@jbrowse/core 3.7.0 → 4.0.1
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.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.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.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.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.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
- package/esm/ui/react-colorful.d.ts +3 -0
- package/esm/ui/react-colorful.js +416 -0
- package/esm/ui/theme.d.ts +58 -0
- package/esm/ui/theme.js +392 -0
- package/esm/ui/useEvent.js +10 -0
- package/esm/util/Base1DUtils.d.ts +38 -0
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- package/ui/AppLogo.js +0 -12
- package/ui/AssemblySelector.d.ts +0 -13
- package/ui/AssemblySelector.js +0 -46
- package/ui/BaseTooltip.js +0 -46
- package/ui/CascadingMenu.d.ts +0 -9
- package/ui/CascadingMenu.js +0 -114
- package/ui/CascadingMenuButton.d.ts +0 -11
- package/ui/CascadingMenuButton.js +0 -29
- package/ui/ColorPicker.js +0 -101
- package/ui/ConfirmDialog.js +0 -18
- 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 -65
- 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.js +0 -35
- package/ui/Logo.js +0 -46
- package/ui/Menu.d.ts +0 -54
- 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 -67
- 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 -102
- package/util/color/cssColorsLevel4.js +0 -160
- package/util/color/index.d.ts +0 -5
- package/util/color/index.js +0 -48
- package/util/colord.d.ts +0 -1
- package/util/colord.js +0 -13
- package/util/compositeMap.js +0 -61
- package/util/convertCodingSequenceToPeptides.d.ts +0 -6
- package/util/convertCodingSequenceToPeptides.js +0 -12
- package/util/dedupe.js +0 -15
- package/util/fetchSeq.d.ts +0 -8
- package/util/fetchSeq.js +0 -27
- package/util/flatbush/index.d.ts +0 -25
- package/util/flatbush/index.js +0 -362
- package/util/flatqueue/index.js +0 -66
- 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 -55
- 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 -30
- package/util/layouts/PrecomputedLayout.js +0 -75
- 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/useFeatureSequence.d.ts +0 -19
- package/util/useFeatureSequence.js +0 -90
- 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/consts.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +0 -0
- /package/{BaseFeatureWidget → esm/BaseFeatureWidget}/SequenceFeatureDetails/util.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}/BaseTooltip.d.ts +0 -0
- /package/{ui → esm/ui}/ColorPicker.d.ts +0 -0
- /package/{ui → esm/ui}/ConfirmDialog.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}/LoadingEllipses.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}/compositeMap.d.ts +0 -0
- /package/{util → esm/util}/dedupe.d.ts +0 -0
- /package/{util → esm/util}/flatqueue/index.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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};
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|
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} & {
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[x: string]: unknown;
|
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}, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
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}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
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|
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}>;
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|
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345
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}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
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|
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|
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}>;
|
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|
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afterCreate(): void;
|
|
349
|
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
|
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350
|
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readonly assemblyNamesList: any[];
|
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351
|
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readonly assemblyList: AnyConfigurationModel[];
|
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352
|
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readonly rpcManager: RpcManager;
|
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353
|
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} & {
|
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354
|
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waitForAssembly(assemblyName: string): Promise<({
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|
355
|
-
configuration: any;
|
|
356
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
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357
|
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error: unknown;
|
|
358
|
-
loadingP: Promise<void> | undefined;
|
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359
|
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|
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360
|
-
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|
|
361
|
-
[x: string]: string;
|
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362
|
-
} | undefined;
|
|
363
|
-
cytobands: import("../util").Feature[] | undefined;
|
|
364
|
-
} & {
|
|
365
|
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getConf(arg: string): any;
|
|
366
|
-
readonly lowerCaseRefNameAliases: {
|
|
367
|
-
[k: string]: string;
|
|
368
|
-
} | undefined;
|
|
369
|
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} & {
|
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|
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|
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371
|
-
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|
|
372
|
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readonly regions: import("./assembly").BasicRegion[] | undefined;
|
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373
|
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|
|
374
|
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|
|
375
|
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hasName(name: string): boolean;
|
|
376
|
-
readonly allAliases: string[];
|
|
377
|
-
readonly allRefNames: string[] | undefined;
|
|
378
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
379
|
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readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
380
|
-
readonly rpcManager: RpcManager;
|
|
381
|
-
readonly refNameColors: string[];
|
|
382
|
-
} & {
|
|
383
|
-
readonly refNames: string[] | undefined;
|
|
384
|
-
} & {
|
|
385
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
386
|
-
getCanonicalRefName2(asmName: string): string;
|
|
387
|
-
getRefNameColor(refName: string): string | undefined;
|
|
388
|
-
isValidRefName(refName: string): boolean;
|
|
389
|
-
} & {
|
|
390
|
-
setLoaded({ regions, refNameAliases, cytobands, }: {
|
|
391
|
-
regions: import("../util").Region[];
|
|
392
|
-
refNameAliases: {
|
|
393
|
-
[x: string]: string;
|
|
394
|
-
};
|
|
395
|
-
cytobands: import("../util").Feature[];
|
|
396
|
-
}): void;
|
|
397
|
-
setError(e: unknown): void;
|
|
398
|
-
setRegions(regions: import("../util").Region[]): void;
|
|
399
|
-
setRefNameAliases(aliases: {
|
|
400
|
-
[x: string]: string;
|
|
401
|
-
}): void;
|
|
402
|
-
setCytobands(cytobands: import("../util").Feature[]): void;
|
|
403
|
-
setLoadingP(p?: Promise<void>): void;
|
|
404
|
-
load(): Promise<void>;
|
|
405
|
-
loadPre(): Promise<void>;
|
|
406
|
-
} & {
|
|
407
|
-
getAdapterMapEntry(adapterConf: {
|
|
408
|
-
[x: string]: unknown;
|
|
409
|
-
}, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
|
|
410
|
-
getRefNameMapForAdapter(adapterConf: {
|
|
411
|
-
[x: string]: unknown;
|
|
412
|
-
}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
413
|
-
[x: string]: string;
|
|
414
|
-
}>;
|
|
415
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
416
|
-
[x: string]: unknown;
|
|
417
|
-
}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
418
|
-
[x: string]: string;
|
|
419
|
-
}>;
|
|
420
|
-
afterCreate(): void;
|
|
421
|
-
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
422
|
-
configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
|
|
423
|
-
}, {
|
|
424
|
-
error: unknown;
|
|
425
|
-
loadingP: Promise<void> | undefined;
|
|
426
|
-
volatileRegions: import("./assembly").BasicRegion[] | undefined;
|
|
427
|
-
refNameAliases: {
|
|
428
|
-
[x: string]: string;
|
|
429
|
-
} | undefined;
|
|
430
|
-
cytobands: import("../util").Feature[] | undefined;
|
|
431
|
-
} & {
|
|
432
|
-
getConf(arg: string): any;
|
|
433
|
-
readonly lowerCaseRefNameAliases: {
|
|
434
|
-
[k: string]: string;
|
|
435
|
-
} | undefined;
|
|
436
|
-
} & {
|
|
437
|
-
readonly initialized: boolean;
|
|
438
|
-
readonly name: string;
|
|
439
|
-
readonly regions: import("./assembly").BasicRegion[] | undefined;
|
|
440
|
-
readonly aliases: string[];
|
|
441
|
-
readonly displayName: string;
|
|
442
|
-
hasName(name: string): boolean;
|
|
443
|
-
readonly allAliases: string[];
|
|
444
|
-
readonly allRefNames: string[] | undefined;
|
|
445
|
-
readonly lowerCaseRefNames: string[] | undefined;
|
|
446
|
-
readonly allRefNamesWithLowerCase: string[] | undefined;
|
|
447
|
-
readonly rpcManager: RpcManager;
|
|
448
|
-
readonly refNameColors: string[];
|
|
449
|
-
} & {
|
|
450
|
-
readonly refNames: string[] | undefined;
|
|
451
|
-
} & {
|
|
452
|
-
getCanonicalRefName(refName: string): string | undefined;
|
|
453
|
-
getCanonicalRefName2(asmName: string): string;
|
|
454
|
-
getRefNameColor(refName: string): string | undefined;
|
|
455
|
-
isValidRefName(refName: string): boolean;
|
|
456
|
-
} & {
|
|
457
|
-
setLoaded({ regions, refNameAliases, cytobands, }: {
|
|
458
|
-
regions: import("../util").Region[];
|
|
459
|
-
refNameAliases: {
|
|
460
|
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[x: string]: string;
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461
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};
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462
|
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cytobands: import("../util").Feature[];
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463
|
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}): void;
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464
|
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setError(e: unknown): void;
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465
|
-
setRegions(regions: import("../util").Region[]): void;
|
|
466
|
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setRefNameAliases(aliases: {
|
|
467
|
-
[x: string]: string;
|
|
468
|
-
}): void;
|
|
469
|
-
setCytobands(cytobands: import("../util").Feature[]): void;
|
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470
|
-
setLoadingP(p?: Promise<void>): void;
|
|
471
|
-
load(): Promise<void>;
|
|
472
|
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loadPre(): Promise<void>;
|
|
473
|
-
} & {
|
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|
-
getAdapterMapEntry(adapterConf: {
|
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475
|
-
[x: string]: unknown;
|
|
476
|
-
}, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
|
|
477
|
-
getRefNameMapForAdapter(adapterConf: {
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|
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[x: string]: unknown;
|
|
479
|
-
}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
480
|
-
[x: string]: string;
|
|
481
|
-
}>;
|
|
482
|
-
getReverseRefNameMapForAdapter(adapterConf: {
|
|
483
|
-
[x: string]: unknown;
|
|
484
|
-
}, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
|
|
485
|
-
[x: string]: string;
|
|
486
|
-
}>;
|
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487
|
-
afterCreate(): void;
|
|
488
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
|
|
489
|
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getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
|
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490
|
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stopToken?: string;
|
|
491
|
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sessionId: string;
|
|
492
|
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}): Promise<{
|
|
493
|
-
[x: string]: string;
|
|
494
|
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} | undefined>;
|
|
495
|
-
getReverseRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
|
|
496
|
-
stopToken?: string;
|
|
497
|
-
sessionId: string;
|
|
498
|
-
}): Promise<{
|
|
499
|
-
[x: string]: string;
|
|
500
|
-
} | undefined>;
|
|
501
|
-
isValidRefName(refName: string, assemblyName: string): boolean;
|
|
502
|
-
} & {
|
|
503
|
-
afterAttach(): void;
|
|
504
|
-
removeAssembly(asm: Assembly): void;
|
|
505
|
-
addAssembly(configuration: any): void;
|
|
506
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
507
|
-
export default assemblyManagerFactory;
|
|
@@ -1,138 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
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3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
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const mobx_1 = require("mobx");
|
|
7
|
-
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
8
|
-
const configuration_1 = require("../configuration");
|
|
9
|
-
const util_1 = require("../util");
|
|
10
|
-
const assembly_1 = __importDefault(require("./assembly"));
|
|
11
|
-
function assemblyManagerFactory(conf, pm) {
|
|
12
|
-
return mobx_state_tree_1.types
|
|
13
|
-
.model({
|
|
14
|
-
assemblies: mobx_state_tree_1.types.array((0, assembly_1.default)(conf, pm)),
|
|
15
|
-
})
|
|
16
|
-
.views(self => ({
|
|
17
|
-
get assemblyNameMap() {
|
|
18
|
-
const obj = {};
|
|
19
|
-
for (const assembly of self.assemblies) {
|
|
20
|
-
for (const name of assembly.allAliases) {
|
|
21
|
-
obj[name] = assembly;
|
|
22
|
-
}
|
|
23
|
-
}
|
|
24
|
-
return obj;
|
|
25
|
-
},
|
|
26
|
-
}))
|
|
27
|
-
.views(self => ({
|
|
28
|
-
getCanonicalAssemblyName(asmName) {
|
|
29
|
-
var _a;
|
|
30
|
-
return (_a = self.assemblyNameMap[asmName]) === null || _a === void 0 ? void 0 : _a.name;
|
|
31
|
-
},
|
|
32
|
-
getCanonicalAssemblyName2(asmName) {
|
|
33
|
-
var _a;
|
|
34
|
-
return ((_a = self.assemblyNameMap[asmName]) === null || _a === void 0 ? void 0 : _a.name) || asmName;
|
|
35
|
-
},
|
|
36
|
-
get(asmName) {
|
|
37
|
-
if (asmName) {
|
|
38
|
-
const assembly = self.assemblyNameMap[asmName];
|
|
39
|
-
if (assembly) {
|
|
40
|
-
return assembly;
|
|
41
|
-
}
|
|
42
|
-
else if (!this.assemblyNamesList.includes(asmName)) {
|
|
43
|
-
pm.evaluateExtensionPoint('Core-handleUnrecognizedAssembly', undefined, {
|
|
44
|
-
assemblyName: asmName,
|
|
45
|
-
session: (0, mobx_state_tree_1.getParent)(self).session,
|
|
46
|
-
});
|
|
47
|
-
}
|
|
48
|
-
}
|
|
49
|
-
return undefined;
|
|
50
|
-
},
|
|
51
|
-
get assemblyNamesList() {
|
|
52
|
-
return this.assemblyList.map(asm => asm.name);
|
|
53
|
-
},
|
|
54
|
-
get assemblyList() {
|
|
55
|
-
const { jbrowse: { assemblies }, session: { sessionAssemblies = [], temporaryAssemblies = [] } = {}, } = (0, mobx_state_tree_1.getParent)(self);
|
|
56
|
-
return [
|
|
57
|
-
...assemblies,
|
|
58
|
-
...sessionAssemblies,
|
|
59
|
-
...temporaryAssemblies,
|
|
60
|
-
];
|
|
61
|
-
},
|
|
62
|
-
get rpcManager() {
|
|
63
|
-
return (0, mobx_state_tree_1.getParent)(self).rpcManager;
|
|
64
|
-
},
|
|
65
|
-
}))
|
|
66
|
-
.views(self => ({
|
|
67
|
-
async waitForAssembly(assemblyName) {
|
|
68
|
-
if (!assemblyName) {
|
|
69
|
-
throw new Error('no assembly name supplied to waitForAssembly');
|
|
70
|
-
}
|
|
71
|
-
let assembly = self.get(assemblyName);
|
|
72
|
-
if (!assembly) {
|
|
73
|
-
try {
|
|
74
|
-
await (0, util_1.when)(() => Boolean(self.get(assemblyName)), {
|
|
75
|
-
timeout: 10000,
|
|
76
|
-
});
|
|
77
|
-
assembly = self.get(assemblyName);
|
|
78
|
-
}
|
|
79
|
-
catch (e) {
|
|
80
|
-
}
|
|
81
|
-
}
|
|
82
|
-
if (!assembly) {
|
|
83
|
-
return undefined;
|
|
84
|
-
}
|
|
85
|
-
await assembly.load();
|
|
86
|
-
await (0, util_1.when)(() => !!(assembly.regions && assembly.refNameAliases) || !!assembly.error);
|
|
87
|
-
if (assembly.error) {
|
|
88
|
-
throw assembly.error;
|
|
89
|
-
}
|
|
90
|
-
return assembly;
|
|
91
|
-
},
|
|
92
|
-
async getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
|
|
93
|
-
if (assemblyName) {
|
|
94
|
-
const asm = await this.waitForAssembly(assemblyName);
|
|
95
|
-
return asm === null || asm === void 0 ? void 0 : asm.getRefNameMapForAdapter(adapterConf, opts);
|
|
96
|
-
}
|
|
97
|
-
return {};
|
|
98
|
-
},
|
|
99
|
-
async getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
|
|
100
|
-
if (assemblyName) {
|
|
101
|
-
const asm = await this.waitForAssembly(assemblyName);
|
|
102
|
-
return asm === null || asm === void 0 ? void 0 : asm.getReverseRefNameMapForAdapter(adapterConf, opts);
|
|
103
|
-
}
|
|
104
|
-
return {};
|
|
105
|
-
},
|
|
106
|
-
isValidRefName(refName, assemblyName) {
|
|
107
|
-
const assembly = self.get(assemblyName);
|
|
108
|
-
if (assembly) {
|
|
109
|
-
return assembly.isValidRefName(refName);
|
|
110
|
-
}
|
|
111
|
-
throw new Error(`Failed to look up refName:${refName} on assemblyName:${assemblyName} (assembly does not exist)`);
|
|
112
|
-
},
|
|
113
|
-
}))
|
|
114
|
-
.actions(self => ({
|
|
115
|
-
afterAttach() {
|
|
116
|
-
(0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => self.assemblyList, assemblyConfs => {
|
|
117
|
-
for (const asm of self.assemblies) {
|
|
118
|
-
if (!asm.configuration) {
|
|
119
|
-
this.removeAssembly(asm);
|
|
120
|
-
}
|
|
121
|
-
}
|
|
122
|
-
for (const conf of assemblyConfs) {
|
|
123
|
-
const name = (0, configuration_1.readConfObject)(conf, 'name');
|
|
124
|
-
if (!self.assemblies.some(a => a.name === name)) {
|
|
125
|
-
this.addAssembly(conf);
|
|
126
|
-
}
|
|
127
|
-
}
|
|
128
|
-
}, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
|
|
129
|
-
},
|
|
130
|
-
removeAssembly(asm) {
|
|
131
|
-
self.assemblies.remove(asm);
|
|
132
|
-
},
|
|
133
|
-
addAssembly(configuration) {
|
|
134
|
-
self.assemblies.push({ configuration });
|
|
135
|
-
},
|
|
136
|
-
}));
|
|
137
|
-
}
|
|
138
|
-
exports.default = assemblyManagerFactory;
|
package/assemblyManager/index.js
DELETED
|
@@ -1,10 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.assemblyConfigSchemaFactory = exports.default = void 0;
|
|
7
|
-
var assemblyManager_1 = require("./assemblyManager");
|
|
8
|
-
Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(assemblyManager_1).default; } });
|
|
9
|
-
var assemblyConfigSchema_1 = require("./assemblyConfigSchema");
|
|
10
|
-
Object.defineProperty(exports, "assemblyConfigSchemaFactory", { enumerable: true, get: function () { return __importDefault(assemblyConfigSchema_1).default; } });
|