@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.10
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/README.md +1476 -265
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +5 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +3 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +34 -29
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +1 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +16 -9
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +15 -31
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +4 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +12 -25
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +6 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +5 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +6 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +7 -18
- package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.d.ts +16 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/jexlFilterActions.js +50 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +0 -8
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +6 -29
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +7 -34
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +2 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +2 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +3 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +12 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +12 -5
- package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
- package/esm/BaseFeatureWidget/formatDetails.d.ts +13 -29
- package/esm/BaseFeatureWidget/formatDetails.js +62 -83
- package/esm/BaseFeatureWidget/index.d.ts +2 -1
- package/esm/BaseFeatureWidget/stateModelFactory.d.ts +42 -29
- package/esm/BaseFeatureWidget/stateModelFactory.js +98 -98
- package/esm/BaseFeatureWidget/types.d.ts +12 -6
- package/esm/BaseFeatureWidget/util.d.ts +0 -10
- package/esm/BaseFeatureWidget/util.js +0 -17
- package/esm/CorePlugin.js +2 -2
- package/esm/PluginLoader.d.ts +24 -13
- package/esm/PluginLoader.js +167 -51
- package/esm/PluginManager.d.ts +130 -24
- package/esm/PluginManager.js +180 -32
- package/esm/ReExports/MuiDataGridReExports.d.ts +1 -0
- package/esm/ReExports/MuiDataGridReExports.js +2 -2
- package/esm/ReExports/coreModules.generated.d.ts +2 -0
- package/esm/ReExports/coreModules.generated.js +528 -0
- package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
- package/esm/ReExports/coreWorkerModules.generated.js +488 -0
- package/esm/ReExports/frameworkModules.d.ts +2 -0
- package/esm/ReExports/frameworkModules.js +68 -0
- package/esm/ReExports/frameworkShared.d.ts +12 -0
- package/esm/ReExports/frameworkShared.js +16 -0
- package/esm/ReExports/frameworkWorkerModules.generated.d.ts +2 -0
- package/esm/ReExports/frameworkWorkerModules.generated.js +130 -0
- package/esm/ReExports/list.js +527 -79
- package/esm/ReExports/modules.d.ts +1 -1
- package/esm/ReExports/modules.js +10 -165
- package/esm/ReExports/registry.d.ts +1 -0
- package/esm/ReExports/registry.js +23 -5
- package/esm/ReExports/uiStub.d.ts +3 -0
- package/esm/ReExports/uiStub.js +33 -0
- package/esm/ReExports/workerModules.d.ts +2 -0
- package/esm/ReExports/workerModules.js +11 -0
- package/esm/TextSearch/TextSearchManager.d.ts +27 -13
- package/esm/TextSearch/TextSearchManager.js +77 -36
- package/esm/TextSearch/places.d.ts +12 -0
- package/esm/TextSearch/places.js +94 -0
- package/esm/assemblyManager/assembly.d.ts +21 -19
- package/esm/assemblyManager/assembly.js +28 -26
- package/esm/assemblyManager/assemblyAdapters.d.ts +1 -1
- package/esm/assemblyManager/assemblyAdapters.js +8 -2
- package/esm/assemblyManager/assemblyConfigSchema.d.ts +31 -90
- package/esm/assemblyManager/assemblyConfigSchema.js +35 -47
- package/esm/assemblyManager/assemblyManager.d.ts +35 -180
- package/esm/assemblyManager/assemblyManager.js +47 -51
- package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +25 -18
- package/esm/assemblyManager/expandAssemblyConfigShorthand.js +78 -49
- package/esm/assemblyManager/geneticCodes.js +2 -5
- package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +10 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.js +10 -0
- package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
- package/esm/assemblyManager/indexAssemblyNames.js +22 -0
- package/esm/assemblyManager/loadRefNameMap.d.ts +1 -1
- package/esm/assemblyManager/loadRefNameMap.js +4 -9
- package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
- package/esm/assemblyManager/refNameMapKey.js +12 -0
- package/esm/checkPlugins.d.ts +2 -0
- package/esm/checkPlugins.js +38 -17
- package/esm/configuration/bamIndexFields.d.ts +49 -0
- package/esm/configuration/bamIndexFields.js +41 -0
- package/esm/configuration/configurationSchema.d.ts +101 -71
- package/esm/configuration/configurationSchema.js +207 -134
- package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
- package/esm/configuration/configurationSchemaUnion.js +56 -0
- package/esm/configuration/configurationSlot.d.ts +150 -60
- package/esm/configuration/configurationSlot.js +103 -75
- package/esm/configuration/fillLocations.d.ts +14 -0
- package/esm/configuration/fillLocations.js +14 -0
- package/esm/configuration/formatAboutConfigSchema.d.ts +7 -21
- package/esm/configuration/formatDetailsConfigSchema.d.ts +11 -37
- package/esm/configuration/formatDetailsConfigSchema.js +10 -13
- package/esm/configuration/fullConfSnapshot.d.ts +4 -19
- package/esm/configuration/fullConfSnapshot.js +30 -52
- package/esm/configuration/getConf.d.ts +45 -41
- package/esm/configuration/getConf.js +111 -44
- package/esm/configuration/index.d.ts +24 -11
- package/esm/configuration/index.js +15 -7
- package/esm/configuration/indexType.d.ts +26 -0
- package/esm/configuration/indexType.js +38 -0
- package/esm/configuration/mergeFormatCallbacks.d.ts +6 -7
- package/esm/configuration/mergeFormatCallbacks.js +13 -10
- package/esm/configuration/readConfObject.d.ts +2 -24
- package/esm/configuration/readConfObject.js +20 -63
- package/esm/configuration/requirements.d.ts +37 -0
- package/esm/configuration/requirements.js +88 -0
- package/esm/configuration/schemaRegistry.d.ts +32 -15
- package/esm/configuration/schemaRegistry.js +33 -35
- package/esm/configuration/schemaTypes.d.ts +21 -5
- package/esm/configuration/schemaTypes.js +66 -55
- package/esm/configuration/slotFacade.d.ts +12 -29
- package/esm/configuration/slotFacade.js +44 -23
- package/esm/configuration/snapshotPreprocess.d.ts +43 -0
- package/esm/configuration/snapshotPreprocess.js +161 -0
- package/esm/configuration/tabixIndexFields.d.ts +30 -4
- package/esm/configuration/tabixIndexFields.js +21 -4
- package/esm/configuration/tabixShorthand.d.ts +34 -17
- package/esm/configuration/tabixShorthand.js +49 -22
- package/esm/configuration/types.d.ts +182 -43
- package/esm/configuration/uriShorthand.d.ts +9 -0
- package/esm/configuration/uriShorthand.js +16 -0
- package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +13 -19
- package/esm/data_adapters/BaseAdapter/BaseAdapter.js +12 -19
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +40 -2
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +68 -5
- package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
- package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
- package/esm/data_adapters/BaseAdapter/index.d.ts +23 -3
- package/esm/data_adapters/BaseAdapter/index.js +1 -0
- package/esm/data_adapters/BaseAdapter/rowSources.d.ts +37 -0
- package/esm/data_adapters/BaseAdapter/rowSources.js +7 -0
- package/esm/data_adapters/BaseAdapter/stats.d.ts +33 -1
- package/esm/data_adapters/BaseAdapter/stats.js +52 -13
- package/esm/data_adapters/BaseAdapter/types.d.ts +8 -12
- package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +1 -1
- package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +7 -11
- package/esm/data_adapters/CytobandAdapter/configSchema.js +3 -17
- package/esm/data_adapters/dataAdapterCache.d.ts +19 -2
- package/esm/data_adapters/dataAdapterCache.js +44 -10
- package/esm/data_adapters/getFeatureAdapter.d.ts +6 -4
- package/esm/data_adapters/getFeatureAdapter.js +8 -8
- package/esm/data_adapters/getSequenceSubAdapter.d.ts +7 -9
- package/esm/data_adapters/getSequenceSubAdapter.js +8 -10
- package/esm/pluggableElementTypes/AdapterType.d.ts +8 -8
- package/esm/pluggableElementTypes/AdapterType.js +1 -1
- package/esm/pluggableElementTypes/DisplayType.d.ts +46 -16
- package/esm/pluggableElementTypes/DisplayType.js +22 -12
- package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
- package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
- package/esm/pluggableElementTypes/PluggableElementBase.d.ts +3 -5
- package/esm/pluggableElementTypes/PluggableElementBase.js +3 -5
- package/esm/pluggableElementTypes/RpcMethodType.d.ts +11 -1
- package/esm/pluggableElementTypes/RpcMethodType.js +25 -9
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +1 -2
- package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
- package/esm/pluggableElementTypes/ViewType.d.ts +20 -4
- package/esm/pluggableElementTypes/ViewType.js +32 -4
- package/esm/pluggableElementTypes/addMenuItems.d.ts +3 -2
- package/esm/pluggableElementTypes/extendElementType.d.ts +1 -2
- package/esm/pluggableElementTypes/extendElementType.js +9 -5
- package/esm/pluggableElementTypes/index.d.ts +2 -1
- package/esm/pluggableElementTypes/index.js +1 -1
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +19 -9
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +65 -27
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +72 -10
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +65 -16
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +179 -117
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +85 -16
- package/esm/pluggableElementTypes/models/BaseViewModel.js +53 -10
- package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +26 -16
- package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +15 -11
- package/esm/pluggableElementTypes/models/assertDisplayContract.js +25 -32
- package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -18
- package/esm/pluggableElementTypes/models/baseConnectionConfig.js +5 -5
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +26 -31
- package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +108 -147
- package/esm/pluggableElementTypes/models/baseTrackConfig.js +96 -73
- package/esm/pluggableElementTypes/models/components/SaveTrackData.js +4 -6
- package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +3 -4
- package/esm/pluggableElementTypes/models/components/fetchTrackData.js +3 -3
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +23 -13
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +80 -48
- package/esm/pluggableElementTypes/models/index.d.ts +2 -3
- package/esm/pluggableElementTypes/models/index.js +2 -3
- package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +15 -1
- package/esm/pluggableElementTypes/models/migrateTrackConfig.js +85 -25
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +4 -3
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +141 -19
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +3 -3
- package/esm/pluginDefinitions.d.ts +34 -7
- package/esm/pluginDefinitions.js +54 -20
- package/esm/rpc/BaseRpcDriver.d.ts +2 -2
- package/esm/rpc/BaseRpcDriver.js +25 -30
- package/esm/rpc/MainThreadRpcDriver.d.ts +2 -2
- package/esm/rpc/MainThreadRpcDriver.js +13 -8
- package/esm/rpc/RpcClient.d.ts +18 -6
- package/esm/rpc/RpcClient.js +51 -16
- package/esm/rpc/RpcManager.d.ts +14 -10
- package/esm/rpc/RpcManager.js +11 -1
- package/esm/rpc/RpcRegistry.d.ts +40 -7
- package/esm/rpc/RpcServer.d.ts +3 -1
- package/esm/rpc/RpcServer.js +19 -12
- package/esm/rpc/WebWorkerRpcDriver.d.ts +11 -4
- package/esm/rpc/WebWorkerRpcDriver.js +64 -68
- package/esm/rpc/byteBudget.d.ts +20 -5
- package/esm/rpc/byteBudget.js +16 -5
- package/esm/rpc/configSchema.d.ts +7 -21
- package/esm/rpc/coreRpcMethods.d.ts +4 -0
- package/esm/rpc/coreRpcMethods.js +4 -0
- package/esm/rpc/methods/CoreGetEncodedFeature.d.ts +13 -0
- package/esm/rpc/methods/CoreGetEncodedFeature.js +32 -0
- package/esm/rpc/methods/CoreGetEncodedLayers.d.ts +16 -0
- package/esm/rpc/methods/CoreGetEncodedLayers.js +59 -0
- package/esm/rpc/methods/CoreGetExportData.js +3 -4
- package/esm/rpc/methods/CoreGetFeatureDensity.d.ts +11 -0
- package/esm/rpc/methods/CoreGetFeatureDensity.js +22 -0
- package/esm/rpc/methods/CoreGetFeatures.js +3 -5
- package/esm/rpc/methods/CoreGetRefNames.js +2 -12
- package/esm/rpc/methods/CoreGetRegionByteEstimate.js +1 -1
- package/esm/rpc/methods/CoreGetSequence.js +2 -2
- package/esm/rpc/methods/CoreLoadAdapterCode.d.ts +13 -0
- package/esm/rpc/methods/CoreLoadAdapterCode.js +16 -0
- package/esm/rpc/methods/layerFeatures.d.ts +33 -0
- package/esm/rpc/methods/layerFeatures.js +29 -0
- package/esm/svg/SvgExport.js +6 -7
- package/esm/svg/SvgThemeProviders.d.ts +12 -0
- package/esm/svg/SvgThemeProviders.js +15 -0
- package/esm/svg/exportViewSvg.d.ts +28 -0
- package/esm/svg/exportViewSvg.js +13 -0
- package/esm/svg/normalizeSvgMarkup.d.ts +7 -0
- package/esm/svg/normalizeSvgMarkup.js +99 -0
- package/esm/svg/serializeSvg.d.ts +7 -0
- package/esm/svg/serializeSvg.js +11 -0
- package/esm/svg/svgId.d.ts +1 -1
- package/esm/svg/svgId.js +1 -1
- package/esm/svg/svgReady.d.ts +9 -7
- package/esm/svg/svgReady.js +8 -7
- package/esm/svg/trackNames.d.ts +7 -5
- package/esm/svg/trackNames.js +12 -9
- package/esm/svg/wrapSvgExport.js +6 -74
- package/esm/ui/AddCustomPluginDialog.js +3 -8
- package/esm/ui/AppReadyMarker.d.ts +45 -0
- package/esm/ui/AppReadyMarker.js +89 -0
- package/esm/ui/BaseExportSvgDialog.d.ts +1 -1
- package/esm/ui/CascadingMenu.js +181 -104
- package/esm/ui/DropDownMenu.js +2 -1
- package/esm/ui/ErrorBanner.js +1 -1
- package/esm/ui/ErrorBoundary.d.ts +2 -2
- package/esm/ui/ErrorMessageStackTraceContents.js +2 -1
- package/esm/ui/ErrorMessageStackTraceDialog.js +5 -11
- package/esm/ui/ExportSvgDialog.d.ts +1 -1
- package/esm/ui/FileDropZone.js +2 -1
- package/esm/ui/FileSelector/useInternetAccounts.d.ts +156 -96
- package/esm/ui/HoverMenu.d.ts +1 -2
- package/esm/ui/HoverMenu.js +6 -3
- package/esm/ui/JexlFilterDialog.d.ts +13 -10
- package/esm/ui/JexlFilterDialog.js +122 -49
- package/esm/ui/JexlFilterRowEditors.d.ts +15 -0
- package/esm/ui/JexlFilterRowEditors.js +90 -0
- package/esm/ui/LazyBaseTooltip.d.ts +4 -0
- package/esm/ui/LazyBaseTooltip.js +9 -0
- package/esm/ui/LegendSwatchGlyph.js +26 -21
- package/esm/ui/LoadingOverlay.d.ts +14 -0
- package/esm/ui/LoadingOverlay.js +4 -2
- package/esm/ui/MenuTypes.d.ts +23 -53
- package/esm/ui/MenuTypes.js +3 -0
- package/esm/ui/MonospaceTextField.d.ts +2 -1
- package/esm/ui/MonospaceTextField.js +23 -20
- package/esm/ui/PaletteContext.d.ts +10 -5
- package/esm/ui/PaletteContext.js +44 -6
- package/esm/ui/RefNameAutocomplete/SearchOption.d.ts +13 -0
- package/esm/ui/RefNameAutocomplete/SearchOption.js +45 -0
- package/esm/ui/RefNameAutocomplete/index.d.ts +1 -2
- package/esm/ui/RefNameAutocomplete/index.js +8 -2
- package/esm/ui/RefNameAutocomplete/util.d.ts +13 -0
- package/esm/ui/RefNameAutocomplete/util.js +42 -1
- package/esm/ui/ResizeHandle.d.ts +3 -1
- package/esm/ui/ResizeHandle.js +44 -11
- package/esm/ui/ScrollChrome.d.ts +13 -0
- package/esm/ui/ScrollChrome.js +11 -0
- package/esm/ui/ScrollEdgeShadow.d.ts +6 -9
- package/esm/ui/ScrollEdgeShadow.js +14 -35
- package/esm/ui/ScrollZoomToggle.d.ts +4 -27
- package/esm/ui/ScrollZoomToggle.js +34 -51
- package/esm/ui/SessionJsonPanel.d.ts +3 -0
- package/esm/ui/SessionJsonPanel.js +14 -0
- package/esm/ui/SettingsChangesTable.d.ts +1 -0
- package/esm/ui/SettingsChangesTable.js +49 -11
- package/esm/ui/ShareLinkField.d.ts +1 -3
- package/esm/ui/ShareLinkField.js +13 -40
- package/esm/ui/SizeSliderRow.d.ts +1 -3
- package/esm/ui/SizeSliderRow.js +4 -6
- package/esm/ui/SnackbarModel.js +79 -67
- package/esm/ui/StatusProgressBar.js +2 -2
- package/esm/ui/SvgColorLegend.d.ts +9 -4
- package/esm/ui/SvgColorLegend.js +82 -41
- package/esm/ui/VerticalScrollbar.d.ts +13 -34
- package/esm/ui/VerticalScrollbar.js +29 -83
- package/esm/ui/ViewLoadingScreen.d.ts +5 -4
- package/esm/ui/ViewLoadingScreen.js +8 -32
- package/esm/ui/colorScale.d.ts +92 -0
- package/esm/ui/colorScale.js +72 -0
- package/esm/ui/colors.d.ts +64 -0
- package/esm/ui/colors.js +230 -1
- package/esm/ui/hoverBoxStyle.d.ts +14 -2
- package/esm/ui/hoverBoxStyle.js +17 -2
- package/esm/ui/index.d.ts +12 -12
- package/esm/ui/index.js +14 -22
- package/esm/ui/launchViewMenu.js +15 -5
- package/esm/ui/legendMenuItem.d.ts +10 -32
- package/esm/ui/legendMenuItem.js +9 -36
- package/esm/ui/legendSpec.d.ts +15 -8
- package/esm/ui/legendSpec.js +14 -23
- package/esm/ui/makeSizeMenu.d.ts +0 -6
- package/esm/ui/makeSizeMenu.js +6 -30
- package/esm/ui/measureLegendText.js +1 -1
- package/esm/ui/menuItemAdornment.d.ts +9 -20
- package/esm/ui/menuItemAdornment.js +10 -32
- package/esm/ui/menuItems.d.ts +2 -7
- package/esm/ui/menuItems.js +1 -6
- package/esm/ui/multiTrackMenuItems.d.ts +6 -0
- package/esm/ui/palette.d.ts +118 -116
- package/esm/ui/palette.js +114 -75
- package/esm/ui/replaceViewAction.d.ts +1 -1
- package/esm/ui/replaceViewAction.js +1 -1
- package/esm/ui/theme.d.ts +43 -119
- package/esm/ui/theme.js +62 -78
- package/esm/ui/toggleMenuItems.d.ts +1 -3
- package/esm/ui/toggleMenuItems.js +6 -5
- package/esm/ui/useAssemblySelection.d.ts +4 -4
- package/esm/ui/viewHeaderHeight.d.ts +1 -0
- package/esm/ui/viewHeaderHeight.js +1 -0
- package/esm/util/Base1DUtils.d.ts +5 -3
- package/esm/util/Base1DUtils.js +14 -6
- package/esm/util/Base1DViewModel.d.ts +2 -1
- package/esm/util/Base1DViewModel.js +3 -2
- package/esm/util/SvgCanvas.d.ts +15 -13
- package/esm/util/SvgCanvas.js +76 -56
- package/esm/util/aborting.d.ts +39 -0
- package/esm/util/aborting.js +88 -6
- package/esm/util/adapterMetadata.d.ts +1 -1
- package/esm/util/adapterMetadata.js +6 -5
- package/esm/util/addAndShowTrack.d.ts +2 -5
- package/esm/util/addAndShowTrack.js +5 -1
- package/esm/util/addRelativeUris.d.ts +17 -5
- package/esm/util/addRelativeUris.js +46 -10
- package/esm/util/addTrackFromWidget.d.ts +2 -5
- package/esm/util/addTrackFromWidget.js +5 -4
- package/esm/util/aggregateFieldName.d.ts +10 -0
- package/esm/util/aggregateFieldName.js +8 -0
- package/esm/util/analytics.js +46 -13
- package/esm/util/animationAllowed.d.ts +9 -0
- package/esm/util/animationAllowed.js +13 -0
- package/esm/util/applyRowResizeWheel.d.ts +10 -5
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- package/esm/util/bandLayout.js +4 -4
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- package/esm/util/bezierConnector.js +38 -45
- package/esm/util/bgzfWorkerPool.d.ts +20 -74
- package/esm/util/bgzfWorkerPool.js +20 -74
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- package/esm/util/cacheBudgets.d.ts +22 -19
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- package/esm/util/categoricalField.js +73 -0
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- package/esm/util/clampToContig.js +19 -0
- package/esm/util/coarseStripHTML.js +1 -2
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- package/esm/util/color/cssColorsLevel4.js +1 -0
- package/esm/util/color/index.d.ts +5 -3
- package/esm/util/color/index.js +7 -4
- package/esm/util/colorBits.d.ts +3 -3
- package/esm/util/colorBits.js +19 -44
- package/esm/util/colorRamp.d.ts +49 -5
- package/esm/util/colorRamp.js +169 -18
- package/esm/util/colorScale.d.ts +156 -0
- package/esm/util/colorScale.js +243 -0
- package/esm/util/colorSchemes.d.ts +21 -0
- package/esm/util/colorSchemes.js +30 -0
- package/esm/util/{createStopTokenRotation.d.ts → createAbortRotation.d.ts} +21 -23
- package/esm/util/{createStopTokenRotation.js → createAbortRotation.js} +21 -52
- package/esm/util/createSvgRasterCanvas.d.ts +10 -0
- package/esm/util/cssColorParse.d.ts +15 -0
- package/esm/util/cssColorParse.js +53 -0
- package/esm/util/diagonalizeRegions.d.ts +2 -3
- package/esm/util/diagonalizeRegions.js +8 -13
- package/esm/util/expandLooseSearchIndex.d.ts +19 -0
- package/esm/util/expandLooseSearchIndex.js +29 -0
- package/esm/util/featureTable.d.ts +224 -0
- package/esm/util/featureTable.js +366 -0
- package/esm/util/featureTransforms.d.ts +80 -0
- package/esm/util/featureTransforms.js +1579 -0
- package/esm/util/featureTypes.d.ts +24 -0
- package/esm/util/featureTypes.js +35 -0
- package/esm/util/fetchAndMaybeUnzip.js +16 -9
- package/esm/util/fetchContext.d.ts +7 -8
- package/esm/util/fetchContext.js +3 -3
- package/esm/util/fetchHub.d.ts +4 -2
- package/esm/util/fetchHub.js +2 -2
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- package/esm/util/fetchSeq.d.ts +2 -3
- package/esm/util/fetchSeq.js +2 -2
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- package/esm/util/fieldReader.js +62 -0
- package/esm/util/freezeDeep.d.ts +8 -10
- package/esm/util/freezeDeep.js +8 -10
- package/esm/util/groupKeys.d.ts +77 -0
- package/esm/util/groupKeys.js +155 -0
- package/esm/util/highlights.d.ts +10 -6
- package/esm/util/highlights.js +12 -25
- package/esm/util/hooks.d.ts +31 -2
- package/esm/util/hooks.js +72 -3
- package/esm/util/index.d.ts +11 -11
- package/esm/util/index.js +11 -10
- package/esm/util/indexCandidates.d.ts +1 -31
- package/esm/util/indexCandidates.js +5 -63
- package/esm/util/installFetch.d.ts +77 -37
- package/esm/util/installFetch.js +65 -38
- package/esm/util/installInitAutorun.d.ts +14 -13
- package/esm/util/installInitAutorun.js +17 -17
- package/esm/util/installPrerequisiteFetch.d.ts +115 -0
- package/esm/util/installPrerequisiteFetch.js +111 -0
- package/esm/util/io/index.js +19 -14
- package/esm/util/isDataCurrent.d.ts +7 -5
- package/esm/util/isDataCurrent.js +9 -6
- package/esm/util/isTextEntryFocused.d.ts +7 -0
- package/esm/util/isTextEntryFocused.js +16 -0
- package/esm/util/jexl.js +24 -21
- package/esm/util/jexlFilterRows.d.ts +89 -0
- package/esm/util/jexlFilterRows.js +252 -0
- package/esm/util/jexlFilters.d.ts +20 -27
- package/esm/util/jexlFilters.js +23 -11
- package/esm/util/jexlStrings.d.ts +3 -4
- package/esm/util/jexlStrings.js +2 -3
- package/esm/util/layouts/GranularRectLayout.d.ts +8 -1
- package/esm/util/layouts/GranularRectLayout.js +25 -8
- package/esm/util/lazyAfterAttach.d.ts +13 -0
- package/esm/util/lazyAfterAttach.js +31 -0
- package/esm/util/lazyWithPreload.d.ts +19 -0
- package/esm/util/lazyWithPreload.js +27 -0
- package/esm/util/legendCandidates.d.ts +72 -0
- package/esm/util/legendCandidates.js +138 -0
- package/esm/util/localStorage.js +4 -4
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- package/esm/util/markEncoding.js +845 -0
- package/esm/util/markEncodingTypes.d.ts +588 -0
- package/esm/util/markEncodingTypes.js +8 -0
- package/esm/util/mst-reflection.d.ts +2 -20
- package/esm/util/mst-reflection.js +3 -53
- package/esm/util/mstUtils.d.ts +31 -23
- package/esm/util/mstUtils.js +39 -24
- package/esm/util/numericUtils.d.ts +7 -0
- package/esm/util/numericUtils.js +16 -0
- package/esm/util/numericValue.d.ts +14 -0
- package/esm/util/numericValue.js +34 -0
- package/esm/util/openFeatureWidget.d.ts +5 -0
- package/esm/util/openFeatureWidget.js +2 -2
- package/esm/util/openViews.d.ts +17 -0
- package/esm/util/openViews.js +22 -0
- package/esm/util/parentWalk.d.ts +1 -1
- package/esm/util/parentWalk.js +1 -1
- package/esm/util/parseLineByLine.d.ts +4 -5
- package/esm/util/parseLineByLine.js +8 -14
- package/esm/util/pluginStore.d.ts +6 -8
- package/esm/util/pluginStore.js +17 -16
- package/esm/util/preloadComponent.d.ts +5 -0
- package/esm/util/preloadComponent.js +11 -0
- package/esm/util/progress.d.ts +22 -22
- package/esm/util/progress.js +27 -26
- package/esm/util/quantileExtent.d.ts +49 -0
- package/esm/util/quantileExtent.js +162 -0
- package/esm/util/range.d.ts +13 -9
- package/esm/util/range.js +17 -8
- package/esm/util/renameRegions.d.ts +26 -6
- package/esm/util/renameRegions.js +68 -54
- package/esm/util/renderToStaticMarkup.js +24 -14
- package/esm/util/rxjs.d.ts +23 -8
- package/esm/util/rxjs.js +61 -15
- package/esm/util/samplesTsv.d.ts +49 -0
- package/esm/util/samplesTsv.js +86 -0
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- package/esm/util/scheduleDetachedDestroy.js +24 -0
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- package/esm/util/scrollLatch.js +8 -0
- package/esm/util/selectEncodedFeature.d.ts +16 -0
- package/esm/util/selectEncodedFeature.js +34 -0
- package/esm/util/sessionSharing.d.ts +7 -5
- package/esm/util/sessionSharing.js +23 -23
- package/esm/util/shapeNameList.d.ts +2 -0
- package/esm/util/shapeNameList.js +6 -0
- package/esm/util/shapeNames.d.ts +7 -0
- package/esm/util/shapeNames.js +11 -0
- package/esm/util/simpleFeature.d.ts +0 -1
- package/esm/util/starFusion.d.ts +26 -0
- package/esm/util/starFusion.js +37 -0
- package/esm/util/stepTables.d.ts +82 -0
- package/esm/util/stepTables.js +243 -0
- package/esm/util/svAlt.d.ts +145 -0
- package/esm/util/svAlt.js +364 -0
- package/esm/util/svgColorProps.d.ts +11 -0
- package/esm/util/svgColorProps.js +28 -1
- package/esm/util/systemColorScheme.d.ts +12 -0
- package/esm/util/systemColorScheme.js +27 -0
- package/esm/util/tabix.d.ts +13 -8
- package/esm/util/tabix.js +17 -12
- package/esm/util/thresholdScale.d.ts +91 -0
- package/esm/util/thresholdScale.js +166 -0
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- package/esm/util/timeGate.js +4 -5
- package/esm/util/trackConfigDelta.d.ts +26 -26
- package/esm/util/trackConfigDelta.js +63 -47
- package/esm/util/tracks.d.ts +121 -40
- package/esm/util/tracks.js +497 -112
- package/esm/util/translateTranscript.d.ts +44 -0
- package/esm/util/translateTranscript.js +102 -0
- package/esm/util/types/data.d.ts +0 -2
- package/esm/util/types/index.d.ts +121 -22
- package/esm/util/types/index.js +9 -0
- package/esm/util/types/mst.d.ts +3 -0
- package/esm/util/types/mst.js +4 -0
- package/esm/util/types/renameIds.d.ts +1 -0
- package/esm/util/types/renameIds.js +29 -0
- package/esm/util/types/services.d.ts +1 -1
- package/esm/util/unknownSnapshotKeys.d.ts +51 -0
- package/esm/util/unknownSnapshotKeys.js +82 -0
- package/esm/util/useFeatureSequence.js +5 -5
- package/esm/util/useFetch.d.ts +3 -4
- package/esm/util/useFetch.js +19 -10
- package/esm/util/useFetchPlugins.d.ts +6 -2
- package/esm/util/useFetchPlugins.js +7 -3
- package/esm/util/usePanelVirtualScroll.d.ts +7 -35
- package/esm/util/usePanelVirtualScroll.js +9 -36
- package/esm/util/useRowVirtualScroll.d.ts +6 -29
- package/esm/util/useRowVirtualScroll.js +8 -49
- package/esm/util/useVirtualScrollWheel.d.ts +20 -4
- package/esm/util/useVirtualScrollWheel.js +40 -74
- package/esm/util/viewHighlights.d.ts +3 -0
- package/esm/util/viewHighlights.js +5 -0
- package/esm/util/viewStatus.d.ts +47 -15
- package/esm/util/viewStatus.js +34 -0
- package/esm/util/wheelZoom.d.ts +7 -1
- package/esm/util/wheelZoom.js +85 -19
- package/esm/util/whenViewSettled.d.ts +55 -8
- package/esm/util/whenViewSettled.js +56 -7
- package/esm/util/withLaunchInput.d.ts +174 -0
- package/esm/util/withLaunchInput.js +274 -0
- package/package.json +70 -20
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -8
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -8
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts +0 -80
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.js +0 -583
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +0 -141
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.js +0 -1116
- package/esm/ReExports/BaseFeatureDetails.d.ts +0 -1
- package/esm/ReExports/BaseFeatureDetails.js +0 -10
- package/esm/ReExports/index.d.ts +0 -1
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- package/esm/ReExports/publicUtil.d.ts +0 -1
- package/esm/ReExports/publicUtil.js +0 -28
- package/esm/configuration/promotableDefaults.d.ts +0 -199
- package/esm/configuration/promotableDefaults.js +0 -326
- package/esm/configuration/promotablePin.d.ts +0 -55
- package/esm/configuration/promotablePin.js +0 -1
- package/esm/configuration/promotableResolve.d.ts +0 -108
- package/esm/configuration/promotableResolve.js +0 -117
- package/esm/configuration/promotableSlots.d.ts +0 -12
- package/esm/configuration/promotableSlots.js +0 -45
- package/esm/configuration/slotShape.d.ts +0 -12
- package/esm/configuration/slotShape.js +0 -84
- package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +0 -51
- package/esm/pluggableElementTypes/models/HighlightsMixin.js +0 -78
- package/esm/ui/PinAdornment.d.ts +0 -5
- package/esm/ui/PinAdornment.js +0 -79
- package/esm/ui/SvgGradientLegend.d.ts +0 -26
- package/esm/ui/SvgGradientLegend.js +0 -26
- package/esm/ui/highlightChipReveal.d.ts +0 -32
- package/esm/ui/highlightChipReveal.js +0 -39
- package/esm/ui/promotableMenuItems.d.ts +0 -19
- package/esm/ui/promotableMenuItems.js +0 -89
- package/esm/ui/promotablePinCoverage.d.ts +0 -44
- package/esm/ui/promotablePinCoverage.js +0 -87
- package/esm/util/applyInitSettings.d.ts +0 -79
- package/esm/util/applyInitSettings.js +0 -91
- package/esm/util/openDisplays.d.ts +0 -23
- package/esm/util/openDisplays.js +0 -79
- package/esm/util/stopToken.d.ts +0 -211
- package/esm/util/stopToken.js +0 -438
- /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/zoomRange.js} +0 -0
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} & {
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|
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};
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|
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} & {
|
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|
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defaultValue: string;
|
|
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|
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|
|
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|
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|
|
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|
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internetAccountId: {
|
|
402
|
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type: "string";
|
|
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|
+
} & {
|
|
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|
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defaultValue: string;
|
|
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|
+
};
|
|
406
|
+
}, import("../../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "internetAccountId", true, import("../../configuration/requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
|
|
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407
|
}> & {
|
|
358
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|
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|
|
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409
|
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|
|
@@ -409,31 +459,41 @@ export default function useInternetAccounts(rootModel?: AbstractRootModel): {
|
|
|
409
459
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
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|
configuration: import("../../configuration/configurationSchema.ts").IConfigurationReference<import("../../configuration/configurationSchema.ts").ConfigurationSchemaType<{
|
|
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|
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|
|
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|
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|
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|
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|
|
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|
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|
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type: "string";
|
|
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|
+
} & {
|
|
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|
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defaultValue: string;
|
|
415
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|
};
|
|
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|
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|
|
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|
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|
|
418
|
-
|
|
419
|
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|
|
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|
+
type: "string";
|
|
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|
+
} & {
|
|
469
|
+
defaultValue: string;
|
|
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470
|
};
|
|
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471
|
readonly authHeader: {
|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
+
type: "string";
|
|
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|
+
} & {
|
|
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|
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defaultValue: string;
|
|
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475
|
};
|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
477
|
+
type: "string";
|
|
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|
+
} & {
|
|
479
|
+
defaultValue: string;
|
|
430
480
|
};
|
|
431
481
|
readonly domains: {
|
|
432
|
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|
|
433
|
-
|
|
434
|
-
|
|
482
|
+
type: "stringArray";
|
|
483
|
+
} & {
|
|
484
|
+
defaultValue: unknown;
|
|
485
|
+
};
|
|
486
|
+
type: {
|
|
487
|
+
type: "string";
|
|
488
|
+
} & {
|
|
489
|
+
defaultValue: string;
|
|
490
|
+
};
|
|
491
|
+
internetAccountId: {
|
|
492
|
+
type: "string";
|
|
493
|
+
} & {
|
|
494
|
+
defaultValue: string;
|
|
435
495
|
};
|
|
436
|
-
}, import("../../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "internetAccountId">>>;
|
|
496
|
+
}, import("../../configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "internetAccountId", true, import("../../configuration/requirements.ts").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>>;
|
|
437
497
|
}, {
|
|
438
498
|
readonly name: string;
|
|
439
499
|
readonly description: string;
|
package/esm/ui/HoverMenu.d.ts
CHANGED
|
@@ -1,6 +1,5 @@
|
|
|
1
1
|
import type { PopoverOrigin } from '@mui/material';
|
|
2
|
-
declare function HoverMenu({
|
|
3
|
-
open: boolean;
|
|
2
|
+
declare function HoverMenu({ anchorEl, onClose, onMouseEnter, paperRef, anchorOrigin, transformOrigin, zIndex, children, }: {
|
|
4
3
|
anchorEl: HTMLElement | null;
|
|
5
4
|
onClose: () => void;
|
|
6
5
|
onMouseEnter?: () => void;
|
package/esm/ui/HoverMenu.js
CHANGED
|
@@ -4,7 +4,10 @@ import { jsx as _jsx } from "react/jsx-runtime";
|
|
|
4
4
|
import { Menu } from '@mui/material';
|
|
5
5
|
// A Menu a hovering pointer can cross into: the root (which spans the viewport)
|
|
6
6
|
// is click-through so the gap between the opener row and the panel doesn't
|
|
7
|
-
// swallow the pointer, while the paper itself stays interactive.
|
|
7
|
+
// swallow the pointer, while the paper itself stays interactive. That root can
|
|
8
|
+
// never deliver a click to a backdrop, so it renders none.
|
|
9
|
+
//
|
|
10
|
+
// Mounted only while its submenu is open, which is why it takes no `open`.
|
|
8
11
|
//
|
|
9
12
|
// Only CascadingMenu's submenus render this, so it takes exactly what they pass
|
|
10
13
|
// — the root's pointer-events and the paper slot are its whole point, and a
|
|
@@ -15,8 +18,8 @@ import { Menu } from '@mui/material';
|
|
|
15
18
|
// and `onMouseEnter`, which fires on the paper rather than the click-through
|
|
16
19
|
// root and so means "the pointer arrived here", not "the pointer is somewhere
|
|
17
20
|
// over the viewport".
|
|
18
|
-
function HoverMenu({
|
|
19
|
-
return (_jsx(Menu, { open:
|
|
21
|
+
function HoverMenu({ anchorEl, onClose, onMouseEnter, paperRef, anchorOrigin, transformOrigin, zIndex, children, }) {
|
|
22
|
+
return (_jsx(Menu, { open: true, anchorEl: anchorEl, onClose: onClose, anchorOrigin: anchorOrigin, transformOrigin: transformOrigin, style: { pointerEvents: 'none', zIndex }, hideBackdrop: true, slotProps: {
|
|
20
23
|
paper: {
|
|
21
24
|
style: { pointerEvents: 'auto' },
|
|
22
25
|
onMouseEnter,
|
|
@@ -1,23 +1,26 @@
|
|
|
1
|
+
import type { JexlFilterField } from '../util/jexlFilterRows.ts';
|
|
1
2
|
import type { JexlFilterModel } from '../util/jexlFilters.ts';
|
|
3
|
+
export type { JexlFilterField } from '../util/jexlFilterRows.ts';
|
|
2
4
|
export interface JexlFilterExample {
|
|
3
5
|
code: string;
|
|
4
6
|
description: string;
|
|
5
7
|
}
|
|
6
8
|
/**
|
|
7
|
-
* Editor for a
|
|
8
|
-
*
|
|
9
|
+
* Editor for a display's jexl feature filters, for any display implementing
|
|
10
|
+
* the two-tier {@link JexlFilterModel} contract. The Conditions tab shows each
|
|
11
|
+
* line as rows of field, operator and value where it can, and as text where it
|
|
12
|
+
* cannot; the Text tab is every line as text.
|
|
9
13
|
*
|
|
10
|
-
*
|
|
11
|
-
*
|
|
12
|
-
*
|
|
13
|
-
*
|
|
14
|
-
* editable) and the others from the raw override (so they did not), and only one
|
|
15
|
-
* of them normalized an emptied list. Both are policy this dialog can state
|
|
16
|
-
* once — the dialog is where "the box is empty" becomes a value.
|
|
14
|
+
* `fields` lists what the field picker offers, then the columns `metadata`
|
|
15
|
+
* describes, if it is an adapter's `{column: description}` map. Either one
|
|
16
|
+
* given as a promise suspends the dialog until it resolves, so it must not
|
|
17
|
+
* reject.
|
|
17
18
|
*/
|
|
18
|
-
declare const JexlFilterDialog: ({ model, handleClose, examples, }: {
|
|
19
|
+
declare const JexlFilterDialog: ({ model, handleClose, examples, fields, metadata, }: {
|
|
19
20
|
model: JexlFilterModel;
|
|
20
21
|
handleClose: () => void;
|
|
21
22
|
examples?: JexlFilterExample[];
|
|
23
|
+
fields?: JexlFilterField[] | Promise<JexlFilterField[]>;
|
|
24
|
+
metadata?: Promise<unknown>;
|
|
22
25
|
}) => import("react").JSX.Element;
|
|
23
26
|
export default JexlFilterDialog;
|
|
@@ -1,34 +1,19 @@
|
|
|
1
|
-
import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
|
|
2
|
-
import { useState } from 'react';
|
|
1
|
+
import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
|
|
2
|
+
import { use, useState } from 'react';
|
|
3
3
|
import { getEnv } from '@jbrowse/mobx-state-tree';
|
|
4
|
+
import AddIcon from '@mui/icons-material/Add';
|
|
5
|
+
import { Button, ListItemText, MenuItem, Tab, Tabs, TextField, } from '@mui/material';
|
|
4
6
|
import { observer } from 'mobx-react';
|
|
7
|
+
import { readConfObject } from '../configuration/readConfObject.js';
|
|
8
|
+
import { addRow, describedColumns, readFilterRows, removeRow, replaceRow, resolveFields, stripJexlPrefix, writeFilterRows, } from '../util/jexlFilterRows.js';
|
|
5
9
|
import { activeJexlFilters } from '../util/jexlFilters.js';
|
|
6
|
-
import { ensureJexlPrefix
|
|
10
|
+
import { ensureJexlPrefix } from '../util/jexlStrings.js';
|
|
11
|
+
import { getContainingTrack } from '../util/mstUtils.js';
|
|
12
|
+
import { makeStyles } from '../util/tss-react/index.js';
|
|
7
13
|
import ExternalLink from './ExternalLink.js';
|
|
14
|
+
import { ConditionRowEditor, TextRowEditor, compileError, } from './JexlFilterRowEditors.js';
|
|
8
15
|
import MonospaceTextField from './MonospaceTextField.js';
|
|
9
16
|
import SubmitDialog from './SubmitDialog.js';
|
|
10
|
-
// Non-blank, trimmed lines — the filter list excludes blank lines a user leaves
|
|
11
|
-
// in the textarea, and the same set is what gets validated.
|
|
12
|
-
function filterLines(text) {
|
|
13
|
-
return text
|
|
14
|
-
.split('\n')
|
|
15
|
-
.map(line => line.trim())
|
|
16
|
-
.filter(line => !!line);
|
|
17
|
-
}
|
|
18
|
-
// jexl compile error for the current text, or undefined when every line parses.
|
|
19
|
-
// Derived during render (compilation is cached on the instance, so no effect
|
|
20
|
-
// needed).
|
|
21
|
-
function jexlError(text, jexl) {
|
|
22
|
-
try {
|
|
23
|
-
for (const line of filterLines(text)) {
|
|
24
|
-
stringToJexlExpression(line, jexl);
|
|
25
|
-
}
|
|
26
|
-
return undefined;
|
|
27
|
-
}
|
|
28
|
-
catch (e) {
|
|
29
|
-
return e;
|
|
30
|
-
}
|
|
31
|
-
}
|
|
32
17
|
/**
|
|
33
18
|
* What a display filtering plain annotation features offers as a starting
|
|
34
19
|
* point. A display whose features are a richer record — a VCF, say — passes its
|
|
@@ -62,33 +47,121 @@ const FEATURE_FILTER_EXAMPLES = [
|
|
|
62
47
|
description: 'show only features with length less than 1Mbp',
|
|
63
48
|
},
|
|
64
49
|
];
|
|
50
|
+
const FEATURE_FIELDS = [
|
|
51
|
+
{ label: 'name', path: ['name'], type: 'text' },
|
|
52
|
+
{ label: 'type', path: ['type'], type: 'text' },
|
|
53
|
+
{ label: 'score', path: ['score'], type: 'number' },
|
|
54
|
+
{ label: 'start', path: ['start'], type: 'number' },
|
|
55
|
+
{ label: 'end', path: ['end'], type: 'number' },
|
|
56
|
+
{ label: 'strand', path: ['strand'], type: 'number' },
|
|
57
|
+
];
|
|
58
|
+
const useStyles = makeStyles()(theme => ({
|
|
59
|
+
body: {
|
|
60
|
+
minHeight: 280,
|
|
61
|
+
},
|
|
62
|
+
tabs: {
|
|
63
|
+
marginBottom: theme.spacing(2),
|
|
64
|
+
},
|
|
65
|
+
hint: {
|
|
66
|
+
marginBottom: theme.spacing(2),
|
|
67
|
+
color: theme.palette.text.secondary,
|
|
68
|
+
},
|
|
69
|
+
examples: {
|
|
70
|
+
minWidth: 220,
|
|
71
|
+
marginBottom: theme.spacing(1),
|
|
72
|
+
},
|
|
73
|
+
}));
|
|
74
|
+
function textLines(text) {
|
|
75
|
+
return text
|
|
76
|
+
.split('\n')
|
|
77
|
+
.map(line => line.trim())
|
|
78
|
+
.filter(line => !!line)
|
|
79
|
+
.map(ensureJexlPrefix);
|
|
80
|
+
}
|
|
81
|
+
function textError(text, jexl) {
|
|
82
|
+
for (const [i, line] of text.split('\n').entries()) {
|
|
83
|
+
const error = line.trim() ? compileError(line, jexl) : undefined;
|
|
84
|
+
if (error) {
|
|
85
|
+
return `Line ${i + 1}: ${error}`;
|
|
86
|
+
}
|
|
87
|
+
}
|
|
88
|
+
return undefined;
|
|
89
|
+
}
|
|
90
|
+
function trackName(model) {
|
|
91
|
+
try {
|
|
92
|
+
return readConfObject(getContainingTrack(model).configuration, 'name');
|
|
93
|
+
}
|
|
94
|
+
catch {
|
|
95
|
+
return undefined;
|
|
96
|
+
}
|
|
97
|
+
}
|
|
98
|
+
function withOneRow(state) {
|
|
99
|
+
return state.rows.length > 0 ? state : addRow(state);
|
|
100
|
+
}
|
|
65
101
|
/**
|
|
66
|
-
* Editor for a
|
|
67
|
-
*
|
|
102
|
+
* Editor for a display's jexl feature filters, for any display implementing
|
|
103
|
+
* the two-tier {@link JexlFilterModel} contract. The Conditions tab shows each
|
|
104
|
+
* line as rows of field, operator and value where it can, and as text where it
|
|
105
|
+
* cannot; the Text tab is every line as text.
|
|
68
106
|
*
|
|
69
|
-
*
|
|
70
|
-
*
|
|
71
|
-
*
|
|
72
|
-
*
|
|
73
|
-
* editable) and the others from the raw override (so they did not), and only one
|
|
74
|
-
* of them normalized an emptied list. Both are policy this dialog can state
|
|
75
|
-
* once — the dialog is where "the box is empty" becomes a value.
|
|
107
|
+
* `fields` lists what the field picker offers, then the columns `metadata`
|
|
108
|
+
* describes, if it is an adapter's `{column: description}` map. Either one
|
|
109
|
+
* given as a promise suspends the dialog until it resolves, so it must not
|
|
110
|
+
* reject.
|
|
76
111
|
*/
|
|
77
|
-
const JexlFilterDialog = observer(function JexlFilterDialog({ model, handleClose, examples = FEATURE_FILTER_EXAMPLES, }) {
|
|
78
|
-
const
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
const
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
112
|
+
const JexlFilterDialog = observer(function JexlFilterDialog({ model, handleClose, examples = FEATURE_FILTER_EXAMPLES, fields = FEATURE_FIELDS, metadata, }) {
|
|
113
|
+
const { classes } = useStyles();
|
|
114
|
+
const jexl = getEnv(model).pluginManager
|
|
115
|
+
.jexl;
|
|
116
|
+
const fieldList = fields instanceof Promise ? use(fields) : fields;
|
|
117
|
+
const described = metadata && use(metadata);
|
|
118
|
+
const [choices] = useState(() => resolveFields([...fieldList, ...describedColumns(described, fieldList)]));
|
|
119
|
+
const [state, setState] = useState(() => withOneRow(readFilterRows(activeJexlFilters(model), jexl, choices)));
|
|
120
|
+
const [tab, setTab] = useState('conditions');
|
|
121
|
+
const [text, setText] = useState({ value: '', shown: '' });
|
|
122
|
+
const textEdited = text.value !== text.shown;
|
|
123
|
+
const error = tab === 'text'
|
|
124
|
+
? textError(text.value, jexl)
|
|
125
|
+
: state.rows.some(row => row.kind === 'text' && compileError(row.text, jexl));
|
|
126
|
+
const name = trackName(model);
|
|
127
|
+
return (_jsx(SubmitDialog, { maxWidth: "md", fullWidth: true, open: true, title: name ? `Filter ${name}` : 'Filter features', submitText: "Apply", submitDisabled: !!error, onCancel: handleClose, onSubmit: () => {
|
|
128
|
+
// An emptied list is "show everything", which is NOT the same as
|
|
129
|
+
// following the config slot, so it is set as an override too
|
|
130
|
+
model.setFilter(tab === 'text' && textEdited
|
|
131
|
+
? textLines(text.value)
|
|
132
|
+
: writeFilterRows(state));
|
|
89
133
|
handleClose();
|
|
90
|
-
}, children:
|
|
91
|
-
|
|
92
|
-
|
|
134
|
+
}, children: _jsxs("div", { className: classes.body, children: [_jsxs(Tabs, { className: classes.tabs, value: tab, onChange: (_, next) => {
|
|
135
|
+
if (next === 'text') {
|
|
136
|
+
const value = writeFilterRows(state)
|
|
137
|
+
.map(stripJexlPrefix)
|
|
138
|
+
.join('\n');
|
|
139
|
+
setText({ value, shown: value });
|
|
140
|
+
}
|
|
141
|
+
else if (textEdited) {
|
|
142
|
+
setState(withOneRow(readFilterRows(textLines(text.value), jexl, choices)));
|
|
143
|
+
}
|
|
144
|
+
setTab(next);
|
|
145
|
+
}, children: [_jsx(Tab, { value: "conditions", label: "Conditions" }), _jsx(Tab, { value: "text", label: "Text", "data-testid": "jexl-filter-text-tab" })] }), tab === 'conditions' ? (_jsxs(_Fragment, { children: [_jsx("div", { className: classes.hint, children: "Show features that match every condition." }), state.rows.map(row => row.kind === 'text' ? (_jsx(TextRowEditor, { row: row, jexl: jexl, onChange: next => {
|
|
146
|
+
setState(replaceRow(state, next));
|
|
147
|
+
}, onRemove: () => {
|
|
148
|
+
setState(removeRow(state, row.id));
|
|
149
|
+
} }, row.id)) : (_jsx(ConditionRowEditor, { row: row, choices: choices, onChange: next => {
|
|
150
|
+
setState(replaceRow(state, next));
|
|
151
|
+
}, onRemove: () => {
|
|
152
|
+
setState(removeRow(state, row.id));
|
|
153
|
+
} }, row.id))), _jsx(Button, { startIcon: _jsx(AddIcon, {}), onClick: () => {
|
|
154
|
+
setState(addRow(state));
|
|
155
|
+
}, children: "Add condition" })] })) : (_jsxs(_Fragment, { children: [_jsx(TextField, { select: true, size: "small", label: "Insert example\u2026", value: "", className: classes.examples, onChange: event => {
|
|
156
|
+
const code = stripJexlPrefix(event.target.value);
|
|
157
|
+
setText({
|
|
158
|
+
...text,
|
|
159
|
+
value: text.value.trim()
|
|
160
|
+
? `${text.value.trimEnd()}\n${code}`
|
|
161
|
+
: code,
|
|
162
|
+
});
|
|
163
|
+
}, children: examples.map(({ code, description }) => (_jsx(MenuItem, { value: code, children: _jsx(ListItemText, { primary: stripJexlPrefix(code), secondary: description }) }, code))) }), _jsx(MonospaceTextField, { fullWidth: true, minRows: 6, maxRows: 14, value: text.value, error: error, helperText: "One filter per line; a feature has to pass every line.", onChange: value => {
|
|
164
|
+
setText({ ...text, value });
|
|
165
|
+
} }), _jsxs("p", { children: ["See the", ' ', _jsx(ExternalLink, { href: "https://jbrowse.org/jb2/docs/config_guides/jexl/", children: "jexl documentation" }), ' ', "for the expression language."] })] }))] }) }));
|
|
93
166
|
});
|
|
94
167
|
export default JexlFilterDialog;
|
|
@@ -0,0 +1,15 @@
|
|
|
1
|
+
import type { ConditionRow, FieldChoice, TextRow } from '../util/jexlFilterRows.ts';
|
|
2
|
+
import type { Jexl } from '@jbrowse/jexl';
|
|
3
|
+
export declare function compileError(line: string, jexl: Pick<Jexl, 'compile'>): string | undefined;
|
|
4
|
+
export declare function ConditionRowEditor({ row, choices, onChange, onRemove, }: {
|
|
5
|
+
row: ConditionRow;
|
|
6
|
+
choices: FieldChoice[];
|
|
7
|
+
onChange: (row: ConditionRow) => void;
|
|
8
|
+
onRemove: () => void;
|
|
9
|
+
}): import("react").JSX.Element;
|
|
10
|
+
export declare function TextRowEditor({ row, jexl, onChange, onRemove, }: {
|
|
11
|
+
row: TextRow;
|
|
12
|
+
jexl: Pick<Jexl, 'compile'>;
|
|
13
|
+
onChange: (row: TextRow) => void;
|
|
14
|
+
onRemove: () => void;
|
|
15
|
+
}): import("react").JSX.Element;
|