@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 { getContainingTrack, getEnv, statusFraction, statusMessageText, } from '../../util/index.js';
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/**
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},
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get DisplayMessageComponent() {
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return undefined;
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},
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*/
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trackMenuItems() {
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get viewMenuActions() {
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return [];
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regionCannotBeRendered() {
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}))
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.actions(self => ({
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/**
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* #action
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*/
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setStatusMessage(status) {
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// derive the indeterminate label and the determinate fraction from the
|
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// one status transport; displays with no bar just ignore statusProgress
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|
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self.statusProgress = statusFraction(status);
|
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/**
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* #action
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*/
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setError(error) {
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self.error = error;
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},
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/**
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* #action
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* Overridable hook (default no-op): drop whatever `hoveredFeature`
|
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* reports. The writing twin of that getter, and what
|
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* `installClearHoverOnViewportChange` calls.
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*
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* A display that STORES its hover owes an override; one that derives it
|
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* from the live pointer (MAF, Hi-C, LD) owes nothing, and the default
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* costs it nothing. Declared here so the clear can be installed for every
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* display rather than remembered per display — forgetting it is the
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* failure ARCHITECTURE.md's stored-hover section is about, and it used to
|
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* be six closures at six call sites, which is six chances to omit one.
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*/
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clearHoveredFeature() { },
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|
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/**
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|
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* #action
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* base display reload does nothing, see specialized displays for details
|
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*/
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reload() { },
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|
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/**
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|
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* #action
|
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215
|
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* Apply a set of display settings to the live display, and report which
|
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|
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* were applied. Each key runs through the display config schema's
|
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* `preProcessSnapshot` (shorthand expansions and legacy-key migrations,
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218
|
+
* as `showTrackGeneric` applies to a session spec's inline track keys),
|
|
219
|
+
* then writes the matching config slot. A key naming a sub-schema
|
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|
+
* (`facet`, `color`) replaces the whole object, its string shorthand
|
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|
+
* lifted by that schema, and `null` clears it. Keys that are not slots
|
|
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|
+
* come back in `unapplied` as `{ key, reason }`, so a caller can tell a
|
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223
|
+
* misspelling from a key that has an action instead of a slot.
|
|
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|
+
*
|
|
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|
+
* `allowSetters` also routes a non-slot key to a single-argument action
|
|
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|
+
* named `set<Key>`. It is off by default because session specs, share
|
|
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|
+
* links and embeds pass untyped JSON here, and a default fallback would
|
|
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|
+
* let them call internal setters (`setError`, `setScrollTop`, ...) and
|
|
229
|
+
* call multi-argument setters with one argument. A caller that wants a
|
|
230
|
+
* specific action can call it directly.
|
|
231
|
+
*
|
|
232
|
+
* A key whose write threw is reported in `failed`. Only `failed` means
|
|
233
|
+
* the caller passed a bad value. `unapplied` needs the caller's own
|
|
234
|
+
* context to read: `showTrackGeneric` spreads the same settings into the
|
|
235
|
+
* display's snapshot, so a declared prop (`resolution`) has already
|
|
236
|
+
* landed by the time it reports here, while the restyle path spreads
|
|
237
|
+
* nothing and every entry there did nothing.
|
|
238
|
+
*
|
|
239
|
+
* A per-key error does not abort the remaining keys. A caller
|
|
240
|
+
* mid-`showTrack` has already pushed the track, and one rejected value
|
|
241
|
+
* should not leave it half-configured.
|
|
242
|
+
*/
|
|
243
|
+
applyDisplaySettings(settings, options) {
|
|
244
|
+
// configuration is the reference every concrete display adds at
|
|
245
|
+
// instantiation (see DisplayModel below); the base model composes
|
|
246
|
+
// before it exists, hence the cast rather than a prop
|
|
247
|
+
const { configuration } = self;
|
|
248
|
+
const { applied, undeclared, failed } = applyConfSettings(configuration, settings);
|
|
249
|
+
const unapplied = [];
|
|
250
|
+
for (const [key, value] of Object.entries(undeclared)) {
|
|
251
|
+
if (!key || key === 'type') {
|
|
252
|
+
unapplied.push({ key, reason: key ? 'display-type' : 'no-slot' });
|
|
253
|
+
continue;
|
|
254
|
+
}
|
|
255
|
+
const setter = self[displaySetterName(key)];
|
|
256
|
+
if (typeof setter !== 'function') {
|
|
257
|
+
unapplied.push({ key, reason: 'no-slot' });
|
|
258
|
+
}
|
|
259
|
+
else if (!options?.allowSetters) {
|
|
260
|
+
unapplied.push({ key, reason: 'setter-only' });
|
|
261
|
+
}
|
|
262
|
+
else {
|
|
263
|
+
try {
|
|
264
|
+
;
|
|
265
|
+
setter(value);
|
|
266
|
+
applied.push(`${key} (via setter)`);
|
|
267
|
+
}
|
|
268
|
+
catch (e) {
|
|
269
|
+
failed.push({ key, error: `${e}` });
|
|
270
|
+
}
|
|
271
|
+
}
|
|
272
|
+
}
|
|
273
|
+
return { applied, unapplied, failed };
|
|
274
|
+
},
|
|
105
275
|
}));
|
|
106
276
|
}
|
|
107
277
|
export const BaseDisplay = stateModelFactory();
|
|
@@ -1,55 +1,264 @@
|
|
|
1
1
|
import type PluginManager from '../../PluginManager.ts';
|
|
2
|
-
import type {
|
|
3
|
-
import type { AnyConfigurationSchemaType } from '../../configuration/index.ts';
|
|
2
|
+
import type { RefNameMismatch } from '../../assemblyManager/refNameMismatch.ts';
|
|
3
|
+
import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '../../configuration/index.ts';
|
|
4
4
|
import type { MenuItem } from '../../ui/index.ts';
|
|
5
|
-
import type {
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
|
|
5
|
+
import type { DisplayModel } from './BaseDisplayModel.tsx';
|
|
6
|
+
import type { FileTypeExporter } from './saveTrackFileTypes/types.ts';
|
|
7
|
+
import type { IType, Instance } from '@jbrowse/mobx-state-tree';
|
|
8
|
+
/**
|
|
9
|
+
* #stateModel BaseTrackModel
|
|
10
|
+
* #category track
|
|
11
|
+
*
|
|
12
|
+
* these MST models only exist for tracks that are *shown*. they should contain
|
|
13
|
+
* only UI state for the track, and have a reference to a track configuration.
|
|
14
|
+
* note that multiple displayed tracks could use the same configuration.
|
|
15
|
+
*/
|
|
13
16
|
export declare function createBaseTrackModel(pm: PluginManager, trackType: string, baseTrackConfig: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
|
|
17
|
+
/**
|
|
18
|
+
* #property
|
|
19
|
+
*/
|
|
14
20
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
21
|
+
/**
|
|
22
|
+
* #property
|
|
23
|
+
*/
|
|
24
|
+
type: import("@jbrowse/mobx-state-tree").ILiteralType<string>;
|
|
25
|
+
/**
|
|
26
|
+
* #property
|
|
27
|
+
*/
|
|
28
|
+
configuration: import("../../configuration/configurationSchema.ts").IConfigurationReference<AnyConfigurationSchemaType>;
|
|
29
|
+
/**
|
|
30
|
+
* #property
|
|
31
|
+
*/
|
|
32
|
+
minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
33
|
+
/**
|
|
34
|
+
* #property
|
|
35
|
+
*/
|
|
36
|
+
pinned: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
37
|
+
/**
|
|
38
|
+
* #property
|
|
39
|
+
* The runtime plugin union (`pluggableMstType`) is typed only as
|
|
40
|
+
* `IAnyType`, erasing the element to `any`. Assert the concrete
|
|
41
|
+
* `DisplayModel` instance every registered display satisfies so reads
|
|
42
|
+
* (`activeDisplay`, `trackMenuItems`) are checked;
|
|
43
|
+
* create/snapshot stay `unknown` since the union's snapshot shape is
|
|
44
|
+
* genuinely dynamic (`replaceDisplay` writes a partial snapshot).
|
|
45
|
+
*/
|
|
46
|
+
displays: import("@jbrowse/mobx-state-tree").IArrayType<IType<unknown, unknown, DisplayModel>>;
|
|
20
47
|
}, {
|
|
48
|
+
/**
|
|
49
|
+
* Whether a height-resize gesture is in progress on this track. Set by
|
|
50
|
+
* whichever handle owns the drag — the view's track resize handle, or a
|
|
51
|
+
* handle a display draws inside itself — and read by displays that sit an
|
|
52
|
+
* expensive per-frame layer out of the gesture.
|
|
53
|
+
*
|
|
54
|
+
* On the track rather than the display because the gesture belongs to the
|
|
55
|
+
* container running it, not to whatever display happens to be active: the
|
|
56
|
+
* view can bracket a drag without knowing which display it landed on, and
|
|
57
|
+
* two handles on one track share one flag rather than racing to clear
|
|
58
|
+
* each other's.
|
|
59
|
+
*/
|
|
60
|
+
resizing: boolean;
|
|
61
|
+
} & {
|
|
62
|
+
/**
|
|
63
|
+
* #getter
|
|
64
|
+
*/
|
|
21
65
|
readonly trackId: string;
|
|
66
|
+
/**
|
|
67
|
+
* #getter
|
|
68
|
+
* determines which webworker to send the track to, currently based on trackId
|
|
69
|
+
*/
|
|
22
70
|
readonly rpcSessionId: string;
|
|
23
|
-
|
|
71
|
+
/**
|
|
72
|
+
* #getter
|
|
73
|
+
*/
|
|
74
|
+
readonly name: string;
|
|
75
|
+
/**
|
|
76
|
+
* #getter
|
|
77
|
+
* this track's own name-search index, from the `textSearching`
|
|
78
|
+
* sub-config. `undefined` when the track has none.
|
|
79
|
+
*
|
|
80
|
+
* The path, not a bare `'textSearchAdapter'`: the slot is
|
|
81
|
+
* `textSearching.textSearchAdapter` (`baseTrackConfig.ts`), and a bare
|
|
82
|
+
* read of a name no schema declares returns `undefined` and reports
|
|
83
|
+
* nothing at any layer, so this getter answered `undefined` for every
|
|
84
|
+
* track ever configured with one. `TextSearchManager` reads the same slot
|
|
85
|
+
* by hand-walking `conf.textSearching.textSearchAdapter`, which is why
|
|
86
|
+
* nothing noticed.
|
|
87
|
+
*/
|
|
24
88
|
readonly textSearchAdapter: any;
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
89
|
+
/**
|
|
90
|
+
* #getter
|
|
91
|
+
*/
|
|
92
|
+
readonly adapterConfig: Record<string, unknown>;
|
|
93
|
+
/**
|
|
94
|
+
* #getter
|
|
95
|
+
* a shown track always has at least one display
|
|
96
|
+
*/
|
|
97
|
+
readonly activeDisplay: DisplayModel & import("@jbrowse/mobx-state-tree").IStateTreeNode<IType<unknown, unknown, DisplayModel>>;
|
|
98
|
+
/**
|
|
99
|
+
* #getter
|
|
100
|
+
* the configured displays the CONTAINING VIEW can draw and the track's
|
|
101
|
+
* adapter feeds, which is the set `replaceDisplay` will accept
|
|
102
|
+
*
|
|
103
|
+
* `configuration.displays` is not that set: baseTrackConfig injects one
|
|
104
|
+
* entry per display type registered for the track TYPE, across every
|
|
105
|
+
* view type, so a VariantTrack carries a ChordVariantDisplay a linear
|
|
106
|
+
* view cannot draw. The track menu's own "Display types" submenu has
|
|
107
|
+
* always filtered them; this exposes the same list to code, because the
|
|
108
|
+
* alternative is every caller re-deriving it from the plugin manager.
|
|
109
|
+
*/
|
|
110
|
+
readonly compatibleDisplays: AnyConfigurationModel[];
|
|
34
111
|
} & {
|
|
35
|
-
|
|
112
|
+
/**
|
|
113
|
+
* #getter
|
|
114
|
+
* Set when this track's file and one of its assemblies share no reference
|
|
115
|
+
* name at all — the `1/2/3` file loaded against a `chr1/chr2/chr3`
|
|
116
|
+
* assembly, which otherwise draws an empty track and says nothing.
|
|
117
|
+
*
|
|
118
|
+
* The verdict is reached in `loadRefNameMap`, which is the only place both
|
|
119
|
+
* name sets are in scope, and recorded on the *assembly* because nothing
|
|
120
|
+
* in the assembly manager can reach a track (the session is a sibling
|
|
121
|
+
* subtree, so `getSession` from there finds only the root). The lookup
|
|
122
|
+
* inverts that: the record is keyed by adapter cache key, which is exactly
|
|
123
|
+
* what `rpcSessionId` already is, so a track finds its own with no
|
|
124
|
+
* plumbing in between.
|
|
125
|
+
*
|
|
126
|
+
* The names come from `getConfAssemblyNamesOrNone`, not from a raw
|
|
127
|
+
* `assemblyNames` slot read: this model is shared by every track type, and
|
|
128
|
+
* `ReferenceSequenceTrack`'s schema does not declare that slot — it names
|
|
129
|
+
* its assembly by being the `sequence` of one. A raw read there returns
|
|
130
|
+
* `undefined` with no diagnostic at any layer, so the getter was inert for
|
|
131
|
+
* that one track type while looking like it worked. The `OrNone` half is
|
|
132
|
+
* what keeps this total: it runs on every render of every track label, and
|
|
133
|
+
* an unanswerable question must not become a thrown getter.
|
|
134
|
+
*
|
|
135
|
+
* Diagnostic only. It gates nothing, and a track carrying one still loads,
|
|
136
|
+
* still fetches and still draws whatever it can.
|
|
137
|
+
*/
|
|
138
|
+
readonly refNameMismatch: RefNameMismatch | undefined;
|
|
139
|
+
/**
|
|
140
|
+
* #getter
|
|
141
|
+
*/
|
|
142
|
+
readonly adapterType: import("../AdapterType.ts").default<any>;
|
|
36
143
|
} & {
|
|
144
|
+
/**
|
|
145
|
+
* #action
|
|
146
|
+
* Write the config to the session now rather than after the 400 ms
|
|
147
|
+
* wait, for an edit that has to be undoable the moment it lands.
|
|
148
|
+
*/
|
|
149
|
+
persistConfigurationNow(): void;
|
|
150
|
+
/**
|
|
151
|
+
* #action
|
|
152
|
+
*/
|
|
37
153
|
setPinned(flag: boolean): void;
|
|
154
|
+
/**
|
|
155
|
+
* #action
|
|
156
|
+
*/
|
|
38
157
|
setMinimized(flag: boolean): void;
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
158
|
+
/**
|
|
159
|
+
* #action
|
|
160
|
+
*/
|
|
161
|
+
setResizing(flag: boolean): void;
|
|
162
|
+
/**
|
|
163
|
+
* #action
|
|
164
|
+
* `applyDisplaySettings` on the display being drawn (`activeDisplay`,
|
|
165
|
+
* which a shown track always has — this is not meaningful on a bare
|
|
166
|
+
* config node) — the track-level entry for "restyle this track in
|
|
167
|
+
* place" (a session spec's inline keys, an agent's settings bag). Only
|
|
168
|
+
* that one display: settings vocabularies are per display type, so
|
|
169
|
+
* broadcasting one bag across a track's other displays would mis-route
|
|
170
|
+
* keys; address a non-active display directly if that is what you mean.
|
|
171
|
+
* See BaseDisplayModel for the routing and the `allowSetters` opt-in.
|
|
172
|
+
*/
|
|
173
|
+
applyDisplaySettings(settings: Record<string, unknown>, options?: {
|
|
174
|
+
allowSetters?: boolean;
|
|
175
|
+
}): {
|
|
176
|
+
applied: string[];
|
|
177
|
+
unapplied: import("../../util/unknownSnapshotKeys.ts").UnappliedSetting[];
|
|
178
|
+
failed: {
|
|
179
|
+
key: string;
|
|
180
|
+
error: string;
|
|
181
|
+
}[];
|
|
182
|
+
};
|
|
183
|
+
/**
|
|
184
|
+
* #action
|
|
185
|
+
*/
|
|
186
|
+
replaceDisplay(oldDisplayId: string, newDisplayId: string, initialSnapshot?: any): void;
|
|
187
|
+
/**
|
|
188
|
+
* #action
|
|
189
|
+
* Persist any config-schema mutation (quick track-menu edits calling
|
|
190
|
+
* `setSlot` directly, or the full Settings dialog) back to the session,
|
|
191
|
+
* debounced, mirroring ConfigurationEditorWidget's own save. Both savers
|
|
192
|
+
* intentionally coexist — this one covers direct setSlot edits on a shown
|
|
193
|
+
* track, the widget covers an unshown track edited from the selector (no
|
|
194
|
+
* BaseTrackModel). When both fire they compute an identical delta, deduped
|
|
195
|
+
* in updateTrackConfiguration; don't drop one to "simplify". `reaction`
|
|
196
|
+
* (not `autorun`) on purpose: `self.configuration` is defined
|
|
197
|
+
* immediately on attach, unlike ConfigurationEditorWidget's `target`
|
|
198
|
+
* (which starts undefined), so an autorun's guaranteed first run would
|
|
199
|
+
* otherwise schedule a spurious flush for every track ever shown, even
|
|
200
|
+
* completely untouched ones — `reaction` only fires on an actual change.
|
|
201
|
+
*
|
|
202
|
+
* `equals: compareStructural` is load-bearing, not an optimization:
|
|
203
|
+
* `self.configuration` is a re-resolving reference, and persisting a save
|
|
204
|
+
* can swap the resolved node identity (the delta path reconciles in place
|
|
205
|
+
* but still churns once, and a session without deltas replaces the frozen
|
|
206
|
+
* `jbrowse.tracks` entry, rehydrating a brand-new MST node every write).
|
|
207
|
+
* Referential comparison would treat every such swap as a fresh change
|
|
208
|
+
* and re-fire the save, an unbounded debounced loop. Structural
|
|
209
|
+
* comparison settles once the content stops changing.
|
|
210
|
+
*/
|
|
211
|
+
afterAttach(): void;
|
|
42
212
|
} & {
|
|
213
|
+
/**
|
|
214
|
+
* #action
|
|
215
|
+
* The awaitable sibling of `replaceDisplay`: loads the target display's
|
|
216
|
+
* state model, then swaps to it carrying whatever settings the outgoing
|
|
217
|
+
* display can hand over.
|
|
218
|
+
*
|
|
219
|
+
* `replaceDisplay` stays a plain sync action and ASSERTS the model is
|
|
220
|
+
* loaded, and every display state model in this tree is a dynamic import
|
|
221
|
+
* until something shows one — so a caller that has not already shown the
|
|
222
|
+
* target needs this. Named like `launchTrack`, which is the same problem
|
|
223
|
+
* one level up.
|
|
224
|
+
*/
|
|
225
|
+
launchDisplay(displayId: string): Promise<void>;
|
|
226
|
+
} & {
|
|
227
|
+
/**
|
|
228
|
+
* #getter
|
|
229
|
+
* Whether this track's adapter writes an export format itself, rather
|
|
230
|
+
* than the save dialog rebuilding one out of rendered features. A claim
|
|
231
|
+
* about the adapter type, not about a given format — the fetch still
|
|
232
|
+
* falls back when the adapter declines the one that was asked for.
|
|
233
|
+
*/
|
|
234
|
+
readonly exportsDataViaAdapter: boolean;
|
|
235
|
+
/**
|
|
236
|
+
* #getter
|
|
237
|
+
* The size in bytes above which "Save track data" asks for confirmation
|
|
238
|
+
* before fetching. Uses the adapter's `fetchSizeLimit` where it declares
|
|
239
|
+
* one, so a save asks at the same size at which the track's display
|
|
240
|
+
* refuses to render; otherwise a default. The default is generous
|
|
241
|
+
* because exceeding it only prompts for confirmation, and the user
|
|
242
|
+
* explicitly requested the data.
|
|
243
|
+
*/
|
|
244
|
+
readonly exportByteLimit: number;
|
|
245
|
+
/**
|
|
246
|
+
* #method
|
|
247
|
+
*/
|
|
43
248
|
saveTrackFileFormatOptions(): Record<string, FileTypeExporter>;
|
|
44
249
|
} & {
|
|
250
|
+
/**
|
|
251
|
+
* #getter
|
|
252
|
+
* the "Save track data" menu entry. Kept separate from trackMenuItems so
|
|
253
|
+
* consumers (e.g. the LGV track-label menu) can place it alongside the
|
|
254
|
+
* session's Settings/Copy/Delete track actions without fishing it back out
|
|
255
|
+
* of the general list
|
|
256
|
+
*/
|
|
257
|
+
readonly saveTrackDataMenuItem: MenuItem;
|
|
258
|
+
/**
|
|
259
|
+
* #method
|
|
260
|
+
*/
|
|
45
261
|
trackMenuItems(): MenuItem[];
|
|
46
|
-
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").
|
|
47
|
-
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
48
|
-
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
49
|
-
configuration: AnyConfigurationSchemaType;
|
|
50
|
-
minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
51
|
-
pinned: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
52
|
-
displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
|
|
53
|
-
}>>;
|
|
262
|
+
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
|
|
54
263
|
export type BaseTrackStateModel = ReturnType<typeof createBaseTrackModel>;
|
|
55
264
|
export type BaseTrackModel = Instance<BaseTrackStateModel>;
|