@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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|
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}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
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onHorizontalScroll?: () => void;
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/**
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model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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/**
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} & {
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/**
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id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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/**
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|
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rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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rendererTypeName: string;
|
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|
error: unknown;
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/**
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* #volatile
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|
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* determinate progress fraction [0,1] for the current status, or
|
|
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|
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* undefined when the in-flight phase is indeterminate. Set alongside
|
|
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|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
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|
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* bar simply leaves it undefined.
|
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*/
|
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statusProgress: number | undefined;
|
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|
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} & {
|
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/**
|
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* #getter
|
|
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|
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*/
|
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|
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readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
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|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
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|
}> | null;
|
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110
|
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|
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111
|
-
|
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/**
|
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* #getter
|
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*/
|
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|
+
readonly adapterConfig: Record<string, unknown>;
|
|
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|
+
/**
|
|
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|
+
* #getter
|
|
373
|
+
* Returns true if the parent track is minimized. Used to skip
|
|
374
|
+
* expensive operations like autoruns when track is not visible.
|
|
375
|
+
*/
|
|
112
376
|
readonly isMinimized: boolean;
|
|
113
|
-
|
|
114
|
-
|
|
377
|
+
/**
|
|
378
|
+
* #getter
|
|
379
|
+
* Overridable hook (default `undefined`): what the pointer is currently
|
|
380
|
+
* over, for readers **outside** the display. `LinearGenomeViewContainer`
|
|
381
|
+
* publishes it to `session.hovered`, the view-wide "what is the user
|
|
382
|
+
* pointing at" channel a plugin can subscribe to.
|
|
383
|
+
*
|
|
384
|
+
* Declared here because a cross-display consumer can only read a name the
|
|
385
|
+
* base declares — the same reason `FetchMixin.fetchInert` is a
|
|
386
|
+
* hook rather than a getter each display invents. The container used to
|
|
387
|
+
* read `featureUnderMouse`, which only the wiggle, alignments and
|
|
388
|
+
* Manhattan families spelled that way — canvas said `hoveredFeature`,
|
|
389
|
+
* variants `hoveredGenotype` — so the channel carried a hover from a third
|
|
390
|
+
* of the display types and nothing said which. It also asked only
|
|
391
|
+
* `displays[0]` of each track.
|
|
392
|
+
*
|
|
393
|
+
* `unknown` because the payload genuinely differs — a read, a wiggle bin,
|
|
394
|
+
* a SNP, a genotype cell — and `session.hovered` is typed to match ("can
|
|
395
|
+
* be anything; code that wants to deal with this should examine it").
|
|
396
|
+
* Narrow it in the override.
|
|
397
|
+
*/
|
|
398
|
+
readonly hoveredFeature: unknown;
|
|
399
|
+
/**
|
|
400
|
+
* #getter
|
|
401
|
+
* Overridable hook (default `'feature'`): the SINGULAR word for one of
|
|
402
|
+
* the things this display draws, as a menu row or a chip says it —
|
|
403
|
+
* "Hide this read", "Showing 3 variants".
|
|
404
|
+
*
|
|
405
|
+
* Declared here for the same reason as `hoveredFeature` above: it is read
|
|
406
|
+
* across the display boundary, by chrome that has no idea which display
|
|
407
|
+
* it is drawing for (`SoloSelectionChip`, alignments' group-label
|
|
408
|
+
* overlay), and a name only the base declares is a name every such
|
|
409
|
+
* consumer can rely on. Two displays declared it independently and one of
|
|
410
|
+
* those declarations WAS this default.
|
|
411
|
+
*
|
|
412
|
+
* **A control keeps the generic word; content takes this one.** "Variant
|
|
413
|
+
* height" reads as a different setting from "Feature height" when it is
|
|
414
|
+
* the same one, so the shared menus stay on "feature" however the display
|
|
415
|
+
* answers here, and the noun varies where it names what the user is
|
|
416
|
+
* looking at — "Showing 3 variants", "Hide this read". A display drawing
|
|
417
|
+
* something the generic word already fits is right to leave this alone.
|
|
418
|
+
*
|
|
419
|
+
* Distinct from the per-hit noun a context menu takes off the clicked
|
|
420
|
+
* item's own `type` ("mRNA", "gene"); that names one annotation, this
|
|
421
|
+
* names what the track holds. The hit noun falls back to this.
|
|
422
|
+
*/
|
|
423
|
+
readonly featureNoun: string;
|
|
424
|
+
/**
|
|
425
|
+
* #getter
|
|
426
|
+
* The widget `openFeatureWidget` opens for one of this display's
|
|
427
|
+
* features. Displays may override it. The default is the generic feature
|
|
428
|
+
* widget, for displays drawing plain features.
|
|
429
|
+
*
|
|
430
|
+
* Displays whose features are a specific kind (a read, a variant, a
|
|
431
|
+
* synteny block) override it, including the `id`: two displays naming
|
|
432
|
+
* one id share the drawer panel, which suits two displays showing the
|
|
433
|
+
* same kind of feature.
|
|
434
|
+
*/
|
|
435
|
+
readonly featureWidgetType: {
|
|
436
|
+
type: string;
|
|
437
|
+
id: string;
|
|
438
|
+
};
|
|
115
439
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
440
|
+
/**
|
|
441
|
+
* #property
|
|
442
|
+
*/
|
|
116
443
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
444
|
+
/**
|
|
445
|
+
* #property
|
|
446
|
+
*/
|
|
117
447
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
118
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
|
119
448
|
}, {
|
|
120
|
-
rendererTypeName: string;
|
|
121
449
|
error: unknown;
|
|
122
450
|
statusMessage: string | undefined;
|
|
451
|
+
/**
|
|
452
|
+
* #volatile
|
|
453
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
454
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
455
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
456
|
+
* bar simply leaves it undefined.
|
|
457
|
+
*/
|
|
458
|
+
statusProgress: number | undefined;
|
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123
459
|
} & {
|
|
460
|
+
/**
|
|
461
|
+
* #getter
|
|
462
|
+
*/
|
|
463
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
464
|
+
} & {
|
|
465
|
+
/**
|
|
466
|
+
* #getter
|
|
467
|
+
*/
|
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124
468
|
readonly RenderingComponent: React.FC<{
|
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125
|
-
model: {
|
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126
|
-
|
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127
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-
|
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128
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-
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129
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-
|
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130
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-
|
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469
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+
model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
470
|
+
/**
|
|
471
|
+
* #property
|
|
472
|
+
*/
|
|
473
|
+
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
474
|
+
/**
|
|
475
|
+
* #property
|
|
476
|
+
*/
|
|
477
|
+
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
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478
|
+
}> & {
|
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131
479
|
error: unknown;
|
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132
480
|
statusMessage: string | undefined;
|
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481
|
+
/**
|
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482
|
+
* #volatile
|
|
483
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
484
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
485
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
486
|
+
* bar simply leaves it undefined.
|
|
487
|
+
*/
|
|
488
|
+
statusProgress: number | undefined;
|
|
489
|
+
} & {
|
|
490
|
+
/**
|
|
491
|
+
* #getter
|
|
492
|
+
*/
|
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493
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
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133
494
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
495
|
+
/**
|
|
496
|
+
* #property
|
|
497
|
+
*/
|
|
134
498
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
499
|
+
/**
|
|
500
|
+
* #property
|
|
501
|
+
*/
|
|
135
502
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
136
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
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137
503
|
}, {
|
|
138
|
-
rendererTypeName: string;
|
|
139
504
|
error: unknown;
|
|
140
505
|
statusMessage: string | undefined;
|
|
506
|
+
/**
|
|
507
|
+
* #volatile
|
|
508
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
509
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
510
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
511
|
+
* bar simply leaves it undefined.
|
|
512
|
+
*/
|
|
513
|
+
statusProgress: number | undefined;
|
|
514
|
+
} & {
|
|
515
|
+
/**
|
|
516
|
+
* #getter
|
|
517
|
+
*/
|
|
518
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
141
519
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
142
|
-
onHorizontalScroll?: () => void;
|
|
143
|
-
blockState?: Record<string,
|
|
520
|
+
onHorizontalScroll?: (distance: number) => void;
|
|
521
|
+
blockState?: Record<string, unknown>;
|
|
144
522
|
}>;
|
|
523
|
+
/**
|
|
524
|
+
* #getter
|
|
525
|
+
*/
|
|
145
526
|
readonly DisplayBlurb: React.FC<{
|
|
146
|
-
model: {
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
527
|
+
model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
528
|
+
/**
|
|
529
|
+
* #property
|
|
530
|
+
*/
|
|
531
|
+
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
532
|
+
/**
|
|
533
|
+
* #property
|
|
534
|
+
*/
|
|
535
|
+
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
536
|
+
}> & {
|
|
152
537
|
error: unknown;
|
|
153
538
|
statusMessage: string | undefined;
|
|
539
|
+
/**
|
|
540
|
+
* #volatile
|
|
541
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
542
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
543
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
544
|
+
* bar simply leaves it undefined.
|
|
545
|
+
*/
|
|
546
|
+
statusProgress: number | undefined;
|
|
547
|
+
} & {
|
|
548
|
+
/**
|
|
549
|
+
* #getter
|
|
550
|
+
*/
|
|
551
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
154
552
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
553
|
+
/**
|
|
554
|
+
* #property
|
|
555
|
+
*/
|
|
155
556
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
557
|
+
/**
|
|
558
|
+
* #property
|
|
559
|
+
*/
|
|
156
560
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
157
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
|
158
561
|
}, {
|
|
159
|
-
rendererTypeName: string;
|
|
160
562
|
error: unknown;
|
|
161
563
|
statusMessage: string | undefined;
|
|
564
|
+
/**
|
|
565
|
+
* #volatile
|
|
566
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
567
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
568
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
569
|
+
* bar simply leaves it undefined.
|
|
570
|
+
*/
|
|
571
|
+
statusProgress: number | undefined;
|
|
572
|
+
} & {
|
|
573
|
+
/**
|
|
574
|
+
* #getter
|
|
575
|
+
*/
|
|
576
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
162
577
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
163
578
|
}> | null;
|
|
164
|
-
|
|
165
|
-
|
|
579
|
+
/**
|
|
580
|
+
* #getter
|
|
581
|
+
*/
|
|
582
|
+
readonly adapterConfig: Record<string, unknown>;
|
|
583
|
+
/**
|
|
584
|
+
* #getter
|
|
585
|
+
* Returns true if the parent track is minimized. Used to skip
|
|
586
|
+
* expensive operations like autoruns when track is not visible.
|
|
587
|
+
*/
|
|
166
588
|
readonly isMinimized: boolean;
|
|
167
|
-
|
|
168
|
-
|
|
589
|
+
/**
|
|
590
|
+
* #getter
|
|
591
|
+
* Overridable hook (default `undefined`): what the pointer is currently
|
|
592
|
+
* over, for readers **outside** the display. `LinearGenomeViewContainer`
|
|
593
|
+
* publishes it to `session.hovered`, the view-wide "what is the user
|
|
594
|
+
* pointing at" channel a plugin can subscribe to.
|
|
595
|
+
*
|
|
596
|
+
* Declared here because a cross-display consumer can only read a name the
|
|
597
|
+
* base declares — the same reason `FetchMixin.fetchInert` is a
|
|
598
|
+
* hook rather than a getter each display invents. The container used to
|
|
599
|
+
* read `featureUnderMouse`, which only the wiggle, alignments and
|
|
600
|
+
* Manhattan families spelled that way — canvas said `hoveredFeature`,
|
|
601
|
+
* variants `hoveredGenotype` — so the channel carried a hover from a third
|
|
602
|
+
* of the display types and nothing said which. It also asked only
|
|
603
|
+
* `displays[0]` of each track.
|
|
604
|
+
*
|
|
605
|
+
* `unknown` because the payload genuinely differs — a read, a wiggle bin,
|
|
606
|
+
* a SNP, a genotype cell — and `session.hovered` is typed to match ("can
|
|
607
|
+
* be anything; code that wants to deal with this should examine it").
|
|
608
|
+
* Narrow it in the override.
|
|
609
|
+
*/
|
|
610
|
+
readonly hoveredFeature: unknown;
|
|
611
|
+
/**
|
|
612
|
+
* #getter
|
|
613
|
+
* Overridable hook (default `'feature'`): the SINGULAR word for one of
|
|
614
|
+
* the things this display draws, as a menu row or a chip says it —
|
|
615
|
+
* "Hide this read", "Showing 3 variants".
|
|
616
|
+
*
|
|
617
|
+
* Declared here for the same reason as `hoveredFeature` above: it is read
|
|
618
|
+
* across the display boundary, by chrome that has no idea which display
|
|
619
|
+
* it is drawing for (`SoloSelectionChip`, alignments' group-label
|
|
620
|
+
* overlay), and a name only the base declares is a name every such
|
|
621
|
+
* consumer can rely on. Two displays declared it independently and one of
|
|
622
|
+
* those declarations WAS this default.
|
|
623
|
+
*
|
|
624
|
+
* **A control keeps the generic word; content takes this one.** "Variant
|
|
625
|
+
* height" reads as a different setting from "Feature height" when it is
|
|
626
|
+
* the same one, so the shared menus stay on "feature" however the display
|
|
627
|
+
* answers here, and the noun varies where it names what the user is
|
|
628
|
+
* looking at — "Showing 3 variants", "Hide this read". A display drawing
|
|
629
|
+
* something the generic word already fits is right to leave this alone.
|
|
630
|
+
*
|
|
631
|
+
* Distinct from the per-hit noun a context menu takes off the clicked
|
|
632
|
+
* item's own `type` ("mRNA", "gene"); that names one annotation, this
|
|
633
|
+
* names what the track holds. The hit noun falls back to this.
|
|
634
|
+
*/
|
|
635
|
+
readonly featureNoun: string;
|
|
636
|
+
/**
|
|
637
|
+
* #getter
|
|
638
|
+
* The widget `openFeatureWidget` opens for one of this display's
|
|
639
|
+
* features. Displays may override it. The default is the generic feature
|
|
640
|
+
* widget, for displays drawing plain features.
|
|
641
|
+
*
|
|
642
|
+
* Displays whose features are a specific kind (a read, a variant, a
|
|
643
|
+
* synteny block) override it, including the `id`: two displays naming
|
|
644
|
+
* one id share the drawer panel, which suits two displays showing the
|
|
645
|
+
* same kind of feature.
|
|
646
|
+
*/
|
|
647
|
+
readonly featureWidgetType: {
|
|
648
|
+
type: string;
|
|
649
|
+
id: string;
|
|
650
|
+
};
|
|
169
651
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
170
652
|
};
|
|
171
|
-
|
|
172
|
-
|
|
653
|
+
/**
|
|
654
|
+
* #method
|
|
655
|
+
*/
|
|
173
656
|
trackMenuItems(): MenuItem[];
|
|
174
|
-
readonly viewMenuActions: MenuItem[];
|
|
175
|
-
regionCannotBeRendered(): null;
|
|
176
657
|
} & {
|
|
177
|
-
|
|
658
|
+
/**
|
|
659
|
+
* #action
|
|
660
|
+
*/
|
|
661
|
+
setStatusMessage(status?: RpcStatus): void;
|
|
662
|
+
/**
|
|
663
|
+
* #action
|
|
664
|
+
*/
|
|
178
665
|
setError(error?: unknown): void;
|
|
179
|
-
|
|
666
|
+
/**
|
|
667
|
+
* #action
|
|
668
|
+
* Overridable hook (default no-op): drop whatever `hoveredFeature`
|
|
669
|
+
* reports. The writing twin of that getter, and what
|
|
670
|
+
* `installClearHoverOnViewportChange` calls.
|
|
671
|
+
*
|
|
672
|
+
* A display that STORES its hover owes an override; one that derives it
|
|
673
|
+
* from the live pointer (MAF, Hi-C, LD) owes nothing, and the default
|
|
674
|
+
* costs it nothing. Declared here so the clear can be installed for every
|
|
675
|
+
* display rather than remembered per display — forgetting it is the
|
|
676
|
+
* failure ARCHITECTURE.md's stored-hover section is about, and it used to
|
|
677
|
+
* be six closures at six call sites, which is six chances to omit one.
|
|
678
|
+
*/
|
|
679
|
+
clearHoveredFeature(): void;
|
|
680
|
+
/**
|
|
681
|
+
* #action
|
|
682
|
+
* base display reload does nothing, see specialized displays for details
|
|
683
|
+
*/
|
|
180
684
|
reload(): void;
|
|
685
|
+
/**
|
|
686
|
+
* #action
|
|
687
|
+
* Apply a set of display settings to the live display, and report which
|
|
688
|
+
* were applied. Each key runs through the display config schema's
|
|
689
|
+
* `preProcessSnapshot` (shorthand expansions and legacy-key migrations,
|
|
690
|
+
* as `showTrackGeneric` applies to a session spec's inline track keys),
|
|
691
|
+
* then writes the matching config slot. A key naming a sub-schema
|
|
692
|
+
* (`facet`, `color`) replaces the whole object, its string shorthand
|
|
693
|
+
* lifted by that schema, and `null` clears it. Keys that are not slots
|
|
694
|
+
* come back in `unapplied` as `{ key, reason }`, so a caller can tell a
|
|
695
|
+
* misspelling from a key that has an action instead of a slot.
|
|
696
|
+
*
|
|
697
|
+
* `allowSetters` also routes a non-slot key to a single-argument action
|
|
698
|
+
* named `set<Key>`. It is off by default because session specs, share
|
|
699
|
+
* links and embeds pass untyped JSON here, and a default fallback would
|
|
700
|
+
* let them call internal setters (`setError`, `setScrollTop`, ...) and
|
|
701
|
+
* call multi-argument setters with one argument. A caller that wants a
|
|
702
|
+
* specific action can call it directly.
|
|
703
|
+
*
|
|
704
|
+
* A key whose write threw is reported in `failed`. Only `failed` means
|
|
705
|
+
* the caller passed a bad value. `unapplied` needs the caller's own
|
|
706
|
+
* context to read: `showTrackGeneric` spreads the same settings into the
|
|
707
|
+
* display's snapshot, so a declared prop (`resolution`) has already
|
|
708
|
+
* landed by the time it reports here, while the restyle path spreads
|
|
709
|
+
* nothing and every entry there did nothing.
|
|
710
|
+
*
|
|
711
|
+
* A per-key error does not abort the remaining keys. A caller
|
|
712
|
+
* mid-`showTrack` has already pushed the track, and one rejected value
|
|
713
|
+
* should not leave it half-configured.
|
|
714
|
+
*/
|
|
715
|
+
applyDisplaySettings(settings: Record<string, unknown>, options?: {
|
|
716
|
+
allowSetters?: boolean;
|
|
717
|
+
}): {
|
|
718
|
+
applied: string[];
|
|
719
|
+
unapplied: UnappliedSetting[];
|
|
720
|
+
failed: {
|
|
721
|
+
key: string;
|
|
722
|
+
error: string;
|
|
723
|
+
}[];
|
|
724
|
+
};
|
|
181
725
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
|
|
182
726
|
export type BaseDisplayStateModel = typeof BaseDisplay;
|
|
183
727
|
export type BaseDisplayModel = Instance<BaseDisplayStateModel>;
|
|
728
|
+
/**
|
|
729
|
+
* The shape every display instance held in a track's `displays` array
|
|
730
|
+
* satisfies: the composed `BaseDisplay` state model (RenderingComponent,
|
|
731
|
+
* DisplayBlurb, trackMenuItems, ...) plus the `configuration`
|
|
732
|
+
* reference every display gains at instantiation. `getPortableSettings` is
|
|
733
|
+
* optional — only display types that support switching type via the track menu
|
|
734
|
+
* implement it. This is the concrete element type behind
|
|
735
|
+
* `BaseTrackModel.displays`, which the runtime plugin union erases to `any`.
|
|
736
|
+
*/
|
|
737
|
+
export interface DisplayModel extends BaseDisplayModel {
|
|
738
|
+
configuration: AnyConfigurationModel & {
|
|
739
|
+
displayId: string;
|
|
740
|
+
};
|
|
741
|
+
getPortableSettings?: (newDisplayId?: string) => Record<string, unknown> | undefined;
|
|
742
|
+
}
|