@jbrowse/core 4.3.0 → 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 +1994 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +14 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +36 -23
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +10 -7
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +124 -21
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.d.ts +2 -8
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseAttributes.js +4 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js +2 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +12 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +19 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +18 -23
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +9 -6
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +33 -30
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.d.ts +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetailsFrame.js +11 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.d.ts +8 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldActionsButton.js +24 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FieldName.js +2 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.d.ts +3 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Formatter.js +19 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.d.ts +4 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ParentFeatureLine.js +17 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +5 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +8 -6
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +7 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +15 -20
- 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 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +9 -10
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.d.ts +18 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceBody.js +10 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.d.ts +7 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceContents.js +35 -24
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.d.ts +10 -5
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js +64 -41
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts +3 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js +17 -8
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceLegend.js +19 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.d.ts +5 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequenceName.js +15 -18
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js +33 -17
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.d.ts +3 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/consts.js +7 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.d.ts +11 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/FeatureSequenceDialog.js +29 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js +4 -6
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.d.ts +18 -6
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js +11 -29
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.d.ts +9 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js +63 -58
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.d.ts +7 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js +38 -51
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js +19 -27
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.d.ts +6 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/dialogs/TranscriptSelector.js +20 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.d.ts +12 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/featureTypeUtil.js +97 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/index.js +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.d.ts +62 -63
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +69 -59
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.d.ts +21 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/panelAssemblyName.js +24 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts +5 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js +93 -75
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js +4 -11
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts +5 -2
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js +21 -48
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.d.ts +8 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/PlainSequence.js +20 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts +6 -3
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js +33 -13
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts +7 -4
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js +67 -11
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.d.ts +14 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/renderSequenceSegments.js +42 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/types.d.ts +8 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.d.ts +9 -9
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js +28 -44
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.d.ts +23 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceFetch.js +31 -0
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts +90 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/util.js +145 -23
- package/esm/BaseFeatureWidget/configSchema.d.ts +1 -1
- package/esm/BaseFeatureWidget/configSchema.js +1 -1
- package/esm/BaseFeatureWidget/formatDetails.d.ts +22 -0
- package/esm/BaseFeatureWidget/formatDetails.js +82 -0
- package/esm/BaseFeatureWidget/index.d.ts +4 -1
- package/esm/BaseFeatureWidget/index.js +2 -2
- package/esm/BaseFeatureWidget/stateModelFactory.d.ts +102 -71
- package/esm/BaseFeatureWidget/stateModelFactory.js +162 -63
- package/esm/BaseFeatureWidget/types.d.ts +15 -8
- package/esm/BaseFeatureWidget/util.d.ts +2 -37
- package/esm/BaseFeatureWidget/util.js +4 -85
- package/esm/CorePlugin.js +12 -7
- package/esm/PhasedScheduler.d.ts +4 -2
- package/esm/PhasedScheduler.js +18 -2
- package/esm/Plugin.d.ts +6 -1
- package/esm/Plugin.js +7 -0
- package/esm/PluginLoader.d.ts +55 -44
- package/esm/PluginLoader.js +290 -90
- package/esm/PluginManager.d.ts +476 -57
- package/esm/PluginManager.js +480 -91
- package/esm/ReExports/MuiDataGridReExports.d.ts +3 -2
- package/esm/ReExports/MuiDataGridReExports.js +58 -130
- package/esm/ReExports/MuiReExports.d.ts +3 -134
- package/esm/ReExports/MuiReExports.js +43 -16
- package/esm/ReExports/MuiStylesReExports.d.ts +66 -0
- package/esm/ReExports/MuiStylesReExports.js +55 -0
- 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/lazify.d.ts +2 -2
- package/esm/ReExports/lazify.js +16 -3
- package/esm/ReExports/list.js +433 -160
- package/esm/ReExports/modules.d.ts +1 -1
- package/esm/ReExports/modules.js +10 -146
- package/esm/ReExports/muiComponentNames.d.ts +18 -0
- package/esm/ReExports/muiComponentNames.js +130 -0
- package/esm/ReExports/registry.d.ts +3 -0
- package/esm/ReExports/registry.js +46 -0
- 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/BaseResults.d.ts +20 -21
- package/esm/TextSearch/BaseResults.js +8 -33
- package/esm/TextSearch/TextSearchManager.d.ts +30 -36
- package/esm/TextSearch/TextSearchManager.js +138 -44
- package/esm/TextSearch/places.d.ts +12 -0
- package/esm/TextSearch/places.js +94 -0
- package/esm/assemblyManager/assembly.d.ts +310 -35
- package/esm/assemblyManager/assembly.js +554 -263
- package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
- package/esm/assemblyManager/assemblyAdapters.js +24 -0
- package/esm/assemblyManager/assemblyConfigSchema.d.ts +135 -19
- package/esm/assemblyManager/assemblyConfigSchema.js +205 -23
- package/esm/assemblyManager/assemblyManager.d.ts +586 -323
- package/esm/assemblyManager/assemblyManager.js +352 -51
- package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +39 -0
- package/esm/assemblyManager/expandAssemblyConfigShorthand.js +114 -0
- package/esm/assemblyManager/geneticCodes.d.ts +21 -0
- package/esm/assemblyManager/geneticCodes.js +44 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +19 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.js +22 -0
- package/esm/assemblyManager/index.d.ts +1 -1
- package/esm/assemblyManager/index.js +2 -2
- package/esm/assemblyManager/indexAssemblyNames.d.ts +9 -0
- package/esm/assemblyManager/indexAssemblyNames.js +22 -0
- package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
- package/esm/assemblyManager/loadRefNameMap.js +75 -0
- package/esm/assemblyManager/refNameColors.d.ts +1 -0
- package/esm/assemblyManager/refNameColors.js +32 -0
- package/esm/assemblyManager/refNameMapKey.d.ts +7 -0
- package/esm/assemblyManager/refNameMapKey.js +12 -0
- package/esm/assemblyManager/refNameMaps.d.ts +26 -0
- package/esm/assemblyManager/refNameMaps.js +87 -0
- package/esm/assemblyManager/refNameMismatch.d.ts +54 -0
- package/esm/assemblyManager/refNameMismatch.js +66 -0
- package/esm/checkPlugins.d.ts +13 -0
- package/esm/checkPlugins.js +98 -0
- package/esm/configuration/bamIndexFields.d.ts +49 -0
- package/esm/configuration/bamIndexFields.js +41 -0
- package/esm/configuration/configurationSchema.d.ts +194 -29
- package/esm/configuration/configurationSchema.js +439 -145
- package/esm/configuration/configurationSchemaUnion.d.ts +39 -0
- package/esm/configuration/configurationSchemaUnion.js +56 -0
- package/esm/configuration/configurationSlot.d.ts +373 -30
- package/esm/configuration/configurationSlot.js +231 -224
- package/esm/configuration/fillLocations.d.ts +14 -0
- package/esm/configuration/fillLocations.js +14 -0
- package/esm/configuration/formatAboutConfigSchema.d.ts +41 -0
- package/esm/configuration/formatAboutConfigSchema.js +58 -0
- package/esm/configuration/formatDetailsConfigSchema.d.ts +54 -0
- package/esm/configuration/formatDetailsConfigSchema.js +87 -0
- package/esm/configuration/fullConfSnapshot.d.ts +13 -0
- package/esm/configuration/fullConfSnapshot.js +44 -0
- package/esm/configuration/getConf.d.ts +92 -0
- package/esm/configuration/getConf.js +141 -0
- package/esm/configuration/index.d.ts +32 -3
- package/esm/configuration/index.js +27 -2
- package/esm/configuration/indexType.d.ts +26 -0
- package/esm/configuration/indexType.js +38 -0
- package/esm/configuration/mergeFormatCallbacks.d.ts +14 -0
- package/esm/configuration/mergeFormatCallbacks.js +27 -0
- package/esm/configuration/readConfObject.d.ts +34 -0
- package/esm/configuration/readConfObject.js +118 -0
- package/esm/configuration/requirements.d.ts +37 -0
- package/esm/configuration/requirements.js +88 -0
- package/esm/configuration/schemaRegistry.d.ts +52 -0
- package/esm/configuration/schemaRegistry.js +48 -0
- package/esm/configuration/schemaTypes.d.ts +39 -0
- package/esm/configuration/schemaTypes.js +105 -0
- package/esm/configuration/slotFacade.d.ts +65 -0
- package/esm/configuration/slotFacade.js +110 -0
- package/esm/configuration/slotValueUtils.d.ts +17 -0
- package/esm/configuration/slotValueUtils.js +25 -0
- package/esm/configuration/snapshotPreprocess.d.ts +43 -0
- package/esm/configuration/snapshotPreprocess.js +161 -0
- package/esm/configuration/tabixIndexFields.d.ts +70 -0
- package/esm/configuration/tabixIndexFields.js +62 -0
- package/esm/configuration/tabixShorthand.d.ts +51 -0
- package/esm/configuration/tabixShorthand.js +72 -0
- package/esm/configuration/types.d.ts +315 -13
- package/esm/configuration/uriShorthand.d.ts +9 -0
- package/esm/configuration/uriShorthand.js +16 -0
- package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +19 -11
- package/esm/data_adapters/BaseAdapter/BaseAdapter.js +19 -18
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +158 -7
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +164 -29
- package/esm/data_adapters/BaseAdapter/BaseRefNameAliasAdapter.d.ts +1 -0
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.d.ts +13 -5
- package/esm/data_adapters/BaseAdapter/BaseSequenceAdapter.js +9 -7
- package/esm/data_adapters/BaseAdapter/BaseTextSearchAdapter.d.ts +2 -1
- package/esm/data_adapters/BaseAdapter/CytobandAdapter.d.ts +7 -0
- package/esm/data_adapters/BaseAdapter/RegionsAdapter.d.ts +2 -1
- package/esm/data_adapters/BaseAdapter/featureDensity.d.ts +40 -0
- package/esm/data_adapters/BaseAdapter/featureDensity.js +31 -0
- package/esm/data_adapters/BaseAdapter/getAdapterId.d.ts +2 -0
- package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
- package/esm/data_adapters/BaseAdapter/index.d.ts +28 -6
- package/esm/data_adapters/BaseAdapter/index.js +6 -5
- 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 +37 -5
- package/esm/data_adapters/BaseAdapter/stats.js +89 -24
- package/esm/data_adapters/BaseAdapter/types.d.ts +11 -13
- package/esm/data_adapters/BaseAdapter/types.js +1 -0
- package/esm/data_adapters/BaseAdapter/util.d.ts +5 -1
- package/esm/data_adapters/BaseAdapter/util.js +14 -3
- package/esm/data_adapters/BaseAdapter/zoomRange.d.ts +10 -0
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.d.ts +1 -1
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +5 -5
- package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +34 -6
- package/esm/data_adapters/CytobandAdapter/configSchema.js +47 -17
- package/esm/data_adapters/CytobandAdapter/index.js +3 -3
- package/esm/data_adapters/adapterSessionRefcount.d.ts +61 -0
- package/esm/data_adapters/adapterSessionRefcount.js +96 -0
- package/esm/data_adapters/dataAdapterCache.d.ts +53 -2
- package/esm/data_adapters/dataAdapterCache.js +99 -25
- package/esm/data_adapters/getFeatureAdapter.d.ts +24 -0
- package/esm/data_adapters/getFeatureAdapter.js +27 -0
- package/esm/data_adapters/getSequenceSubAdapter.d.ts +19 -0
- package/esm/data_adapters/getSequenceSubAdapter.js +42 -0
- package/esm/pluggableElementTypes/AdapterType.d.ts +57 -7
- package/esm/pluggableElementTypes/AdapterType.js +44 -5
- package/esm/pluggableElementTypes/AddTrackWorkflowType.d.ts +6 -1
- package/esm/pluggableElementTypes/AddTrackWorkflowType.js +3 -1
- package/esm/pluggableElementTypes/ConnectionType.d.ts +5 -5
- package/esm/pluggableElementTypes/ConnectionType.js +1 -1
- package/esm/pluggableElementTypes/DisplayType.d.ts +54 -14
- package/esm/pluggableElementTypes/DisplayType.js +30 -7
- package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
- package/esm/pluggableElementTypes/LazyStateModelElement.d.ts +32 -0
- package/esm/pluggableElementTypes/LazyStateModelElement.js +77 -0
- package/esm/pluggableElementTypes/PluggableElementBase.d.ts +11 -0
- package/esm/pluggableElementTypes/PluggableElementBase.js +11 -0
- package/esm/pluggableElementTypes/RpcMethodType.d.ts +142 -12
- package/esm/pluggableElementTypes/RpcMethodType.js +279 -98
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +18 -9
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.js +26 -20
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.d.ts +5 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegion.js +18 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.d.ts +5 -0
- package/esm/pluggableElementTypes/RpcMethodTypeWithRenameRegions.js +10 -0
- package/esm/pluggableElementTypes/TextSearchAdapterType.d.ts +7 -7
- package/esm/pluggableElementTypes/TextSearchAdapterType.js +3 -1
- package/esm/pluggableElementTypes/TrackType.d.ts +2 -1
- package/esm/pluggableElementTypes/TrackType.js +1 -1
- package/esm/pluggableElementTypes/ViewType.d.ts +22 -5
- package/esm/pluggableElementTypes/ViewType.js +40 -5
- package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
- package/esm/pluggableElementTypes/WidgetType.js +1 -1
- package/esm/pluggableElementTypes/addMenuItems.d.ts +88 -0
- package/esm/pluggableElementTypes/addMenuItems.js +82 -0
- package/esm/pluggableElementTypes/extendElementType.d.ts +29 -0
- package/esm/pluggableElementTypes/extendElementType.js +72 -0
- package/esm/pluggableElementTypes/index.d.ts +8 -7
- package/esm/pluggableElementTypes/index.js +24 -14
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +80 -15
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +643 -84
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +230 -60
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +246 -37
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +416 -107
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +236 -16
- package/esm/pluggableElementTypes/models/BaseViewModel.js +154 -16
- package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +169 -25
- package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
- package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +178 -0
- package/esm/pluggableElementTypes/models/assertDisplayContract.js +239 -0
- package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +26 -8
- package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +31 -17
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
- package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +142 -65
- package/esm/pluggableElementTypes/models/baseTrackConfig.js +215 -90
- package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
- package/esm/pluggableElementTypes/models/components/SaveTrackData.js +111 -139
- package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +54 -0
- package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +50 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +147 -0
- package/esm/pluggableElementTypes/models/index.d.ts +5 -3
- package/esm/pluggableElementTypes/models/index.js +9 -8
- package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +48 -0
- package/esm/pluggableElementTypes/models/migrateTrackConfig.js +114 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +10 -3
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +272 -100
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
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- package/esm/util/useFetchPlugins.d.ts +16 -0
- package/esm/util/useFetchPlugins.js +18 -0
- package/esm/util/useMeasure.d.ts +11 -1
- package/esm/util/useMeasure.js +20 -6
- package/esm/util/usePanZoom.d.ts +75 -0
- package/esm/util/usePanZoom.js +175 -0
- package/esm/util/usePanelVirtualScroll.d.ts +9 -0
- package/esm/util/usePanelVirtualScroll.js +15 -0
- package/esm/util/usePointerDrag.d.ts +37 -0
- package/esm/util/usePointerDrag.js +61 -0
- package/esm/util/useRafCommit.d.ts +4 -0
- package/esm/util/useRafCommit.js +50 -0
- package/esm/util/useResizeDrag.d.ts +91 -0
- package/esm/util/useResizeDrag.js +105 -0
- package/esm/util/useRowVirtualScroll.d.ts +9 -0
- package/esm/util/useRowVirtualScroll.js +22 -0
- package/esm/util/useVirtualScrollWheel.d.ts +23 -0
- package/esm/util/useVirtualScrollWheel.js +74 -0
- package/esm/util/viewHighlights.d.ts +3 -0
- package/esm/util/viewHighlights.js +5 -0
- package/esm/util/viewStatus.d.ts +90 -0
- package/esm/util/viewStatus.js +54 -0
- package/esm/util/virtualRange.d.ts +36 -0
- package/esm/util/virtualRange.js +26 -0
- package/esm/util/webStorage.d.ts +26 -0
- package/esm/util/webStorage.js +92 -0
- package/esm/util/wheelZoom.d.ts +65 -0
- package/esm/util/wheelZoom.js +297 -0
- package/esm/util/whenViewSettled.d.ts +74 -0
- package/esm/util/whenViewSettled.js +77 -0
- package/esm/util/withFeatureDetails.d.ts +34 -0
- package/esm/util/withFeatureDetails.js +59 -0
- package/esm/util/withLaunchInput.d.ts +174 -0
- package/esm/util/withLaunchInput.js +274 -0
- package/package.json +290 -820
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +0 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +0 -14
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +0 -7
- 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 -9
- package/esm/ReExports/DataGrid.d.ts +0 -1
- package/esm/ReExports/DataGrid.js +0 -1
- package/esm/ReExports/index.d.ts +0 -1
- package/esm/ReExports/index.js +0 -1
- package/esm/configuration/util.d.ts +0 -10
- package/esm/configuration/util.js +0 -123
- package/esm/data_adapters/BaseAdapter/BaseOptions.d.ts +0 -18
- package/esm/data_adapters/util.d.ts +0 -1
- package/esm/data_adapters/util.js +0 -6
- package/esm/pluggableElementTypes/GlyphType.d.ts +0 -43
- package/esm/pluggableElementTypes/GlyphType.js +0 -18
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.d.ts +0 -5
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/fetchSequence.js +0 -17
- package/esm/pluggableElementTypes/renderers/BoxRendererType.d.ts +0 -52
- package/esm/pluggableElementTypes/renderers/BoxRendererType.js +0 -78
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.d.ts +0 -4
- package/esm/pluggableElementTypes/renderers/CircularChordRendererType.js +0 -4
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.d.ts +0 -58
- package/esm/pluggableElementTypes/renderers/FeatureRendererType.js +0 -77
- package/esm/pluggableElementTypes/renderers/LayoutSession.d.ts +0 -31
- package/esm/pluggableElementTypes/renderers/LayoutSession.js +0 -40
- package/esm/pluggableElementTypes/renderers/RendererType.d.ts +0 -28
- package/esm/pluggableElementTypes/renderers/RendererType.js +0 -20
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.d.ts +0 -58
- package/esm/pluggableElementTypes/renderers/ServerSideRendererType.js +0 -108
- package/esm/pluggableElementTypes/renderers/index.d.ts +0 -6
- package/esm/pluggableElementTypes/renderers/index.js +0 -6
- package/esm/pluggableElementTypes/renderers/util.d.ts +0 -3
- package/esm/pluggableElementTypes/renderers/util.js +0 -14
- package/esm/rpc/baseRpcConfig.d.ts +0 -8
- package/esm/rpc/baseRpcConfig.js +0 -10
- package/esm/rpc/mainThreadRpcConfig.d.ts +0 -8
- package/esm/rpc/mainThreadRpcConfig.js +0 -8
- package/esm/rpc/methods/CoreGetFeatureDensityStats.d.ts +0 -17
- package/esm/rpc/methods/CoreGetFeatureDensityStats.js +0 -25
- package/esm/rpc/methods/CoreGetFeatureDetails.d.ts +0 -11
- package/esm/rpc/methods/CoreGetFeatureDetails.js +0 -24
- package/esm/rpc/methods/CoreGetFileInfo.d.ts +0 -9
- package/esm/rpc/methods/CoreGetFileInfo.js +0 -15
- package/esm/rpc/methods/CoreRender.d.ts +0 -14
- package/esm/rpc/methods/CoreRender.js +0 -40
- package/esm/rpc/methods/CoreSaveFeatureData.d.ts +0 -16
- package/esm/rpc/methods/CoreSaveFeatureData.js +0 -32
- package/esm/rpc/methods/util.d.ts +0 -15
- package/esm/rpc/methods/util.js +0 -7
- package/esm/rpc/webWorkerRpcConfig.d.ts +0 -8
- package/esm/rpc/webWorkerRpcConfig.js +0 -8
- package/esm/ui/MenuButton.d.ts +0 -1
- package/esm/ui/MenuButton.js +0 -1
- package/esm/ui/MenuItems.d.ts +0 -15
- package/esm/ui/MenuItems.js +0 -59
- package/esm/ui/useEvent.d.ts +0 -1
- package/esm/ui/useEvent.js +0 -10
- package/esm/util/blobToDataURL.d.ts +0 -1
- package/esm/util/blobToDataURL.js +0 -14
- package/esm/util/compositeMap.d.ts +0 -11
- package/esm/util/compositeMap.js +0 -59
- package/esm/util/flatqueue/index.d.ts +0 -11
- package/esm/util/flatqueue/index.js +0 -61
- package/esm/util/layouts/BaseLayout.d.ts +0 -30
- package/esm/util/layouts/MultiLayout.d.ts +0 -12
- package/esm/util/layouts/MultiLayout.js +0 -40
- package/esm/util/layouts/PileupLayout.d.ts +0 -41
- package/esm/util/layouts/PileupLayout.js +0 -202
- package/esm/util/layouts/PrecomputedLayout.d.ts +0 -30
- package/esm/util/layouts/PrecomputedLayout.js +0 -71
- package/esm/util/layouts/SceneGraph.d.ts +0 -31
- package/esm/util/layouts/SceneGraph.js +0 -121
- package/esm/util/makeAbortableReaction.d.ts +0 -3
- package/esm/util/makeAbortableReaction.js +0 -47
- package/esm/util/map-obj/index.d.ts +0 -13
- package/esm/util/map-obj/index.js +0 -92
- package/esm/util/nextTick.d.ts +0 -1
- package/esm/util/nextTick.js +0 -3
- package/esm/util/offscreenCanvasGetSerializingSvg.d.ts +0 -5
- package/esm/util/offscreenCanvasGetSerializingSvg.js +0 -9
- package/esm/util/offscreenCanvasUtils.d.ts +0 -12
- package/esm/util/offscreenCanvasUtils.js +0 -19
- package/esm/util/renderToAbstractCanvas.d.ts +0 -17
- package/esm/util/renderToAbstractCanvas.js +0 -53
- package/esm/util/stopToken.d.ts +0 -19
- package/esm/util/stopToken.js +0 -90
- package/esm/util/transferables.d.ts +0 -2
- package/esm/util/transferables.js +0 -35
- package/esm/util/tss-react/mui/index.d.ts +0 -1
- package/esm/util/tss-react/mui/index.js +0 -1
- package/esm/util/tss-react/mui/mui.d.ts +0 -10
- package/esm/util/tss-react/mui/mui.js +0 -5
- package/esm/util/when.d.ts +0 -1
- package/esm/util/when.js +0 -1
- /package/esm/{BaseFeatureWidget/BaseFeatureDetail/types.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
- /package/esm/data_adapters/BaseAdapter/{BaseOptions.js → zoomRange.js} +0 -0
- /package/esm/{util/layouts/BaseLayout.js → rpc/RpcRegistry.js} +0 -0
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import type { ZoomRange } from '../data_adapters/BaseAdapter/zoomRange.ts';
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import type { ColorSchemeName } from './colorSchemes.ts';
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/**
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* #api
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* Where a channel's value comes from: a feature field name, read natively
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* (`feature.get(name)`), or a `jexl:` expression over `feature` — the opt-in
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* escape, measured at 1.5x to 2.0x native per feature (MARK_ENCODING.md
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*/
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export type FieldRef = string;
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/**
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* A field bound to a categorical scale: each distinct value takes one entry
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* of the channel's `range` — a colour for `color`, a shape name for
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* `shape`. Every value derives its entry from itself (an integer takes the
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* slot it names, anything else hashes in), so every region agrees on a value
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* it shares with another at the cost of an occasional collision. A `domain`
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* spends the range deliberately: the listed values take it in order, and a
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* value the domain leaves out never takes a listed value's entry. The domain
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* orders and spends; it never adds a value the data lacks.
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*/
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export interface CategoricalRef {
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field: FieldRef;
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scale: 'categorical';
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domain?: (string | number)[];
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/** What a key names each `domain` value, one each in order. */
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labels?: string[];
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}
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/**
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* A numeric field cut into intervals: `domain` is the ascending cut points
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* and `range` holds one colour more, so a value paints the entry for the
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field: FieldRef;
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scale: 'threshold';
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domain?: (string | number)[];
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range?: string[];
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/** What the key names each bin, one each from the lowest. */
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labels?: string[];
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}
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/**
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* A numeric field read through a linear or log scale into a ramp. Each end of
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export interface ContinuousRef {
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field: FieldRef;
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scale: 'linear' | 'log';
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domainMin?: number;
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domainMax?: number;
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reverse?: boolean;
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/**
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domainQuantile?: number;
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}
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/**
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* returning one paints per feature with no scale; the object forms bind a
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}) | ContinuousRef | ThresholdRef;
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/**
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* and the field holding its 0-based coordinate, as a paired record states
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* its mate (`{ chrom: 'mate.refName', pos: 'mate.start' }`). Spelt the way
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pos: FieldRef;
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* A numeric field read through a linear or log scale into a width in CSS px:
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scale?: 'linear' | 'log';
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}
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/**
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* #api
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* How a mark's `size` channel resolves: a number is a constant width in CSS
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* the object binds the field to a scale.
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*/
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export type SizeEncoding = number | FieldRef | SizeRef;
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/**
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* #api
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* The declared mapping from a feature's fields to a mark's channels. Every
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* positional channel is a field: `x` defaults to `start` and `x2` to `end`, a
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* mark that plots no value leaves `y` off, and the scale `y` is read through
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* belongs to the display rather than to the encoding. `shape` is read by the
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* `point` mark alone, `row` — an integer field, 0 where missing — by every
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* mark, which stands a feature in the band it names.
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export interface MarkEncoding {
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row?: FieldRef;
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/** The field a `text` mark prints, read by that mark alone. */
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}
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/**
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* #api
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* The lanes a caller asks the encoder to fill, beyond `x` and `x2`, which
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* every payload carries, and `featureIndex`, which one carries where a
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* feature was skipped: a mark's channels, and `index` for the Flatbush a
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* hover reads. A lane not asked for is neither
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* allocated nor transferred, and a caller that never hovers declines the
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* index, which is most of the encoder's cost after the walk.
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*/
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export type LaneName = 'y' | 'color' | 'colorValue' | 'glyph' | 'row' | 'text' | 'size' | 'x2Ref' | 'index';
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/**
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* #api
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* The scale a colour channel was resolved through, as the legend reads it —
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* the same table the colours in the payload came from, so the key cannot
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* disagree with the painting.
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*/
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export type ColorScaleTable = {
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kind: 'categorical';
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field: string;
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domain: string[];
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/** The declared range, the other half of what assigns a key its colour. */
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range?: string[];
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/**
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* Whether every non-empty key met here parsed as a finite number: a
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* numeric field the declaration landed on a categorical scale, which
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* the key can then say rather than the encoder typing the field from
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* the data.
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*/
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numericKeys?: boolean;
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/** Each key met, in the field's order, `''` for no value. */
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entries: {
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color: number;
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}[];
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} | {
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kind: 'threshold';
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field: string;
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/** The cut points, ascending, as numbers. */
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domain: number[];
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/**
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* The declared interval colours, one more than the cuts; the default
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* palette fills what the declaration leaves.
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*/
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range?: string[];
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/**
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* Whether a feature with no value painted here, in the no-value grey:
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* the key's `(no value)` row, as the feature display's threshold gives
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* it (ADR-156).
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*/
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missing?: boolean;
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/**
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* Whether text that is no number painted here, in the misconfiguration
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* grey: the key's `(not a number)` row.
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*/
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notNumber?: boolean;
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} | {
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kind: 'ramp';
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field: string;
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scale: 'linear' | 'log';
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/** What the ramp spans here: each declared end, else `extent`'s. */
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domain: [number, number];
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/**
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* Whether each end was declared, and so already agrees across regions;
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* an open end is what a display widens to the union of theirs.
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*/
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pinned: [boolean, boolean];
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/**
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* The declared {@link ColorEncoding} `domainMid`: where the middle stop
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* of the straight `lut` sits, which every reader places through
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* render-core's `rampMidNorm` and `rampMidT`.
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*/
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domainMid?: number;
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/**
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* The declared stops — `range`'s colours or the `scheme` — and
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* `reverse`, which with both ends pinned make up the whole declaration,
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* so marks declaring one ramp alike share a key on it.
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*/
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range?: string[];
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scheme?: ColorSchemeName;
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reverse?: boolean;
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/**
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* This region's own extremes of the field, what a display unions;
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* `[Infinity, -Infinity]` where it holds no number, so a union passes
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* over it.
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*/
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extent: [number, number];
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/**
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|
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* The declared `domainQuantile` `extent` follows, below 1 only, so a
|
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* display re-measuring a subset of the instances clips it alike.
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*/
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|
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quantile?: number;
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|
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lut: Uint8Array;
|
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|
+
/**
|
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|
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* Whether a feature with no value painted here, in the no-value grey:
|
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* the key's `(no value)` row, as a threshold's.
|
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*/
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|
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missing?: boolean;
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/** Whether text that is no number painted here, in the misconfiguration grey. */
|
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|
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notNumber?: boolean;
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|
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};
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/**
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* #api
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* The scale a shape channel was resolved through: which shape each value of
|
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* the field took.
|
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*/
|
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|
+
export interface ShapeScaleTable {
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kind: 'shape';
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field: string;
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domain: string[];
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range?: ShapeName[];
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entries: {
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|
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value: string;
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|
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shape: ShapeName;
|
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|
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}[];
|
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|
+
}
|
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|
+
/**
|
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|
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* #api
|
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260
|
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* The scale a size channel is read through: the `size` lane holds the raw
|
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|
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* values and the shape maps them to px through this, so a display unions
|
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|
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* `extent` over its loaded regions into the open ends of `domain` and every
|
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|
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* region strokes the same value at the same width.
|
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|
+
*/
|
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|
+
export interface SizeScaleTable {
|
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266
|
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field: string;
|
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267
|
+
scale: 'linear' | 'log';
|
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|
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domain: [number, number];
|
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|
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pinned: [boolean, boolean];
|
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|
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range: [number, number];
|
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|
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extent: [number, number];
|
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|
+
}
|
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|
+
/**
|
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|
+
* #api
|
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275
|
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* The table behind a channel a key is drawn from: a colour's, whose `kind`
|
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|
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* names the scale it resolved through, or a shape's. A `size` channel's
|
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|
+
* ({@link SizeScaleTable}) draws no key and stands outside.
|
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278
|
+
*/
|
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279
|
+
export type ScaleTable = ColorScaleTable | ShapeScaleTable;
|
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|
+
/**
|
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281
|
+
* #api
|
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282
|
+
* One encoding's channels over one region's features, dense and
|
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283
|
+
* index-aligned: instance `i` of every array is the same feature, and
|
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284
|
+
* `featureIndex[i]` says which one of the input list it was, or it is absent
|
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285
|
+
* where instance `i` is feature `i` ({@link featureIndexAt}). A lane is
|
|
286
|
+
* present when the caller asked for it ({@link LaneName}); {@link Encoded}
|
|
287
|
+
* is this type with a known lane set required.
|
|
288
|
+
*/
|
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289
|
+
export interface EncodedChannels {
|
|
290
|
+
count: number;
|
|
291
|
+
/**
|
|
292
|
+
* Features the walk left out: one whose `x`, `x2` or `y` read as missing
|
|
293
|
+
* or not a number. A mistyped field skips every feature, so a display
|
|
294
|
+
* reads this beside `count` to say so.
|
|
295
|
+
*/
|
|
296
|
+
skipped: number;
|
|
297
|
+
/**
|
|
298
|
+
* Of `skipped`, the features whose `x` or `x2` read no number, such as
|
|
299
|
+
* the edges a `bin` writes for a feature lacking its field. Absent where
|
|
300
|
+
* the layer placed nothing by a field, as the density sidecar's does.
|
|
301
|
+
*/
|
|
302
|
+
skippedPosition?: number;
|
|
303
|
+
x: Uint32Array;
|
|
304
|
+
x2: Uint32Array;
|
|
305
|
+
featureIndex?: Uint32Array;
|
|
306
|
+
y?: Float32Array;
|
|
307
|
+
/**
|
|
308
|
+
* Each instance's packed ABGR, or one number every instance paints where
|
|
309
|
+
* the colour is a constant; {@link colorAt} reads either.
|
|
310
|
+
*/
|
|
311
|
+
color?: Uint32Array | number;
|
|
312
|
+
/**
|
|
313
|
+
* The raw values of a quantitative colour channel — a ramp's or a
|
|
314
|
+
* threshold's — for a caller that named the `colorValue` lane: the scale
|
|
315
|
+
* then resolves on the main thread and in the shader, a ramp against a
|
|
316
|
+
* domain unioned over the loaded regions (`scale.extent` is this region's
|
|
317
|
+
* contribution) and a threshold against its cuts as uniforms. Where the
|
|
318
|
+
* colour reads the field `y` plots, this IS the `y` array, not a copy.
|
|
319
|
+
*/
|
|
320
|
+
colorValue?: Float32Array;
|
|
321
|
+
/** The point painter's code for each feature's `shape`. */
|
|
322
|
+
glyph?: Uint8Array;
|
|
323
|
+
row?: Uint32Array;
|
|
324
|
+
/**
|
|
325
|
+
* Each feature's `text` channel as text, `''` where the field holds
|
|
326
|
+
* nothing; a list joins its members with commas. Strings, so the lane is
|
|
327
|
+
* cloned across the wire where the typed lanes are transferred.
|
|
328
|
+
*/
|
|
329
|
+
text?: string[];
|
|
330
|
+
/** Each feature's raw `size` value, NaN where it holds no number. */
|
|
331
|
+
size?: Float32Array;
|
|
332
|
+
/**
|
|
333
|
+
* Which sequence each feature's `x2` lies on, as an index into
|
|
334
|
+
* `x2RefNames`: the far end's own where `x2` is a {@link LocusRef}, else
|
|
335
|
+
* the feature's, in the adapter's naming either way.
|
|
336
|
+
*/
|
|
337
|
+
x2Ref?: Uint32Array;
|
|
338
|
+
x2RefNames?: string[];
|
|
339
|
+
/** The finite `y` extremes, `Infinity`/`-Infinity` when nothing plotted. */
|
|
340
|
+
yMin: number;
|
|
341
|
+
yMax: number;
|
|
342
|
+
/** A Flatbush over (x, y, x2, y), when `index` was asked for and `count` is not 0. */
|
|
343
|
+
flatbushData?: ArrayBuffer;
|
|
344
|
+
/** The colour channel's table, when `color` is a scale. */
|
|
345
|
+
scale?: ColorScaleTable;
|
|
346
|
+
/** The shape channel's table, when `shape` is a scale. */
|
|
347
|
+
shapeScale?: ShapeScaleTable;
|
|
348
|
+
/** The size channel's table, when the `size` lane was filled. */
|
|
349
|
+
sizeScale?: SizeScaleTable;
|
|
350
|
+
}
|
|
351
|
+
/**
|
|
352
|
+
* #api
|
|
353
|
+
* {@link EncodedChannels} with the lanes in `L` present — what
|
|
354
|
+
* `encodeFeatures` answers a caller that named them.
|
|
355
|
+
*/
|
|
356
|
+
export type Encoded<L extends LaneName> = EncodedChannels & Required<Pick<EncodedChannels, Exclude<L, 'index'>>>;
|
|
357
|
+
/**
|
|
358
|
+
* #api
|
|
359
|
+
* One layer of a `CoreGetEncodedLayers` request: the encoding to evaluate and
|
|
360
|
+
* the lanes the display's mark reads.
|
|
361
|
+
*/
|
|
362
|
+
export interface LayerRequest {
|
|
363
|
+
encoding: MarkEncoding;
|
|
364
|
+
lanes: LaneName[];
|
|
365
|
+
/** This layer's own steps, run after the request's shared ones. */
|
|
366
|
+
transform?: TransformStep[];
|
|
367
|
+
}
|
|
368
|
+
/**
|
|
369
|
+
* #api
|
|
370
|
+
* What `CoreGetEncodedLayers` answers for one region: `layers[i]` is the
|
|
371
|
+
* request's `layers[i]` over the region's features, so a display's mark
|
|
372
|
+
* list indexes straight into it.
|
|
373
|
+
*/
|
|
374
|
+
export interface EncodedLayersResult {
|
|
375
|
+
layers: EncodedChannels[];
|
|
376
|
+
/** The sections a facet stacked every layer's rows into. */
|
|
377
|
+
facet?: FacetSection[];
|
|
378
|
+
bytes?: number;
|
|
379
|
+
zoomRange?: ZoomRange;
|
|
380
|
+
/** What the adapter said about this answer that the features cannot show. */
|
|
381
|
+
notices?: string[];
|
|
382
|
+
}
|
|
383
|
+
/**
|
|
384
|
+
* #api
|
|
385
|
+
* Keep the features a `jexl:` expression over `feature` admits.
|
|
386
|
+
*/
|
|
387
|
+
export interface FilterStep {
|
|
388
|
+
type: 'filter';
|
|
389
|
+
expr: string;
|
|
390
|
+
}
|
|
391
|
+
/**
|
|
392
|
+
* #api
|
|
393
|
+
* Write a `jexl:` expression's value over `feature` into the field `as` of
|
|
394
|
+
* every feature.
|
|
395
|
+
*/
|
|
396
|
+
export interface FormulaStep {
|
|
397
|
+
type: 'formula';
|
|
398
|
+
expr: string;
|
|
399
|
+
as: string;
|
|
400
|
+
}
|
|
401
|
+
/**
|
|
402
|
+
* #api
|
|
403
|
+
* Place every feature in a genome-aligned bin of `step` bp, writing the bin's
|
|
404
|
+
* edges over the fields `as` names — `start` and `end` by default, so an
|
|
405
|
+
* `aggregate` grouped by those counts per bin and the bar spans the bin.
|
|
406
|
+
*
|
|
407
|
+
* With `field` (`start` by default) a feature lands in the one bin that field
|
|
408
|
+
* falls in. With `fields`, an interval's start and end, it is cut at the bin
|
|
409
|
+
* edges into one piece per bin it overlaps, each piece writing `overlap`, the
|
|
410
|
+
* bases of the interval inside its bin; a zero-length interval (an insertion)
|
|
411
|
+
* is one piece of overlap 0 in the bin holding its position, and one whose
|
|
412
|
+
* ends are not numbers is none. A piece is its feature with those fields
|
|
413
|
+
* beside it, so its id and hover are the feature's, and an `aggregate` over
|
|
414
|
+
* the pieces weighted by `overlap` is a mean per base.
|
|
415
|
+
*/
|
|
416
|
+
export type BinStep = {
|
|
417
|
+
type: 'bin';
|
|
418
|
+
step: number;
|
|
419
|
+
as?: [string, string];
|
|
420
|
+
} & ({
|
|
421
|
+
field?: FieldRef;
|
|
422
|
+
fields?: never;
|
|
423
|
+
} | {
|
|
424
|
+
fields: [FieldRef, FieldRef];
|
|
425
|
+
field?: never;
|
|
426
|
+
});
|
|
427
|
+
/**
|
|
428
|
+
* #api
|
|
429
|
+
* One summary over a group: `count` needs no field; `sum`, `mean`, `min` and
|
|
430
|
+
* `max` read one, skipping values that are not numbers. The output field is
|
|
431
|
+
* `as`, else `count` or `<op>_<field>`.
|
|
432
|
+
*
|
|
433
|
+
* `weight` names a field each row counts by: `count` is then the sum of the
|
|
434
|
+
* weights, `sum` the sum of value times weight, and `mean` that over the sum
|
|
435
|
+
* of the weights, a row whose weight is not a number counting for nothing. A
|
|
436
|
+
* weight moves no minimum or maximum, so `min` and `max` read none.
|
|
437
|
+
*/
|
|
438
|
+
export interface AggregateOp {
|
|
439
|
+
op: 'count' | 'sum' | 'mean' | 'min' | 'max';
|
|
440
|
+
field?: FieldRef;
|
|
441
|
+
weight?: FieldRef;
|
|
442
|
+
as?: string;
|
|
443
|
+
}
|
|
444
|
+
/**
|
|
445
|
+
* #api
|
|
446
|
+
* One feature per distinct `groupby` value set (one for the whole region
|
|
447
|
+
* with none), spanning its members' extent, carrying the group's fields and
|
|
448
|
+
* every `ops` entry.
|
|
449
|
+
*/
|
|
450
|
+
export interface AggregateStep {
|
|
451
|
+
type: 'aggregate';
|
|
452
|
+
groupby?: FieldRef[];
|
|
453
|
+
ops: AggregateOp[];
|
|
454
|
+
}
|
|
455
|
+
/**
|
|
456
|
+
* #api
|
|
457
|
+
* Replace the features with runs of constant depth: how many of them overlap
|
|
458
|
+
* each stretch of the region, in a field `as` (`coverage` by default), with
|
|
459
|
+
* the stretches nothing overlaps left out.
|
|
460
|
+
*/
|
|
461
|
+
export interface CoverageStep {
|
|
462
|
+
type: 'coverage';
|
|
463
|
+
as?: string;
|
|
464
|
+
}
|
|
465
|
+
/**
|
|
466
|
+
* #api
|
|
467
|
+
* Fan each feature out into one feature per element of an array-valued field
|
|
468
|
+
* — `subfeatures`, so a gene answers its transcripts and a transcript its
|
|
469
|
+
* exons — or per entry of a record keyed by name, so a VCF record answers one
|
|
470
|
+
* feature per sample and a MAF block one per species, each with its key in
|
|
471
|
+
* `key`. Each answer reads the element's own fields first and the feature it
|
|
472
|
+
* came from for everything else, so an exon still knows its gene's name and
|
|
473
|
+
* strand and a species row its block's reference span. A feature whose field
|
|
474
|
+
* holds no array and no record drops out unless `keepEmpty` says otherwise.
|
|
475
|
+
*/
|
|
476
|
+
export interface FlattenStep {
|
|
477
|
+
type: 'flatten';
|
|
478
|
+
field?: FieldRef;
|
|
479
|
+
/** Written with the element's position in its parent's array. */
|
|
480
|
+
index?: string;
|
|
481
|
+
/** Written with the entry's key, where the field is a record. */
|
|
482
|
+
key?: string;
|
|
483
|
+
keepEmpty?: boolean;
|
|
484
|
+
}
|
|
485
|
+
/**
|
|
486
|
+
* #api
|
|
487
|
+
* Replace each aligned row with its cells against the reference: one feature
|
|
488
|
+
* per run of columns in one `state` — `match`, `mismatch` or `gap` — on the
|
|
489
|
+
* row's own reference span, a mismatch run carrying its `base` and a match or
|
|
490
|
+
* mismatch run `match` as 1 or 0, and one interbase feature per `insertion`,
|
|
491
|
+
* standing at the reference base it precedes with the inserted bases in
|
|
492
|
+
* `base` and their count in `length`. The row's `field` (`seq`) is the
|
|
493
|
+
* aligned text, and the reference's is the same field on the feature the row
|
|
494
|
+
* was fanned out of, so a `flatten` over a MAF block's `alignments` stands in
|
|
495
|
+
* front. A gap run reaching either end of the row is no cell, and a feature
|
|
496
|
+
* with no parent answers none.
|
|
497
|
+
*/
|
|
498
|
+
export interface CellsStep {
|
|
499
|
+
type: 'cells';
|
|
500
|
+
field?: FieldRef;
|
|
501
|
+
}
|
|
502
|
+
/**
|
|
503
|
+
* #api
|
|
504
|
+
* Assign every feature the lowest row on which it overlaps nothing already
|
|
505
|
+
* there — greedy first fit in start order, the packing a pileup is — and
|
|
506
|
+
* write it to the field `as` (`row`). `fields` names the interval read
|
|
507
|
+
* (`start`, `end`); `padding` is bp of clearance kept between two features
|
|
508
|
+
* sharing a row. The answer is the input in start order, so a `span`
|
|
509
|
+
* encoding `row` stacks it. Under a facet it packs each section on its own.
|
|
510
|
+
*/
|
|
511
|
+
export interface PileupStep {
|
|
512
|
+
type: 'pileup';
|
|
513
|
+
as?: string;
|
|
514
|
+
fields?: [FieldRef, FieldRef];
|
|
515
|
+
padding?: number;
|
|
516
|
+
}
|
|
517
|
+
/**
|
|
518
|
+
* #api
|
|
519
|
+
* One feature per other end a record states: the `mate` a paired adapter
|
|
520
|
+
* fills in (BEDPE, STAR-Fusion), or each VCF `ALT` naming a locus, a
|
|
521
|
+
* breakend's mate or a symbolic allele's `END` on `CHR2` or its own
|
|
522
|
+
* sequence. Each answer carries `mate` (`refName`, `start`, `end`, 0-based
|
|
523
|
+
* and half-open, and the far end's `mateDirection`), its own end's
|
|
524
|
+
* `mateDirection`, the `alt` it came from and `svType`, the structural
|
|
525
|
+
* class the allele states (`svClassOfAlt`). A record naming no other end drops
|
|
526
|
+
* out, and two records or alleles stating one pair of ends answer once.
|
|
527
|
+
*/
|
|
528
|
+
export interface MateStep {
|
|
529
|
+
type: 'mate';
|
|
530
|
+
}
|
|
531
|
+
/**
|
|
532
|
+
* #api
|
|
533
|
+
* One step over the features before a layer is encoded, named by `type` the
|
|
534
|
+
* way GenomeSpy spells a transform; every step runs in order and the next
|
|
535
|
+
* reads what the last answered.
|
|
536
|
+
*/
|
|
537
|
+
export type TransformStep = FilterStep | FormulaStep | FlattenStep | CellsStep | BinStep | AggregateStep | CoverageStep | PileupStep | MateStep;
|
|
538
|
+
export type CoreGetEncodedLayersArgs = {
|
|
539
|
+
adapterConfig: Record<string, unknown>;
|
|
540
|
+
region: {
|
|
541
|
+
refName: string;
|
|
542
|
+
start: number;
|
|
543
|
+
end: number;
|
|
544
|
+
assemblyName: string;
|
|
545
|
+
};
|
|
546
|
+
layers: LayerRequest[];
|
|
547
|
+
/** The steps over the features, in order, before every layer encodes. */
|
|
548
|
+
transform?: TransformStep[];
|
|
549
|
+
/** Split the features after the shared steps, before each layer's own. */
|
|
550
|
+
facet?: FacetSpec;
|
|
551
|
+
/**
|
|
552
|
+
* The zoom the adapter reads at, for one with zoom levels (BigWig); absent
|
|
553
|
+
* is full resolution.
|
|
554
|
+
*/
|
|
555
|
+
bpPerPx?: number;
|
|
556
|
+
/**
|
|
557
|
+
* What the adapter's `getFeatures` takes beside the region and the zoom, for
|
|
558
|
+
* an adapter whose answer depends on more than those: the GWAS adapter reads
|
|
559
|
+
* its LD join here.
|
|
560
|
+
*/
|
|
561
|
+
opts?: object;
|
|
562
|
+
byteLimit?: number;
|
|
563
|
+
};
|
|
564
|
+
/**
|
|
565
|
+
* #api
|
|
566
|
+
* A row facet: split the features on `field`'s value, run `transform` and then
|
|
567
|
+
* every layer's own steps over each section alone, and stack the sections,
|
|
568
|
+
* each starting on the row after the one above it ends.
|
|
569
|
+
*/
|
|
570
|
+
export interface FacetSpec {
|
|
571
|
+
field: FieldRef;
|
|
572
|
+
/**
|
|
573
|
+
* Steps over each section's features, before every layer's own: a `pileup`
|
|
574
|
+
* here packs each section on its own rows, which every layer then stands
|
|
575
|
+
* in.
|
|
576
|
+
*/
|
|
577
|
+
transform?: TransformStep[];
|
|
578
|
+
}
|
|
579
|
+
/**
|
|
580
|
+
* #api
|
|
581
|
+
* One faceted section as the worker stacked it: its key, the row it starts on
|
|
582
|
+
* and how many rows it holds.
|
|
583
|
+
*/
|
|
584
|
+
export interface FacetSection {
|
|
585
|
+
key: string;
|
|
586
|
+
firstRow: number;
|
|
587
|
+
rowCount: number;
|
|
588
|
+
}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
// The declared shape of a mark encoding and what evaluating one produces —
|
|
2
|
+
// split from markEncoding.ts because that file's runtime half reaches
|
|
3
|
+
// render-core's whole HAL/color-ramp graph for encodeFeatures' native scale
|
|
4
|
+
// tables, and RpcRegistry.ts needs only these types for CoreGetEncodedLayers'
|
|
5
|
+
// wire shape. Importing them from markEncoding.ts would carry that graph into
|
|
6
|
+
// every leaf that reaches the RPC registry. scripts/moduleClosure.test.ts
|
|
7
|
+
// holds the ceiling.
|
|
8
|
+
export {};
|
|
@@ -0,0 +1,11 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Test whether a `trackId` matches any of the given patterns, exactly as
|
|
3
|
+
* written. A session copy of a track carries a timestamp suffix on its id (see
|
|
4
|
+
* {@link makeTrackId} / {@link copyTrackSnapshot}), so a plain string misses
|
|
5
|
+
* the user's copies and matching them means passing a `RegExp` yourself.
|
|
6
|
+
*
|
|
7
|
+
* To scope an extension point contribution to a track, use
|
|
8
|
+
* `matchesTrackSelector` from `@jbrowse/core/ui` instead: it takes the same
|
|
9
|
+
* patterns and normalizes the copy suffix, which is the part nobody remembers.
|
|
10
|
+
*/
|
|
11
|
+
export declare function matchTrackId(trackId: string | undefined, patterns: (string | RegExp)[]): boolean;
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Test whether a `trackId` matches any of the given patterns, exactly as
|
|
3
|
+
* written. A session copy of a track carries a timestamp suffix on its id (see
|
|
4
|
+
* {@link makeTrackId} / {@link copyTrackSnapshot}), so a plain string misses
|
|
5
|
+
* the user's copies and matching them means passing a `RegExp` yourself.
|
|
6
|
+
*
|
|
7
|
+
* To scope an extension point contribution to a track, use
|
|
8
|
+
* `matchesTrackSelector` from `@jbrowse/core/ui` instead: it takes the same
|
|
9
|
+
* patterns and normalizes the copy suffix, which is the part nobody remembers.
|
|
10
|
+
*/
|
|
11
|
+
export function matchTrackId(trackId, patterns) {
|
|
12
|
+
return (trackId !== undefined &&
|
|
13
|
+
patterns.some(pattern => typeof pattern === 'string' ? pattern === trackId : pattern.test(trackId)));
|
|
14
|
+
}
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
export declare function measureText(str: unknown, fontSize?: number, fontFamily?: string): number;
|
|
2
|
+
export interface MeasuredFont {
|
|
3
|
+
/** assign to `ctx.font` */
|
|
4
|
+
css: string;
|
|
5
|
+
/** width of `text` in that same font, in px */
|
|
6
|
+
measure: (text: string) => number;
|
|
7
|
+
}
|
|
8
|
+
/**
|
|
9
|
+
* A CSS font string and its own measurement, built from one set of inputs so a
|
|
10
|
+
* caller cannot paint in one font and reserve room in another.
|
|
11
|
+
*
|
|
12
|
+
* Two files describing one font is the normal shape — something measures to
|
|
13
|
+
* decide whether a label fits, something else sets `ctx.font` and draws it — and
|
|
14
|
+
* the two drift silently, because a label that overflows its box by a pixel
|
|
15
|
+
* looks like a label. plugin-maf drew its deletion count in `bold 10px Courier
|
|
16
|
+
* New,monospace` and measured it here without naming the family, so a monospace
|
|
17
|
+
* label was answered from the Helvetica table above: 0.55px short per digit,
|
|
18
|
+
* which its 2px of padding covered for exactly three digits and no more.
|
|
19
|
+
*
|
|
20
|
+
* `weight` reaches the CSS and not the measurement, which is right for the
|
|
21
|
+
* digits these callers measure — monospace bold and regular share an advance,
|
|
22
|
+
* and Helvetica's ten digits are one width in either.
|
|
23
|
+
*/
|
|
24
|
+
export declare function measuredFont(fontSize: number, fontFamily: string, weight?: string): MeasuredFont;
|