounts.js +18 -0
- package/esm/ui/HoverMenu.js +15 -0
- package/esm/ui/Icons.js +14 -0
- package/esm/ui/LoadingEllipses.d.ts +7 -0
- package/esm/ui/LoadingEllipses.js +31 -0
- package/esm/ui/Logo.js +42 -0
- package/esm/ui/Menu.d.ts +2 -0
- package/esm/ui/Menu.js +1 -0
- package/esm/ui/MenuButton.d.ts +1 -0
- package/esm/ui/MenuButton.js +1 -0
- package/esm/ui/MenuItems.d.ts +15 -0
- package/esm/ui/MenuItems.js +59 -0
- package/esm/ui/MenuTypes.d.ts +39 -0
- package/esm/ui/MenuTypes.js +1 -0
- package/esm/ui/PrerenderedCanvas.d.ts +10 -0
- package/esm/ui/PrerenderedCanvas.js +33 -0
- package/esm/ui/RedErrorMessageBox.js +16 -0
- package/esm/ui/ResizeHandle.js +67 -0
- package/esm/ui/ReturnToImportFormDialog.js +13 -0
- package/esm/ui/SanitizedHTML.js +61 -0
- package/esm/ui/Snackbar.d.ts +10 -0
- package/esm/ui/Snackbar.js +14 -0
- package/esm/ui/SnackbarContents.d.ts +5 -0
- package/esm/ui/SnackbarContents.js +11 -0
- package/esm/ui/SnackbarModel.d.ts +17 -0
- package/esm/ui/SnackbarModel.js +55 -0
- package/esm/ui/colors.js +67 -0
- package/esm/ui/index.d.ts +20 -0
- package/esm/ui/index.js +20 -0
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- package/stories/JBrowseCore.stories.js +0 -10
- package/stories/examples/WithSequencePanel.d.ts +0 -6
- package/stories/examples/WithSequencePanel.js +0 -42
- package/stories/examples/index.d.ts +0 -1
- package/stories/examples/index.js +0 -17
- package/stories/examples/util.d.ts +0 -33
- package/stories/examples/util.js +0 -235
- package/tsconfig.build.tsbuildinfo +0 -1
- package/ui/AppLogo.d.ts +0 -7
- package/ui/AppLogo.js +0 -12
- package/ui/AssemblySelector.d.ts +0 -13
- package/ui/AssemblySelector.js +0 -46
- package/ui/BaseTooltip.d.ts +0 -8
- package/ui/BaseTooltip.js +0 -46
- package/ui/CascadingMenu.d.ts +0 -9
- package/ui/CascadingMenu.js +0 -92
- package/ui/CascadingMenuButton.d.ts +0 -11
- package/ui/CascadingMenuButton.js +0 -29
- package/ui/ColorPicker.js +0 -101
- package/ui/DataGridFlexContainer.d.ts +0 -3
- package/ui/DataGridFlexContainer.js +0 -15
- package/ui/Dialog.d.ts +0 -7
- package/ui/Dialog.js +0 -50
- package/ui/DraggableDialog.js +0 -32
- package/ui/DropDownMenu.d.ts +0 -8
- package/ui/DropDownMenu.js +0 -37
- package/ui/EditableTypography.js +0 -72
- package/ui/ErrorBoundary.d.ts +0 -17
- package/ui/ErrorBoundary.js +0 -19
- package/ui/ErrorMessage.js +0 -94
- package/ui/ErrorMessageStackTraceDialog.js +0 -149
- package/ui/ExternalLink.js +0 -13
- package/ui/FactoryResetDialog.js +0 -24
- package/ui/FatalErrorDialog.js +0 -24
- package/ui/FileSelector/FileSelector.d.ts +0 -11
- package/ui/FileSelector/FileSelector.js +0 -102
- package/ui/FileSelector/LocalFileChooser.d.ts +0 -6
- package/ui/FileSelector/LocalFileChooser.js +0 -42
- package/ui/FileSelector/UrlChooser.d.ts +0 -8
- package/ui/FileSelector/UrlChooser.js +0 -19
- package/ui/FileSelector/index.d.ts +0 -1
- package/ui/FileSelector/index.js +0 -8
- package/ui/HoverMenu.js +0 -50
- package/ui/Icons.js +0 -23
- package/ui/LoadingEllipses.d.ts +0 -6
- package/ui/LoadingEllipses.js +0 -35
- package/ui/Logo.js +0 -46
- package/ui/Menu.d.ts +0 -53
- package/ui/Menu.js +0 -233
- package/ui/MenuButton.d.ts +0 -10
- package/ui/MenuButton.js +0 -28
- package/ui/PrerenderedCanvas.d.ts +0 -10
- package/ui/PrerenderedCanvas.js +0 -34
- package/ui/RedErrorMessageBox.js +0 -19
- package/ui/ResizeHandle.js +0 -72
- package/ui/ReturnToImportFormDialog.js +0 -18
- package/ui/SanitizedHTML.js +0 -64
- package/ui/Snackbar.d.ts +0 -10
- package/ui/Snackbar.js +0 -49
- package/ui/SnackbarContents.d.ts +0 -5
- package/ui/SnackbarContents.js +0 -16
- package/ui/SnackbarModel.d.ts +0 -17
- package/ui/SnackbarModel.js +0 -96
- package/ui/colors.js +0 -78
- package/ui/hooks.d.ts +0 -66
- package/ui/hooks.js +0 -185
- package/ui/index.d.ts +0 -19
- package/ui/index.js +0 -56
- package/ui/react-colorful.d.ts +0 -17
- package/ui/react-colorful.js +0 -466
- package/ui/theme.d.ts +0 -59
- package/ui/theme.js +0 -381
- package/ui/useEvent.js +0 -47
- package/util/Base1DUtils.d.ts +0 -38
- package/util/Base1DUtils.js +0 -198
- package/util/Base1DViewModel.d.ts +0 -61
- package/util/Base1DViewModel.js +0 -135
- package/util/QuickLRU.d.ts +0 -32
- package/util/QuickLRU.js +0 -237
- package/util/TimeTraveller.d.ts +0 -19
- package/util/TimeTraveller.js +0 -90
- package/util/aborting.js +0 -48
- package/util/analytics.js +0 -86
- package/util/blobToDataURL.js +0 -17
- package/util/blockTypes.d.ts +0 -58
- package/util/blockTypes.js +0 -110
- package/util/calculateDynamicBlocks.d.ts +0 -3
- package/util/calculateDynamicBlocks.js +0 -100
- package/util/calculateStaticBlocks.d.ts +0 -13
- package/util/calculateStaticBlocks.js +0 -102
- package/util/cluster.d.ts +0 -17
- package/util/cluster.js +0 -96
- package/util/color/cssColorsLevel4.js +0 -160
- package/util/color/index.d.ts +0 -4
- package/util/color/index.js +0 -40
- package/util/colord.d.ts +0 -1
- package/util/colord.js +0 -13
- package/util/compositeMap.d.ts +0 -11
- package/util/compositeMap.js +0 -61
- package/util/dedupe.js +0 -15
- package/util/formatFastaStrings.js +0 -12
- package/util/idMaker.js +0 -24
- package/util/index.d.ts +0 -274
- package/util/index.js +0 -1052
- package/util/io/RemoteFileWithRangeCache.js +0 -76
- package/util/io/index.d.ts +0 -7
- package/util/io/index.js +0 -103
- package/util/jexl.d.ts +0 -4
- package/util/jexl.js +0 -54
- package/util/jexlStrings.js +0 -23
- package/util/layouts/BaseLayout.d.ts +0 -30
- package/util/layouts/BaseLayout.js +0 -2
- package/util/layouts/GranularRectLayout.d.ts +0 -37
- package/util/layouts/GranularRectLayout.js +0 -343
- package/util/layouts/MultiLayout.d.ts +0 -12
- package/util/layouts/MultiLayout.js +0 -42
- package/util/layouts/PrecomputedLayout.d.ts +0 -28
- package/util/layouts/PrecomputedLayout.js +0 -66
- package/util/layouts/PrecomputedMultiLayout.d.ts +0 -4
- package/util/layouts/PrecomputedMultiLayout.js +0 -21
- package/util/layouts/SceneGraph.js +0 -115
- package/util/layouts/index.d.ts +0 -7
- package/util/layouts/index.js +0 -31
- package/util/makeAbortableReaction.d.ts +0 -2
- package/util/makeAbortableReaction.js +0 -50
- package/util/map-obj.d.ts +0 -3
- package/util/map-obj.js +0 -37
- package/util/mst-reflection.d.ts +0 -11
- package/util/mst-reflection.js +0 -62
- package/util/nanoid.d.ts +0 -5
- package/util/nanoid.js +0 -43
- package/util/nextTick.js +0 -6
- package/util/offscreenCanvasPonyfill.d.ts +0 -7
- package/util/offscreenCanvasPonyfill.js +0 -65
- package/util/offscreenCanvasUtils.d.ts +0 -28
- package/util/offscreenCanvasUtils.js +0 -99
- package/util/parseLineByLine.js +0 -25
- package/util/range.js +0 -26
- package/util/rxjs.d.ts +0 -3
- package/util/rxjs.js +0 -21
- package/util/simpleFeature.d.ts +0 -44
- package/util/simpleFeature.js +0 -82
- package/util/stats.d.ts +0 -21
- package/util/stats.js +0 -78
- package/util/stopToken.d.ts +0 -3
- package/util/stopToken.js +0 -29
- package/util/tracks.d.ts +0 -55
- package/util/tracks.js +0 -168
- package/util/types/index.d.ts +0 -254
- package/util/types/index.js +0 -172
- package/util/types/mst.d.ts +0 -107
- package/util/types/mst.js +0 -72
- package/util/types/util.d.ts +0 -6
- package/util/types/util.js +0 -2
- package/util/useMeasure.js +0 -33
- package/util/when.js +0 -5
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/ArrayValue.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/BasicValue.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/DataGridDetails.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/FieldName.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/SimpleField.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/UriField.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/BaseFeatureDetail/util.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +0 -0
- /package/{PhasedScheduler.d.ts → esm/PhasedScheduler.d.ts} +0 -0
- /package/{ReExports → esm/ReExports}/BaseFeatureDetails.d.ts +0 -0
- /package/{ReExports → esm/ReExports}/DataGrid.d.ts +0 -0
- /package/{ReExports → esm/ReExports}/MuiDataGridReExports.d.ts +0 -0
- /package/{ReExports → esm/ReExports}/lazify.d.ts +0 -0
- /package/{ReExports → esm/ReExports}/list.d.ts +0 -0
- /package/{ReExports → esm/ReExports}/modules.d.ts +0 -0
- /package/{data_adapters → esm/data_adapters}/util.d.ts +0 -0
- /package/{pluggableElementTypes → esm/pluggableElementTypes}/PluggableElementBase.d.ts +0 -0
- /package/{pluggableElementTypes → esm/pluggableElementTypes}/renderers/util/serializableFilterChain.d.ts +0 -0
- /package/{ui → esm/ui}/ColorPicker.d.ts +0 -0
- /package/{ui → esm/ui}/DraggableDialog.d.ts +0 -0
- /package/{ui → esm/ui}/EditableTypography.d.ts +0 -0
- /package/{ui → esm/ui}/ErrorMessage.d.ts +0 -0
- /package/{ui → esm/ui}/ErrorMessageStackTraceDialog.d.ts +0 -0
- /package/{ui → esm/ui}/ExternalLink.d.ts +0 -0
- /package/{ui → esm/ui}/FactoryResetDialog.d.ts +0 -0
- /package/{ui → esm/ui}/FatalErrorDialog.d.ts +0 -0
- /package/{ui → esm/ui}/HoverMenu.d.ts +0 -0
- /package/{ui → esm/ui}/Icons.d.ts +0 -0
- /package/{ui → esm/ui}/Logo.d.ts +0 -0
- /package/{ui → esm/ui}/RedErrorMessageBox.d.ts +0 -0
- /package/{ui → esm/ui}/ResizeHandle.d.ts +0 -0
- /package/{ui → esm/ui}/ReturnToImportFormDialog.d.ts +0 -0
- /package/{ui → esm/ui}/SanitizedHTML.d.ts +0 -0
- /package/{ui → esm/ui}/colors.d.ts +0 -0
- /package/{ui → esm/ui}/useEvent.d.ts +0 -0
- /package/{util → esm/util}/aborting.d.ts +0 -0
- /package/{util → esm/util}/analytics.d.ts +0 -0
- /package/{util → esm/util}/blobToDataURL.d.ts +0 -0
- /package/{util → esm/util}/color/cssColorsLevel4.d.ts +0 -0
- /package/{util → esm/util}/dedupe.d.ts +0 -0
- /package/{util → esm/util}/formatFastaStrings.d.ts +0 -0
- /package/{util → esm/util}/idMaker.d.ts +0 -0
- /package/{util → esm/util}/io/RemoteFileWithRangeCache.d.ts +0 -0
- /package/{util → esm/util}/jexlStrings.d.ts +0 -0
- /package/{util → esm/util}/layouts/SceneGraph.d.ts +0 -0
- /package/{util → esm/util}/nextTick.d.ts +0 -0
- /package/{util → esm/util}/parseLineByLine.d.ts +0 -0
- /package/{util → esm/util}/range.d.ts +0 -0
- /package/{util → esm/util}/useMeasure.d.ts +0 -0
- /package/{util → esm/util}/when.d.ts +0 -0
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export declare const genomeColor = "rgb(200,280,200)";
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function splitString({ str, charactersPerRow, showCoordinates, currRemainder = 0, splitSize = 10, }) {
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import type PluginManager from '../PluginManager';
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export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
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type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
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trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
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showCoordinatesSetting: string;
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intronBp: number;
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upDownBp: number;
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upperCaseCDS: boolean;
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charactersPerRow: number;
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feature: SimpleFeatureSerialized | undefined;
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mode: string;
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} & {
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setFeature(f: SimpleFeatureSerialized): void;
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setUpDownBp(f: number): void;
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setIntronBp(f: number): void;
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setUpperCaseCDS(f: boolean): void;
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setShowCoordinates(f: "none" | "relative" | "genomic"): void;
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setMode(mode: string): void;
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} & {
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readonly showCoordinates: boolean;
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readonly showGenomicCoordsOption: boolean;
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readonly hasCDS: boolean | undefined;
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readonly hasExon: boolean | undefined;
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readonly hasExonOrCDS: boolean | undefined;
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} & {
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afterAttach(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
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descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
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}, {
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error: unknown;
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} & {
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setFeatureData(featureData: SimpleFeatureSerialized): void;
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clearFeatureData(): void;
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setFormattedData(feat: SimpleFeatureSerialized): void;
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setExtra(type?: string, trackId?: string, maxDepth?: number): void;
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setError(e: unknown): void;
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} & {
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afterCreate(): void;
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}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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featureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
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formattedFields: import("mobx-state-tree").IType<any, any, any>;
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unformattedFeatureData: import("mobx-state-tree").IType<MaybeSerializedFeat, MaybeSerializedFeat, MaybeSerializedFeat>;
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trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
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showCoordinatesSetting: string;
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intronBp: number;
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upDownBp: number;
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upperCaseCDS: boolean;
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charactersPerRow: number;
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feature: SimpleFeatureSerialized | undefined;
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mode: string;
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} & {
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setFeature(f: SimpleFeatureSerialized): void;
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setUpDownBp(f: number): void;
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setIntronBp(f: number): void;
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setUpperCaseCDS(f: boolean): void;
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setShowCoordinates(f: "none" | "relative" | "genomic"): void;
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} & {
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readonly showCoordinates: boolean;
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readonly showGenomicCoordsOption: boolean;
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readonly hasCDS: boolean | undefined;
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readonly hasExon: boolean | undefined;
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readonly hasExonOrCDS: boolean | undefined;
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} & {
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afterAttach(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
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descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
|
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}>>, {
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type: "BaseFeatureWidget";
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id: string;
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track: import("mobx-state-tree").ReferenceIdentifier | undefined;
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view: import("mobx-state-tree").ReferenceIdentifier | undefined;
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trackId: string | undefined;
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trackType: string | undefined;
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maxDepth: number | undefined;
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sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
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formattedFields: any;
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descriptions: Record<string, unknown> | undefined;
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finalizedFeatureData: any;
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}>;
|
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|
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export type BaseFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
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|
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export type BaseFeatureWidgetModel = Instance<BaseFeatureWidgetStateModel>;
|
|
@@ -1,99 +0,0 @@
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|
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"use strict";
|
|
2
|
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Object.defineProperty(exports, "__esModule", { value: true });
|
|
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|
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exports.stateModelFactory = stateModelFactory;
|
|
4
|
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const mobx_1 = require("mobx");
|
|
5
|
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const mobx_state_tree_1 = require("mobx-state-tree");
|
|
6
|
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const configuration_1 = require("../configuration");
|
|
7
|
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const util_1 = require("../util");
|
|
8
|
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const model_1 = require("./SequenceFeatureDetails/model");
|
|
9
|
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const util_2 = require("./util");
|
|
10
|
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const mst_1 = require("../util/types/mst");
|
|
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|
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function stateModelFactory(pluginManager) {
|
|
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|
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return mobx_state_tree_1.types
|
|
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|
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.model('BaseFeatureWidget', {
|
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|
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id: mst_1.ElementId,
|
|
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|
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type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
|
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|
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featureData: mobx_state_tree_1.types.frozen(),
|
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|
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formattedFields: mobx_state_tree_1.types.frozen(),
|
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|
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unformattedFeatureData: mobx_state_tree_1.types.frozen(),
|
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|
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view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
|
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|
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track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
|
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21
|
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trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
|
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|
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trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
|
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|
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maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
|
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24
|
-
sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
|
|
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|
-
descriptions: mobx_state_tree_1.types.frozen(),
|
|
26
|
-
})
|
|
27
|
-
.volatile(() => ({
|
|
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|
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error: undefined,
|
|
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|
-
}))
|
|
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|
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.actions(self => ({
|
|
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|
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setFeatureData(featureData) {
|
|
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|
-
self.unformattedFeatureData = featureData;
|
|
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|
-
},
|
|
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;
|
|
@@ -1,48 +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 => {
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|
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formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
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parse(sub);
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}
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package/CorePlugin.d.ts
DELETED
package/CorePlugin.js
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@@ -1,66 +0,0 @@
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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var desc = Object.getOwnPropertyDescriptor(m, k);
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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desc = { enumerable: true, get: function() { return m[k]; } };
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|
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}
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Object.defineProperty(o, k2, desc);
|
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}) : (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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o[k2] = m[k];
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}));
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-
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
|
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|
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}) : function(o, v) {
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o["default"] = v;
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|
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});
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|
-
var __importStar = (this && this.__importStar) || (function () {
|
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var ownKeys = function(o) {
|
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|
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ownKeys = Object.getOwnPropertyNames || function (o) {
|
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var ar = [];
|
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for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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return ar;
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};
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return ownKeys(o);
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};
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return function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
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__setModuleDefault(result, mod);
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return result;
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|
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|
-
};
|
|
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-
})();
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|
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|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
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|
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return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
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|
-
};
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|
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|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
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|
-
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;
|
package/PhasedScheduler.js
DELETED
|
@@ -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
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 {};
|