@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.11
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 +1709 -390
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +5 -5
- 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 +37 -14
- 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 +49 -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/SequenceFeatureDetails/useSequenceData.js +8 -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 +34 -3
- 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 +530 -0
- package/esm/ReExports/coreWorkerModules.generated.d.ts +2 -0
- package/esm/ReExports/coreWorkerModules.generated.js +490 -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 +528 -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 +26 -11
- package/esm/configuration/index.js +16 -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/plot.d.ts +61 -0
- package/esm/configuration/plot.js +142 -0
- 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 +53 -16
- package/esm/pluggableElementTypes/DisplayType.js +28 -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/WidgetType.d.ts +6 -0
- package/esm/pluggableElementTypes/WidgetType.js +6 -0
- 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 +2 -9
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +19 -9
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +122 -28
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +155 -11
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +65 -16
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +179 -117
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +87 -18
- package/esm/pluggableElementTypes/models/BaseViewModel.js +54 -11
- 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 -50
- 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/TimeTraveller.d.ts +3 -0
- package/esm/util/TimeTraveller.js +34 -2
- 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
- package/esm/util/applyRowResizeWheel.js +10 -21
- package/esm/util/bandHeight.d.ts +10 -0
- package/esm/util/bandHeight.js +29 -0
- package/esm/util/bandLayout.d.ts +4 -4
- package/esm/util/bandLayout.js +4 -4
- package/esm/util/baseDisplayConfig.d.ts +8 -0
- package/esm/util/baseDisplayConfig.js +27 -0
- package/esm/util/bezierConnector.d.ts +4 -3
- package/esm/util/bezierConnector.js +38 -45
- package/esm/util/bgzfWorkerPool.d.ts +20 -74
- package/esm/util/bgzfWorkerPool.js +20 -74
- package/esm/util/binnedAggregate.d.ts +17 -0
- package/esm/util/binnedAggregate.js +275 -0
- package/esm/util/cacheBudgets.d.ts +22 -19
- package/esm/util/cacheBudgets.js +22 -19
- package/esm/util/cachedSetup.d.ts +16 -6
- package/esm/util/cachedSetup.js +108 -38
- package/esm/util/categoricalField.d.ts +56 -0
- package/esm/util/categoricalField.js +73 -0
- package/esm/util/cellMatches.d.ts +23 -0
- package/esm/util/cellMatches.js +264 -0
- package/esm/util/cellsStep.d.ts +29 -0
- package/esm/util/cellsStep.js +437 -0
- package/esm/util/clampToContig.d.ts +17 -0
- package/esm/util/clampToContig.js +19 -0
- package/esm/util/coarseStripHTML.js +1 -2
- package/esm/util/color/cssColorsLevel4.d.ts +1 -0
- 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/copyToClipboard.js +8 -1
- 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 +81 -0
- package/esm/util/featureTransforms.js +1231 -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
- package/esm/util/fetchPhases.d.ts +10 -10
- package/esm/util/fetchSeq.d.ts +2 -3
- package/esm/util/fetchSeq.js +2 -2
- package/esm/util/fieldReader.d.ts +17 -0
- package/esm/util/fieldReader.js +62 -0
- package/esm/util/formatBytes.js +1 -1
- package/esm/util/formatGuessers.d.ts +25 -14
- package/esm/util/formatGuessers.js +42 -27
- package/esm/util/formatRelativeTime.js +1 -1
- package/esm/util/freezeDeep.d.ts +8 -10
- package/esm/util/freezeDeep.js +8 -10
- package/esm/util/getLocationUri.d.ts +2 -1
- package/esm/util/getLocationUri.js +8 -2
- package/esm/util/groupKeys.d.ts +76 -0
- package/esm/util/groupKeys.js +156 -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/intervals.js +9 -4
- package/esm/util/io/index.js +22 -15
- 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 +32 -57
- package/esm/util/jexlFilters.js +31 -29
- 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/locString.js +5 -2
- package/esm/util/localStorage.js +4 -4
- package/esm/util/markEncoding.d.ts +150 -0
- package/esm/util/markEncoding.js +885 -0
- package/esm/util/markEncodingTypes.d.ts +595 -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
- package/esm/util/scheduleDetachedDestroy.d.ts +18 -0
- package/esm/util/scheduleDetachedDestroy.js +24 -0
- package/esm/util/scrollLatch.d.ts +1 -0
- 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/springAnimate.js +1 -1
- package/esm/util/starFusion.d.ts +26 -0
- package/esm/util/starFusion.js +37 -0
- package/esm/util/stepTables.d.ts +96 -0
- package/esm/util/stepTables.js +277 -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 +19 -10
- package/esm/util/tabix.js +19 -14
- package/esm/util/thresholdScale.d.ts +91 -0
- package/esm/util/thresholdScale.js +166 -0
- package/esm/util/timeGate.d.ts +4 -5
- 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 +120 -66
- package/esm/util/tracks.js +501 -151
- 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 +53 -0
- package/esm/util/unknownSnapshotKeys.js +76 -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/usePanZoom.js +10 -3
- package/esm/util/usePanelVirtualScroll.d.ts +7 -35
- package/esm/util/usePanelVirtualScroll.js +9 -36
- package/esm/util/useRafCommit.js +1 -0
- 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/withFeatureDetails.js +4 -0
- package/esm/util/withLaunchInput.d.ts +174 -0
- package/esm/util/withLaunchInput.js +274 -0
- package/package.json +75 -24
- 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
- package/esm/ReExports/index.js +0 -1
- 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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export function setterOnlyMessage(label, keys) {
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return `${label} did not apply ${keys.join(', ')}: no config slot takes ${keys.length > 1 ? 'them' : 'it'}. Call ${keys.map(displaySetterName).join(', ')} on the display instead.`;
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}
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/**
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}
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}
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/**
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* Name the row lists a view refused whole. `withLaunchInput` splits an authored
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* restores, per entry — but a row list is indexed against the view's `levels`
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const message = `${viewLabel(self)} refused ${keys.join(', ')}: the list mixes built view snapshots with recipes to open one, and the rows index against the levels between them. Write all of them one way.`;
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assemblyName: asmName,
|
|
34
34
|
session: s,
|
|
35
|
-
|
|
35
|
+
signal,
|
|
36
36
|
statusCallback: slot(),
|
|
37
37
|
}),
|
|
38
38
|
upDownBp > 0
|
|
@@ -42,7 +42,7 @@ export function useFeatureSequence({ session, start, end, refName, upDownBp, for
|
|
|
42
42
|
refName,
|
|
43
43
|
assemblyName: asmName,
|
|
44
44
|
session: s,
|
|
45
|
-
|
|
45
|
+
signal,
|
|
46
46
|
statusCallback: slot(),
|
|
47
47
|
})
|
|
48
48
|
: Promise.resolve(''),
|
|
@@ -53,7 +53,7 @@ export function useFeatureSequence({ session, start, end, refName, upDownBp, for
|
|
|
53
53
|
refName,
|
|
54
54
|
assemblyName: asmName,
|
|
55
55
|
session: s,
|
|
56
|
-
|
|
56
|
+
signal,
|
|
57
57
|
statusCallback: slot(),
|
|
58
58
|
})
|
|
59
59
|
: Promise.resolve(''),
|
package/esm/util/useFetch.d.ts
CHANGED
|
@@ -1,5 +1,4 @@
|
|
|
1
1
|
import type { RpcStatus, StatusCallback } from './progress.ts';
|
|
2
|
-
import type { StopToken } from './stopToken.ts';
|
|
3
2
|
export type FetchKey = string | readonly unknown[] | null | undefined | false;
|
|
4
3
|
type FetchingKey<Key> = Exclude<Key, null | undefined | false>;
|
|
5
4
|
/**
|
|
@@ -10,8 +9,8 @@ type FetchingKey<Key> = Exclude<Key, null | undefined | false>;
|
|
|
10
9
|
* single argument (`useGenomesData`). Most fetchers close over what they need
|
|
11
10
|
* and declare no parameters at all, which stays assignable either way.
|
|
12
11
|
*
|
|
13
|
-
* A
|
|
14
|
-
* created per fetch and
|
|
12
|
+
* A signal and a status callback follow the key arguments. The signal is
|
|
13
|
+
* created per fetch and aborted when the key changes or the component unmounts,
|
|
15
14
|
* so a fetcher that forwards it to an RPC cancels the worker instead of leaving
|
|
16
15
|
* it grinding on an answer nobody is waiting for. The callback is what the RPC's
|
|
17
16
|
* own progress comes back through, and it surfaces on the hook's `status` — a
|
|
@@ -19,7 +18,7 @@ type FetchingKey<Key> = Exclude<Key, null | undefined | false>;
|
|
|
19
18
|
* works, instead of a bare spinner over an uninterruptible whole-chromosome
|
|
20
19
|
* read. Fetchers that take neither are unaffected.
|
|
21
20
|
*/
|
|
22
|
-
type FetcherArgs<Key> = FetchingKey<Key> extends readonly unknown[] ? [...FetchingKey<Key>,
|
|
21
|
+
type FetcherArgs<Key> = FetchingKey<Key> extends readonly unknown[] ? [...FetchingKey<Key>, AbortSignal, StatusCallback] : [FetchingKey<Key>, AbortSignal, StatusCallback];
|
|
23
22
|
interface FetchState<Data> {
|
|
24
23
|
data: Data | undefined;
|
|
25
24
|
error: unknown;
|
package/esm/util/useFetch.js
CHANGED
|
@@ -1,11 +1,20 @@
|
|
|
1
1
|
import { useCallback, useEffect, useRef, useState } from 'react';
|
|
2
2
|
import { createStatusWindow } from './progress.js';
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
//
|
|
6
|
-
|
|
3
|
+
// The whole key as the "don't fetch" sentinel: `cond && [...]`, `cond ? [...] :
|
|
4
|
+
// null`. `false` belongs here and NOT in the element check below, which is what
|
|
5
|
+
// this used to share with it.
|
|
6
|
+
const isNoKey = (k) => k === null || k === undefined || k === false;
|
|
7
|
+
// An element that has not resolved yet — an offset still being computed, an
|
|
8
|
+
// assembly still loading. **`false` is not one of them**: it is a resolved
|
|
9
|
+
// boolean, and a caller with a `false`-valued setting in its key meant to fetch
|
|
10
|
+
// under that setting. Sharing one predicate with the sentinel above made every
|
|
11
|
+
// such key unfetchable, which the MAF sequence widget shipped — its
|
|
12
|
+
// `includeInsertions` defaults to `false`, so the widget sat on its loading
|
|
13
|
+
// animation forever and issued no RPC at all. `SaveTrackData` hit the same
|
|
14
|
+
// thing and encoded its boolean as a string rather than fixing it here.
|
|
15
|
+
const isUnresolved = (k) => k === null || k === undefined;
|
|
7
16
|
function serializeKey(key) {
|
|
8
|
-
return
|
|
17
|
+
return isNoKey(key) || (Array.isArray(key) && key.some(isUnresolved))
|
|
9
18
|
? null
|
|
10
19
|
: JSON.stringify(key);
|
|
11
20
|
}
|
|
@@ -85,7 +94,7 @@ export function useFetch(key, fetcher, options = {}) {
|
|
|
85
94
|
// fetch resolved is a different case, and the stream's own `clear` drops
|
|
86
95
|
// that one.)
|
|
87
96
|
let settled = false;
|
|
88
|
-
const
|
|
97
|
+
const controller = new AbortController();
|
|
89
98
|
// A refetch under the same key — mutate(), or the cross-component
|
|
90
99
|
// mutate(key) — is the same question asked again, so what is on screen is
|
|
91
100
|
// a stale answer to it rather than an answer to something else: leave it
|
|
@@ -107,7 +116,7 @@ export function useFetch(key, fetcher, options = {}) {
|
|
|
107
116
|
setStatus(undefined);
|
|
108
117
|
// The runtime counterpart of FetcherArgs: an array key becomes one
|
|
109
118
|
// argument per element, anything else a single argument, then the stop
|
|
110
|
-
//
|
|
119
|
+
// signal and the status callback. A conditional type over an unresolved
|
|
111
120
|
// `Key` can't be discharged
|
|
112
121
|
// inside the function body, so the parameter list is erased for this one
|
|
113
122
|
// call — callers still get the precise arity, and the looseness stops
|
|
@@ -127,7 +136,7 @@ export function useFetch(key, fetcher, options = {}) {
|
|
|
127
136
|
const { statusCallback, clear: clearStatus } = statusWindow.open({
|
|
128
137
|
isCurrent: () => alive && !settled,
|
|
129
138
|
});
|
|
130
|
-
const args = [...keyArgs,
|
|
139
|
+
const args = [...keyArgs, controller.signal, statusCallback];
|
|
131
140
|
const call = fetcher;
|
|
132
141
|
Promise.resolve()
|
|
133
142
|
.then(() => call(...args))
|
|
@@ -151,9 +160,9 @@ export function useFetch(key, fetcher, options = {}) {
|
|
|
151
160
|
});
|
|
152
161
|
return () => {
|
|
153
162
|
alive = false;
|
|
154
|
-
// the
|
|
163
|
+
// the signal's lifetime is this fetch's. An abort rejection lands in the
|
|
155
164
|
// catch above with alive already false, so it never surfaces as an error
|
|
156
|
-
|
|
165
|
+
controller.abort();
|
|
157
166
|
// and the window's lifetime is too: `alive` already makes a queued
|
|
158
167
|
// trailing write a no-op, but the timer behind it would otherwise stand
|
|
159
168
|
// for up to a window past unmount
|
|
@@ -1,12 +1,16 @@
|
|
|
1
|
-
import type { JBrowsePlugin } from './types/data.ts';
|
|
2
1
|
/**
|
|
3
2
|
* The plugin store listing. Shared by every surface that installs plugins (the
|
|
4
3
|
* in-session plugin store widget, Desktop's global plugins dialog) so they read
|
|
5
4
|
* the same manifest version and get the same integrity hashes and compatibility
|
|
6
5
|
* ranges — a second copy of this fetch is how one of them silently ends up on
|
|
7
6
|
* the unhashed v1 list.
|
|
7
|
+
*
|
|
8
|
+
* Through `fetchPlugins`, which memoizes its request, rather than fetching the
|
|
9
|
+
* url directly: `useFetch` holds no data cache, so every open of the store
|
|
10
|
+
* widget was a fresh round trip beside whatever the boot path had already
|
|
11
|
+
* asked for.
|
|
8
12
|
*/
|
|
9
13
|
export declare function useFetchPlugins(): {
|
|
10
|
-
plugins: JBrowsePlugin[] | undefined;
|
|
14
|
+
plugins: import("./index.ts").JBrowsePlugin[] | undefined;
|
|
11
15
|
error: unknown;
|
|
12
16
|
};
|
|
@@ -1,5 +1,4 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import { fetchJson } from './fetchJson.js';
|
|
1
|
+
import { fetchPlugins } from '../checkPlugins.js';
|
|
3
2
|
import { useFetch } from './useFetch.js';
|
|
4
3
|
/**
|
|
5
4
|
* The plugin store listing. Shared by every surface that installs plugins (the
|
|
@@ -7,8 +6,13 @@ import { useFetch } from './useFetch.js';
|
|
|
7
6
|
* the same manifest version and get the same integrity hashes and compatibility
|
|
8
7
|
* ranges — a second copy of this fetch is how one of them silently ends up on
|
|
9
8
|
* the unhashed v1 list.
|
|
9
|
+
*
|
|
10
|
+
* Through `fetchPlugins`, which memoizes its request, rather than fetching the
|
|
11
|
+
* url directly: `useFetch` holds no data cache, so every open of the store
|
|
12
|
+
* widget was a fresh round trip beside whatever the boot path had already
|
|
13
|
+
* asked for.
|
|
10
14
|
*/
|
|
11
15
|
export function useFetchPlugins() {
|
|
12
|
-
const { data, error } = useFetch('jbrowse-plugin-store-v2',
|
|
16
|
+
const { data, error } = useFetch('jbrowse-plugin-store-v2', fetchPlugins);
|
|
13
17
|
return { plugins: data?.plugins, error };
|
|
14
18
|
}
|
package/esm/util/usePanZoom.js
CHANGED
|
@@ -113,6 +113,9 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
|
|
|
113
113
|
};
|
|
114
114
|
}, [ref, touchAction]);
|
|
115
115
|
function endDrag(event) {
|
|
116
|
+
if (dragRef.current?.pointerId !== event.pointerId) {
|
|
117
|
+
return;
|
|
118
|
+
}
|
|
116
119
|
dragRef.current = undefined;
|
|
117
120
|
// release only what the move handler took — a press that stayed under the
|
|
118
121
|
// threshold never captured anything
|
|
@@ -131,7 +134,7 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
|
|
|
131
134
|
// lands on an icon inside the control. Shift is left alone too: it is
|
|
132
135
|
// what a range-select of the host's own would want, and it is what
|
|
133
136
|
// JBrowse's own view uses it for.
|
|
134
|
-
if (event.button !== 0 || event.shiftKey) {
|
|
137
|
+
if (!event.isPrimary || event.button !== 0 || event.shiftKey) {
|
|
135
138
|
return;
|
|
136
139
|
}
|
|
137
140
|
if (event.target instanceof Element &&
|
|
@@ -139,11 +142,15 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
|
|
|
139
142
|
return;
|
|
140
143
|
}
|
|
141
144
|
// Note what this does *not* do: capture the pointer. See onPointerMove.
|
|
142
|
-
dragRef.current = {
|
|
145
|
+
dragRef.current = {
|
|
146
|
+
x: event.clientX,
|
|
147
|
+
panning: false,
|
|
148
|
+
pointerId: event.pointerId,
|
|
149
|
+
};
|
|
143
150
|
},
|
|
144
151
|
onPointerMove(event) {
|
|
145
152
|
const drag = dragRef.current;
|
|
146
|
-
if (!drag) {
|
|
153
|
+
if (!drag || drag.pointerId !== event.pointerId) {
|
|
147
154
|
return;
|
|
148
155
|
}
|
|
149
156
|
if (!drag.panning) {
|
|
@@ -1,37 +1,9 @@
|
|
|
1
|
-
|
|
2
|
-
scrollTop: number;
|
|
3
|
-
scrollableHeight: number;
|
|
4
|
-
setScrollTop: (n: number) => void;
|
|
5
|
-
}
|
|
1
|
+
import type { VirtualScrollModel } from './useVirtualScrollWheel.ts';
|
|
6
2
|
/**
|
|
7
|
-
* Wheel gestures over a **scrolled canvas panel** — the alignments pileup
|
|
8
|
-
*
|
|
9
|
-
* once `scrollZoom` has
|
|
10
|
-
* left to the browser and the view's pinch-zoom.
|
|
11
|
-
*
|
|
12
|
-
* These panels paint a fixed-size canvas at `-scrollTop` rather than living in a
|
|
13
|
-
* DOM overflow container, so nothing scrolls them without this. The latch (inside
|
|
14
|
-
* `applyScroll`) owns `preventDefault` but never `stopPropagation`, so a diagonal
|
|
15
|
-
* wheel still bubbles its horizontal component to the LGV for panning.
|
|
16
|
-
*
|
|
17
|
-
* ADR-027 keeps wheel-*intent* dispatch per handler, because the panels do not
|
|
18
|
-
* agree on what a gesture means. This is the second of the two rules that
|
|
19
|
-
* survived that split — the row-stack rule (`useRowVirtualScroll`, where `shift`
|
|
20
|
-
* resizes) is the other — and the two displays sharing it had byte-identical
|
|
21
|
-
* copies differing only in which getter named the viewport. The canvas display
|
|
22
|
-
* converged here when it moved off a native overflow container; the ADR's table
|
|
23
|
-
* still described its pre-virtual-scroll rule and has been corrected.
|
|
24
|
-
*
|
|
25
|
-
* `scrollZoom` and `viewportHeight` are inputs rather than reads off the model,
|
|
26
|
-
* so core needs no view typing and each display keeps naming its own viewport
|
|
27
|
-
* (the pileup's excludes the sticky coverage band; the canvas display's is the
|
|
28
|
-
* whole track).
|
|
29
|
-
*
|
|
30
|
-
* `panel` is the element wrapping the canvas AND the DOM overlays drawn over it,
|
|
31
|
-
* never the canvas alone — see `useVirtualScrollWheel`, which says why.
|
|
3
|
+
* Wheel gestures over a **scrolled canvas panel** — the alignments pileup, the
|
|
4
|
+
* canvas feature display, multi-way synteny: a plain wheel scrolls it, `shift`
|
|
5
|
+
* still scrolls it once `scrollZoom` has given the plain wheel to the view, and
|
|
6
|
+
* ctrl/meta is left to the browser and the view's pinch-zoom. The row-stack
|
|
7
|
+
* rule, where `shift` resizes, is `useRowVirtualScroll` (ADR-027).
|
|
32
8
|
*/
|
|
33
|
-
export declare function usePanelVirtualScroll(panel: HTMLElement | null, model:
|
|
34
|
-
viewportHeight: number;
|
|
35
|
-
scrollZoom: boolean;
|
|
36
|
-
}): void;
|
|
37
|
-
export {};
|
|
9
|
+
export declare function usePanelVirtualScroll(panel: HTMLElement | null, model: VirtualScrollModel, scrollZoom: boolean): void;
|
|
@@ -1,42 +1,15 @@
|
|
|
1
1
|
import { useVirtualScrollWheel } from './useVirtualScrollWheel.js';
|
|
2
2
|
/**
|
|
3
|
-
* Wheel gestures over a **scrolled canvas panel** — the alignments pileup
|
|
4
|
-
*
|
|
5
|
-
* once `scrollZoom` has
|
|
6
|
-
* left to the browser and the view's pinch-zoom.
|
|
7
|
-
*
|
|
8
|
-
* These panels paint a fixed-size canvas at `-scrollTop` rather than living in a
|
|
9
|
-
* DOM overflow container, so nothing scrolls them without this. The latch (inside
|
|
10
|
-
* `applyScroll`) owns `preventDefault` but never `stopPropagation`, so a diagonal
|
|
11
|
-
* wheel still bubbles its horizontal component to the LGV for panning.
|
|
12
|
-
*
|
|
13
|
-
* ADR-027 keeps wheel-*intent* dispatch per handler, because the panels do not
|
|
14
|
-
* agree on what a gesture means. This is the second of the two rules that
|
|
15
|
-
* survived that split — the row-stack rule (`useRowVirtualScroll`, where `shift`
|
|
16
|
-
* resizes) is the other — and the two displays sharing it had byte-identical
|
|
17
|
-
* copies differing only in which getter named the viewport. The canvas display
|
|
18
|
-
* converged here when it moved off a native overflow container; the ADR's table
|
|
19
|
-
* still described its pre-virtual-scroll rule and has been corrected.
|
|
20
|
-
*
|
|
21
|
-
* `scrollZoom` and `viewportHeight` are inputs rather than reads off the model,
|
|
22
|
-
* so core needs no view typing and each display keeps naming its own viewport
|
|
23
|
-
* (the pileup's excludes the sticky coverage band; the canvas display's is the
|
|
24
|
-
* whole track).
|
|
25
|
-
*
|
|
26
|
-
* `panel` is the element wrapping the canvas AND the DOM overlays drawn over it,
|
|
27
|
-
* never the canvas alone — see `useVirtualScrollWheel`, which says why.
|
|
3
|
+
* Wheel gestures over a **scrolled canvas panel** — the alignments pileup, the
|
|
4
|
+
* canvas feature display, multi-way synteny: a plain wheel scrolls it, `shift`
|
|
5
|
+
* still scrolls it once `scrollZoom` has given the plain wheel to the view, and
|
|
6
|
+
* ctrl/meta is left to the browser and the view's pinch-zoom. The row-stack
|
|
7
|
+
* rule, where `shift` resizes, is `useRowVirtualScroll` (ADR-027).
|
|
28
8
|
*/
|
|
29
|
-
export function usePanelVirtualScroll(panel, model,
|
|
30
|
-
useVirtualScrollWheel(panel, (e,
|
|
31
|
-
if ((scrollZoom
|
|
32
|
-
|
|
9
|
+
export function usePanelVirtualScroll(panel, model, scrollZoom) {
|
|
10
|
+
useVirtualScrollWheel(panel, model, (e, scroll) => {
|
|
11
|
+
if ((!scrollZoom || e.shiftKey) && !e.ctrlKey && !e.metaKey) {
|
|
12
|
+
scroll();
|
|
33
13
|
}
|
|
34
|
-
applyScroll(e, {
|
|
35
|
-
scrollTop: model.scrollTop,
|
|
36
|
-
viewportHeight,
|
|
37
|
-
scrollableHeight: model.scrollableHeight,
|
|
38
|
-
}, n => {
|
|
39
|
-
model.setScrollTop(n);
|
|
40
|
-
});
|
|
41
14
|
});
|
|
42
15
|
}
|
package/esm/util/useRafCommit.js
CHANGED
|
@@ -1,32 +1,9 @@
|
|
|
1
|
-
|
|
2
|
-
effectiveRowHeight: number;
|
|
3
|
-
scrollTop: number;
|
|
4
|
-
nrow: number;
|
|
5
|
-
scrollableHeight: number;
|
|
6
|
-
setRowHeight: (n: number) => void;
|
|
7
|
-
setScrollTop: (n: number) => void;
|
|
8
|
-
}
|
|
1
|
+
import type { RowResizeTarget } from './applyRowResizeWheel.ts';
|
|
9
2
|
/**
|
|
10
3
|
* Wheel gestures over a **row-stack** panel — the multi-sample variant displays
|
|
11
|
-
* and MAF: `shift`+wheel resizes the rows
|
|
12
|
-
*
|
|
13
|
-
*
|
|
14
|
-
*
|
|
15
|
-
* These panels paint a fixed-size canvas at `-scrollTop` rather than living in a
|
|
16
|
-
* DOM overflow container, so nothing scrolls them without this.
|
|
17
|
-
*
|
|
18
|
-
* ADR-027 keeps wheel-*intent* dispatch per handler, because the four panels do
|
|
19
|
-
* not agree on what a gesture means — and that still holds. This is the one rule
|
|
20
|
-
* two of them genuinely share, which the ADR states outright ("same rule as the
|
|
21
|
-
* variant displays, and deliberately so: same sample-row shape, same coupled
|
|
22
|
-
* row-height axis"). It is unified for exactly that reason, and no further: the
|
|
23
|
-
* pileup / canvas-basic rule (`shift` scrolls, nothing resizes) stays where it
|
|
24
|
-
* is. `scrollZoom` and `viewportHeight` are inputs rather than reads off the
|
|
25
|
-
* model, so core needs no view typing and each display keeps naming its own
|
|
26
|
-
* rows-area height.
|
|
4
|
+
* and MAF: `shift`+wheel resizes the rows, keeping the row under the cursor
|
|
5
|
+
* put, and a plain wheel scrolls them unless `scrollZoom` gave it to the view.
|
|
6
|
+
* ctrl/meta is the browser's zoom whatever else is held. The canvas-panel rule,
|
|
7
|
+
* where `shift` scrolls, is `usePanelVirtualScroll` (ADR-027).
|
|
27
8
|
*/
|
|
28
|
-
export declare function useRowVirtualScroll(el: HTMLElement | null, model:
|
|
29
|
-
viewportHeight: number;
|
|
30
|
-
scrollZoom: boolean;
|
|
31
|
-
}): void;
|
|
32
|
-
export {};
|
|
9
|
+
export declare function useRowVirtualScroll(el: HTMLElement | null, model: RowResizeTarget, scrollZoom: boolean): void;
|
|
@@ -2,62 +2,21 @@ import { applyRowResizeWheel } from './applyRowResizeWheel.js';
|
|
|
2
2
|
import { useVirtualScrollWheel } from './useVirtualScrollWheel.js';
|
|
3
3
|
/**
|
|
4
4
|
* Wheel gestures over a **row-stack** panel — the multi-sample variant displays
|
|
5
|
-
* and MAF: `shift`+wheel resizes the rows
|
|
6
|
-
*
|
|
7
|
-
*
|
|
8
|
-
*
|
|
9
|
-
* These panels paint a fixed-size canvas at `-scrollTop` rather than living in a
|
|
10
|
-
* DOM overflow container, so nothing scrolls them without this.
|
|
11
|
-
*
|
|
12
|
-
* ADR-027 keeps wheel-*intent* dispatch per handler, because the four panels do
|
|
13
|
-
* not agree on what a gesture means — and that still holds. This is the one rule
|
|
14
|
-
* two of them genuinely share, which the ADR states outright ("same rule as the
|
|
15
|
-
* variant displays, and deliberately so: same sample-row shape, same coupled
|
|
16
|
-
* row-height axis"). It is unified for exactly that reason, and no further: the
|
|
17
|
-
* pileup / canvas-basic rule (`shift` scrolls, nothing resizes) stays where it
|
|
18
|
-
* is. `scrollZoom` and `viewportHeight` are inputs rather than reads off the
|
|
19
|
-
* model, so core needs no view typing and each display keeps naming its own
|
|
20
|
-
* rows-area height.
|
|
5
|
+
* and MAF: `shift`+wheel resizes the rows, keeping the row under the cursor
|
|
6
|
+
* put, and a plain wheel scrolls them unless `scrollZoom` gave it to the view.
|
|
7
|
+
* ctrl/meta is the browser's zoom whatever else is held. The canvas-panel rule,
|
|
8
|
+
* where `shift` scrolls, is `usePanelVirtualScroll` (ADR-027).
|
|
21
9
|
*/
|
|
22
|
-
export function useRowVirtualScroll(el, model,
|
|
23
|
-
useVirtualScrollWheel(el, (e,
|
|
24
|
-
// ctrl/meta is the browser's own zoom (and the view's pinch-zoom) and is
|
|
25
|
-
// never ours, whatever else is held. Tested first rather than only in the
|
|
26
|
-
// scroll branch: ctrl+shift+wheel used to reach the resize below, which
|
|
27
|
-
// `preventDefault`s — so a row-stack display swallowed page zoom where
|
|
28
|
-
// every other display passes it through.
|
|
10
|
+
export function useRowVirtualScroll(el, model, scrollZoom) {
|
|
11
|
+
useVirtualScrollWheel(el, model, (e, scroll, rowsEl) => {
|
|
29
12
|
if (e.ctrlKey || e.metaKey) {
|
|
30
13
|
return;
|
|
31
14
|
}
|
|
32
15
|
if (e.shiftKey) {
|
|
33
|
-
|
|
34
|
-
// the gesture meaningful: the fit height is exactly the floor it shrinks
|
|
35
|
-
// to, so there is nothing to zoom while the sentinel is set.
|
|
36
|
-
applyRowResizeWheel(e, rowsEl, {
|
|
37
|
-
effectiveRowHeight: model.effectiveRowHeight,
|
|
38
|
-
scrollTop: model.scrollTop,
|
|
39
|
-
nrow: model.nrow,
|
|
40
|
-
viewportHeight,
|
|
41
|
-
setRowHeight: n => {
|
|
42
|
-
model.setRowHeight(n);
|
|
43
|
-
},
|
|
44
|
-
setScrollTop: n => {
|
|
45
|
-
model.setScrollTop(n);
|
|
46
|
-
},
|
|
47
|
-
});
|
|
16
|
+
applyRowResizeWheel(e, rowsEl, model);
|
|
48
17
|
}
|
|
49
18
|
else if (!scrollZoom) {
|
|
50
|
-
|
|
51
|
-
// the track (`scrollableHeight === 0`, always true in fit-to-height mode)
|
|
52
|
-
// the wheel reaches the view and zooms or scrolls the page exactly as it
|
|
53
|
-
// does over any other track. Same for the explicit zoom gestures.
|
|
54
|
-
applyScroll(e, {
|
|
55
|
-
scrollTop: model.scrollTop,
|
|
56
|
-
viewportHeight,
|
|
57
|
-
scrollableHeight: model.scrollableHeight,
|
|
58
|
-
}, n => {
|
|
59
|
-
model.setScrollTop(n);
|
|
60
|
-
});
|
|
19
|
+
scroll();
|
|
61
20
|
}
|
|
62
21
|
});
|
|
63
22
|
}
|
|
@@ -1,7 +1,23 @@
|
|
|
1
|
-
|
|
1
|
+
/**
|
|
2
|
+
* What a virtually scrolled panel reads and writes. `TrackHeightMixin`
|
|
3
|
+
* implements it, so a display passes itself.
|
|
4
|
+
*/
|
|
5
|
+
export interface VirtualScrollModel {
|
|
2
6
|
scrollTop: number;
|
|
3
|
-
|
|
7
|
+
/** 0 when the content fits; never sub-pixel */
|
|
4
8
|
scrollableHeight: number;
|
|
9
|
+
scrollViewportHeight: number;
|
|
10
|
+
setScrollTop: (scrollTop: number) => void;
|
|
5
11
|
}
|
|
6
|
-
|
|
7
|
-
|
|
12
|
+
/**
|
|
13
|
+
* Non-passive wheel wiring for a canvas-backed virtual scroll. Owns the scroll
|
|
14
|
+
* latch (and so `preventDefault`), per-frame coalescing of `setScrollTop`, and
|
|
15
|
+
* the listener lifecycle. `onWheel` decides what the gesture means and calls
|
|
16
|
+
* `scroll` when it means scrolling `model`.
|
|
17
|
+
*
|
|
18
|
+
* **Bind this to the panel, not to the `<canvas>`.** A canvas holds no DOM
|
|
19
|
+
* children, so the clickable overlays drawn over it are siblings, and a wheel
|
|
20
|
+
* over one never reaches a listener on the canvas. Overlays that run their own
|
|
21
|
+
* gestures opt out with `[data-gesture-owner]`.
|
|
22
|
+
*/
|
|
23
|
+
export declare function useVirtualScrollWheel(panel: HTMLElement | null, model: VirtualScrollModel, onWheel: (e: WheelEvent, scroll: () => void, panel: HTMLElement) => void): void;
|