@jbrowse/core 4.3.0 → 5.0.0-beta.1
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 +783 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts +13 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js +33 -22
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts +8 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Attributes.js +117 -19
- 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 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BaseCoreDetails.js +4 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js +12 -5
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js +28 -17
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js +19 -40
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts +6 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js +46 -30
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.d.ts +20 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/FeatureWash.js +66 -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 +17 -0
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts +1 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/Position.js +3 -9
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js +3 -3
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts +3 -2
- package/esm/BaseFeatureWidget/BaseFeatureDetail/UriField.js +7 -14
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.d.ts +2 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/index.js +19 -13
- package/esm/BaseFeatureWidget/BaseFeatureDetail/types.d.ts +5 -4
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.d.ts +8 -1
- package/esm/BaseFeatureWidget/BaseFeatureDetail/util.js +32 -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 +62 -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 +1 -1
- 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 +18 -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 +50 -63
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/model.js +62 -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/test_data/DLGAP3.d.ts +1 -1
- package/esm/BaseFeatureWidget/SequenceFeatureDetails/test_data/NCDN.d.ts +7 -7
- 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.js +1 -1
- package/esm/BaseFeatureWidget/formatDetails.d.ts +38 -0
- package/esm/BaseFeatureWidget/formatDetails.js +103 -0
- package/esm/BaseFeatureWidget/index.d.ts +3 -1
- package/esm/BaseFeatureWidget/index.js +2 -2
- package/esm/BaseFeatureWidget/stateModelFactory.d.ts +80 -62
- package/esm/BaseFeatureWidget/stateModelFactory.js +128 -29
- package/esm/BaseFeatureWidget/types.d.ts +4 -3
- package/esm/BaseFeatureWidget/util.d.ts +4 -29
- package/esm/BaseFeatureWidget/util.js +20 -84
- package/esm/CorePlugin.js +11 -6
- 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 +40 -40
- package/esm/PluginLoader.js +166 -82
- package/esm/PluginManager.d.ts +368 -55
- package/esm/PluginManager.js +326 -85
- package/esm/ReExports/BaseFeatureDetails.js +7 -6
- package/esm/ReExports/MuiDataGridReExports.d.ts +2 -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/index.js +1 -1
- package/esm/ReExports/lazify.d.ts +2 -2
- package/esm/ReExports/lazify.js +16 -3
- package/esm/ReExports/list.js +54 -229
- package/esm/ReExports/modules.js +84 -65
- package/esm/ReExports/muiComponentNames.d.ts +18 -0
- package/esm/ReExports/muiComponentNames.js +130 -0
- package/esm/ReExports/publicUtil.d.ts +1 -0
- package/esm/ReExports/publicUtil.js +28 -0
- package/esm/ReExports/registry.d.ts +2 -0
- package/esm/ReExports/registry.js +28 -0
- package/esm/TextSearch/BaseResults.d.ts +20 -21
- package/esm/TextSearch/BaseResults.js +8 -33
- package/esm/TextSearch/TextSearchManager.d.ts +14 -34
- package/esm/TextSearch/TextSearchManager.js +87 -34
- package/esm/assemblyManager/assembly.d.ts +307 -34
- package/esm/assemblyManager/assembly.js +551 -262
- package/esm/assemblyManager/assemblyAdapters.d.ts +12 -0
- package/esm/assemblyManager/assemblyAdapters.js +18 -0
- package/esm/assemblyManager/assemblyConfigSchema.d.ts +192 -17
- package/esm/assemblyManager/assemblyConfigSchema.js +213 -19
- package/esm/assemblyManager/assemblyManager.d.ts +711 -303
- package/esm/assemblyManager/assemblyManager.js +351 -46
- package/esm/assemblyManager/expandAssemblyConfigShorthand.d.ts +32 -0
- package/esm/assemblyManager/expandAssemblyConfigShorthand.js +85 -0
- package/esm/assemblyManager/geneticCodes.d.ts +21 -0
- package/esm/assemblyManager/geneticCodes.js +47 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.d.ts +9 -0
- package/esm/assemblyManager/getSequenceAdapterConfig.js +12 -0
- package/esm/assemblyManager/index.d.ts +1 -1
- package/esm/assemblyManager/index.js +2 -2
- package/esm/assemblyManager/loadRefNameMap.d.ts +5 -0
- package/esm/assemblyManager/loadRefNameMap.js +80 -0
- package/esm/assemblyManager/refNameColors.d.ts +1 -0
- package/esm/assemblyManager/refNameColors.js +32 -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 +11 -0
- package/esm/checkPlugins.js +77 -0
- package/esm/configuration/configurationSchema.d.ts +154 -19
- package/esm/configuration/configurationSchema.js +359 -138
- package/esm/configuration/configurationSlot.d.ts +283 -30
- package/esm/configuration/configurationSlot.js +205 -226
- package/esm/configuration/formatAboutConfigSchema.d.ts +55 -0
- package/esm/configuration/formatAboutConfigSchema.js +58 -0
- package/esm/configuration/formatDetailsConfigSchema.d.ts +80 -0
- package/esm/configuration/formatDetailsConfigSchema.js +90 -0
- package/esm/configuration/fullConfSnapshot.d.ts +28 -0
- package/esm/configuration/fullConfSnapshot.js +66 -0
- package/esm/configuration/getConf.d.ts +88 -0
- package/esm/configuration/getConf.js +74 -0
- package/esm/configuration/index.d.ts +19 -3
- package/esm/configuration/index.js +19 -2
- package/esm/configuration/mergeFormatCallbacks.d.ts +15 -0
- package/esm/configuration/mergeFormatCallbacks.js +24 -0
- package/esm/configuration/promotableDefaults.d.ts +199 -0
- package/esm/configuration/promotableDefaults.js +326 -0
- package/esm/configuration/promotablePin.d.ts +55 -0
- package/esm/configuration/promotableResolve.d.ts +108 -0
- package/esm/configuration/promotableResolve.js +117 -0
- package/esm/configuration/promotableSlots.d.ts +12 -0
- package/esm/configuration/promotableSlots.js +45 -0
- package/esm/configuration/readConfObject.d.ts +56 -0
- package/esm/configuration/readConfObject.js +161 -0
- package/esm/configuration/schemaRegistry.d.ts +35 -0
- package/esm/configuration/schemaRegistry.js +50 -0
- package/esm/configuration/schemaTypes.d.ts +23 -0
- package/esm/configuration/schemaTypes.js +94 -0
- package/esm/configuration/slotFacade.d.ts +82 -0
- package/esm/configuration/slotFacade.js +89 -0
- package/esm/configuration/slotShape.d.ts +12 -0
- package/esm/configuration/slotShape.js +84 -0
- package/esm/configuration/slotValueUtils.d.ts +17 -0
- package/esm/configuration/slotValueUtils.js +25 -0
- package/esm/configuration/tabixIndexFields.d.ts +44 -0
- package/esm/configuration/tabixIndexFields.js +45 -0
- package/esm/configuration/tabixShorthand.d.ts +34 -0
- package/esm/configuration/tabixShorthand.js +45 -0
- package/esm/configuration/types.d.ts +170 -7
- package/esm/data_adapters/BaseAdapter/BaseAdapter.d.ts +24 -10
- package/esm/data_adapters/BaseAdapter/BaseAdapter.js +23 -15
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts +120 -7
- package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.js +99 -27
- 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/getAdapterId.d.ts +2 -0
- package/esm/data_adapters/BaseAdapter/getAdapterId.js +9 -0
- package/esm/data_adapters/BaseAdapter/index.d.ts +6 -4
- package/esm/data_adapters/BaseAdapter/index.js +5 -5
- package/esm/data_adapters/BaseAdapter/stats.d.ts +5 -5
- package/esm/data_adapters/BaseAdapter/stats.js +48 -22
- package/esm/data_adapters/BaseAdapter/types.d.ts +10 -8
- 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/CytobandAdapter/CytobandAdapter.d.ts +1 -1
- package/esm/data_adapters/CytobandAdapter/CytobandAdapter.js +4 -4
- package/esm/data_adapters/CytobandAdapter/configSchema.d.ts +36 -4
- package/esm/data_adapters/CytobandAdapter/configSchema.js +46 -2
- 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 +35 -1
- package/esm/data_adapters/dataAdapterCache.js +62 -22
- package/esm/data_adapters/getFeatureAdapter.d.ts +22 -0
- package/esm/data_adapters/getFeatureAdapter.js +27 -0
- package/esm/data_adapters/getSequenceSubAdapter.d.ts +21 -0
- package/esm/data_adapters/getSequenceSubAdapter.js +44 -0
- package/esm/pluggableElementTypes/AdapterType.d.ts +52 -2
- 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 +10 -0
- package/esm/pluggableElementTypes/DisplayType.js +14 -1
- package/esm/pluggableElementTypes/InternetAccountType.js +1 -1
- package/esm/pluggableElementTypes/PluggableElementBase.d.ts +13 -0
- package/esm/pluggableElementTypes/PluggableElementBase.js +13 -0
- package/esm/pluggableElementTypes/RpcMethodType.d.ts +132 -12
- package/esm/pluggableElementTypes/RpcMethodType.js +263 -98
- package/esm/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions.d.ts +19 -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 +3 -3
- 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 +2 -1
- package/esm/pluggableElementTypes/ViewType.js +9 -2
- package/esm/pluggableElementTypes/WidgetType.d.ts +2 -2
- package/esm/pluggableElementTypes/WidgetType.js +1 -1
- package/esm/pluggableElementTypes/addMenuItems.d.ts +87 -0
- package/esm/pluggableElementTypes/addMenuItems.js +82 -0
- package/esm/pluggableElementTypes/extendElementType.d.ts +30 -0
- package/esm/pluggableElementTypes/extendElementType.js +68 -0
- package/esm/pluggableElementTypes/index.d.ts +7 -7
- package/esm/pluggableElementTypes/index.js +24 -14
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.d.ts +70 -15
- package/esm/pluggableElementTypes/models/BaseConnectionModelFactory.js +90 -10
- package/esm/pluggableElementTypes/models/BaseDisplayModel.d.ts +605 -84
- package/esm/pluggableElementTypes/models/BaseDisplayModel.js +172 -64
- package/esm/pluggableElementTypes/models/BaseTrackModel.d.ts +195 -35
- package/esm/pluggableElementTypes/models/BaseTrackModel.js +332 -85
- package/esm/pluggableElementTypes/models/BaseViewModel.d.ts +167 -16
- package/esm/pluggableElementTypes/models/BaseViewModel.js +111 -16
- package/esm/pluggableElementTypes/models/HighlightsMixin.d.ts +51 -0
- package/esm/pluggableElementTypes/models/HighlightsMixin.js +78 -0
- package/esm/pluggableElementTypes/models/InternetAccountModel.d.ts +163 -29
- package/esm/pluggableElementTypes/models/InternetAccountModel.js +218 -48
- package/esm/pluggableElementTypes/models/assertDisplayContract.d.ts +174 -0
- package/esm/pluggableElementTypes/models/assertDisplayContract.js +246 -0
- package/esm/pluggableElementTypes/models/baseConnectionConfig.d.ts +22 -8
- package/esm/pluggableElementTypes/models/baseConnectionConfig.js +18 -2
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.d.ts +39 -20
- package/esm/pluggableElementTypes/models/baseInternetAccountConfig.js +23 -2
- package/esm/pluggableElementTypes/models/baseTrackConfig.d.ts +181 -65
- package/esm/pluggableElementTypes/models/baseTrackConfig.js +191 -89
- package/esm/pluggableElementTypes/models/components/SaveTrackData.d.ts +3 -8
- package/esm/pluggableElementTypes/models/components/SaveTrackData.js +113 -139
- package/esm/pluggableElementTypes/models/components/fetchTrackData.d.ts +55 -0
- package/esm/pluggableElementTypes/models/components/fetchTrackData.js +83 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.d.ts +40 -0
- package/esm/pluggableElementTypes/models/expandTrackConfigShorthand.js +115 -0
- package/esm/pluggableElementTypes/models/index.d.ts +6 -3
- package/esm/pluggableElementTypes/models/index.js +10 -8
- package/esm/pluggableElementTypes/models/migrateTrackConfig.d.ts +34 -0
- package/esm/pluggableElementTypes/models/migrateTrackConfig.js +54 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/bed.js +75 -7
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.d.ts +9 -3
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/genbank.js +153 -103
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.d.ts +6 -1
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/gff3.js +70 -74
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/types.d.ts +9 -1
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.d.ts +21 -0
- package/esm/pluggableElementTypes/models/saveTrackFileTypes/util.js +51 -0
- package/esm/pluggableElementTypes/models/uriMatchesDomains.d.ts +29 -0
- package/esm/pluggableElementTypes/models/uriMatchesDomains.js +62 -0
- package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.d.ts +5 -4
- package/esm/pluggableElementTypes/renderers/util/serializableFilterChain.js +20 -10
- package/esm/pluginDefinitions.d.ts +198 -0
- package/esm/pluginDefinitions.js +220 -0
- package/esm/rpc/BaseRpcDriver.d.ts +27 -35
- package/esm/rpc/BaseRpcDriver.js +74 -107
- package/esm/rpc/MainThreadRpcDriver.d.ts +9 -10
- package/esm/rpc/MainThreadRpcDriver.js +18 -29
- package/esm/rpc/RpcClient.d.ts +38 -0
- package/esm/rpc/RpcClient.js +154 -0
- package/esm/rpc/RpcManager.d.ts +116 -27
- package/esm/rpc/RpcManager.js +177 -50
- package/esm/rpc/RpcRegistry.d.ts +265 -0
- package/esm/rpc/RpcRegistry.js +1 -0
- package/esm/rpc/RpcServer.d.ts +41 -0
- package/esm/rpc/RpcServer.js +235 -0
- package/esm/rpc/WebWorkerRpcDriver.d.ts +71 -24
- package/esm/rpc/WebWorkerRpcDriver.js +312 -27
- package/esm/rpc/byteBudget.d.ts +49 -0
- package/esm/rpc/byteBudget.js +50 -0
- package/esm/rpc/configSchema.d.ts +27 -5
- package/esm/rpc/configSchema.js +40 -16
- package/esm/rpc/coreRpcMethods.d.ts +2 -5
- package/esm/rpc/coreRpcMethods.js +9 -12
- package/esm/rpc/explainTransferError.d.ts +35 -0
- package/esm/rpc/explainTransferError.js +158 -0
- package/esm/rpc/methods/CoreFreeResources.d.ts +19 -4
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- package/esm/util/when.js +0 -1
- /package/esm/{data_adapters/BaseAdapter/BaseOptions.js → configuration/promotablePin.js} +0 -0
- /package/esm/{util/layouts/BaseLayout.js → data_adapters/BaseAdapter/CytobandAdapter.js} +0 -0
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import type
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import type { AnyConfigurationModel } from '../../configuration/index.ts';
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import type { MenuItem } from '../../ui/index.ts';
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import type { RpcStatus } from '../../util/progress.ts';
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import type { Instance } from '@jbrowse/mobx-state-tree';
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import type React from 'react';
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export declare const BaseDisplay: import("@jbrowse/mobx-state-tree").IModelType<{
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/**
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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*/
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readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
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} & {
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/**
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* #getter
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*/
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readonly RenderingComponent: React.FC<{
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model: {
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model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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/**
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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}> & {
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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*/
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readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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/**
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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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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onHorizontalScroll?: () => void;
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blockState?: Record<string,
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onHorizontalScroll?: (distance: number) => void;
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blockState?: Record<string, unknown>;
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}>;
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/**
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* #getter
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*/
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readonly DisplayBlurb: React.FC<{
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model: {
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model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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/**
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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}> & {
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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*/
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readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
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} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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}, {
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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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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/**
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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
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* Returns true if the parent track is minimized. Used to skip
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* expensive operations like autoruns when track is not visible.
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*/
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readonly isMinimized: boolean;
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/**
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* #getter
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* Overridable hook (default `undefined`): what the pointer is currently
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* over, for readers **outside** the display. `LinearGenomeViewContainer`
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* publishes it to `session.hovered`, the view-wide "what is the user
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* pointing at" channel a plugin can subscribe to.
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*
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* Declared here because a cross-display consumer can only read a name the
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* base declares — the same reason `SyntenyFetchStateMixin.fetchInert` is a
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* hook rather than a getter each display invents. The container used to
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* read `featureUnderMouse`, which only the wiggle, alignments and
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* Manhattan families spelled that way — canvas said `hoveredFeature`,
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* variants `hoveredGenotype` — so the channel carried a hover from a third
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* of the display types and nothing said which. It also asked only
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* `displays[0]` of each track.
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*
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* `unknown` because the payload genuinely differs — a read, a wiggle bin,
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* a SNP, a genotype cell — and `session.hovered` is typed to match ("can
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* be anything; code that wants to deal with this should examine it").
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* Narrow it in the override.
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*/
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readonly hoveredFeature: unknown;
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/**
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* #getter
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* Overridable hook (default `'feature'`): the SINGULAR word for one of
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* the things this display draws, as a menu row or a chip says it —
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* "Hide this read", "Showing 3 variants".
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*
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* Declared here for the same reason as `hoveredFeature` above: it is read
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* across the display boundary, by chrome that has no idea which display
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* it is drawing for (`SoloSelectionChip`, alignments' group-label
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* overlay), and a name only the base declares is a name every such
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* consumer can rely on. Two displays declared it independently and one of
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* those declarations WAS this default.
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*
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* **A control keeps the generic word; content takes this one.** "Variant
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* height" reads as a different setting from "Feature height" when it is
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* the same one, so the shared menus stay on "feature" however the display
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* answers here, and the noun varies where it names what the user is
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* looking at — "Showing 3 variants", "Hide this read". A display drawing
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* something the generic word already fits is right to leave this alone.
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*
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* Distinct from the per-hit noun a context menu takes off the clicked
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* item's own `type` ("mRNA", "gene"); that names one annotation, this
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* names what the track holds. The hit noun falls back to this.
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*/
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readonly featureNoun: string;
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/**
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* #getter
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* Overridable hook: which widget `openFeatureWidget` opens for one of
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* this display's features. The default is the generic one, which is what
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* a display drawing plain features wants and what the canvas base spelled
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* out by hand.
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*
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* An override is a display whose features have a vocabulary of their own —
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* a read, a variant, a synteny block — and the `id` is deliberately part
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* of it: two displays naming one id share the drawer panel, which is the
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* behaviour when the two are showing the same kind of thing.
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*/
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readonly featureWidgetType: {
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type: string;
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id: string;
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};
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} & {
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/**
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* #method
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* props passed to the renderer's React "Rendering" component.
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* these are client-side only and never sent to the worker.
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* includes displayModel and callbacks
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*/
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renderingProps(): {
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displayModel: {
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displayModel: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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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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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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}> & {
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* bar simply leaves it undefined.
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*/
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statusProgress: number | undefined;
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} & {
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* #getter
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} & {
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/**
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* #getter
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*/
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model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
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/**
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* #property
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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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* #property
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*/
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type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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}> & {
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statusMessage: string | undefined;
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/**
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* #volatile
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* determinate progress fraction [0,1] for the current status, or
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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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* 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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* #getter
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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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rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
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rendererTypeName: string;
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* determinate progress fraction [0,1] for the current status, or
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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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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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readonly adapterConfig: Record<string, unknown>;
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/**
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* #getter
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* Returns true if the parent track is minimized. Used to skip
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*/
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* over, for readers **outside** the display. `LinearGenomeViewContainer`
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* publishes it to `session.hovered`, the view-wide "what is the user
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* pointing at" channel a plugin can subscribe to.
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*
|
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* Declared here because a cross-display consumer can only read a name the
|
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* base declares — the same reason `SyntenyFetchStateMixin.fetchInert` is a
|
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* hook rather than a getter each display invents. The container used to
|
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* read `featureUnderMouse`, which only the wiggle, alignments and
|
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|
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* Manhattan families spelled that way — canvas said `hoveredFeature`,
|
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389
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* variants `hoveredGenotype` — so the channel carried a hover from a third
|
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|
+
* of the display types and nothing said which. It also asked only
|
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391
|
+
* `displays[0]` of each track.
|
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|
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*
|
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|
+
* `unknown` because the payload genuinely differs — a read, a wiggle bin,
|
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|
+
* 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
|
+
*/
|
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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
|
+
* Overridable hook: which widget `openFeatureWidget` opens for one of
|
|
427
|
+
* this display's features. The default is the generic one, which is what
|
|
428
|
+
* a display drawing plain features wants and what the canvas base spelled
|
|
429
|
+
* out by hand.
|
|
430
|
+
*
|
|
431
|
+
* An override is a display whose features have a vocabulary of their own —
|
|
432
|
+
* a read, a variant, a synteny block — and the `id` is deliberately part
|
|
433
|
+
* of it: two displays naming one id share the drawer panel, which is the
|
|
434
|
+
* behaviour when the two are showing the same kind of thing.
|
|
435
|
+
*/
|
|
436
|
+
readonly featureWidgetType: {
|
|
437
|
+
type: string;
|
|
438
|
+
id: string;
|
|
439
|
+
};
|
|
115
440
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
441
|
+
/**
|
|
442
|
+
* #property
|
|
443
|
+
*/
|
|
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|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
445
|
+
/**
|
|
446
|
+
* #property
|
|
447
|
+
*/
|
|
117
448
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
118
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
|
119
449
|
}, {
|
|
120
|
-
rendererTypeName: string;
|
|
121
450
|
error: unknown;
|
|
122
451
|
statusMessage: string | undefined;
|
|
452
|
+
/**
|
|
453
|
+
* #volatile
|
|
454
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
455
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
456
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
457
|
+
* bar simply leaves it undefined.
|
|
458
|
+
*/
|
|
459
|
+
statusProgress: number | undefined;
|
|
123
460
|
} & {
|
|
461
|
+
/**
|
|
462
|
+
* #getter
|
|
463
|
+
*/
|
|
464
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
465
|
+
} & {
|
|
466
|
+
/**
|
|
467
|
+
* #getter
|
|
468
|
+
*/
|
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469
|
readonly RenderingComponent: React.FC<{
|
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125
|
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model: {
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126
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|
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|
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|
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128
|
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|
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|
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130
|
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|
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470
|
+
model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
471
|
+
/**
|
|
472
|
+
* #property
|
|
473
|
+
*/
|
|
474
|
+
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
475
|
+
/**
|
|
476
|
+
* #property
|
|
477
|
+
*/
|
|
478
|
+
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
479
|
+
}> & {
|
|
131
480
|
error: unknown;
|
|
132
481
|
statusMessage: string | undefined;
|
|
482
|
+
/**
|
|
483
|
+
* #volatile
|
|
484
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
485
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
486
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
487
|
+
* bar simply leaves it undefined.
|
|
488
|
+
*/
|
|
489
|
+
statusProgress: number | undefined;
|
|
490
|
+
} & {
|
|
491
|
+
/**
|
|
492
|
+
* #getter
|
|
493
|
+
*/
|
|
494
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
133
495
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
496
|
+
/**
|
|
497
|
+
* #property
|
|
498
|
+
*/
|
|
134
499
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
500
|
+
/**
|
|
501
|
+
* #property
|
|
502
|
+
*/
|
|
135
503
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
136
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
|
137
504
|
}, {
|
|
138
|
-
rendererTypeName: string;
|
|
139
505
|
error: unknown;
|
|
140
506
|
statusMessage: string | undefined;
|
|
507
|
+
/**
|
|
508
|
+
* #volatile
|
|
509
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
510
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
511
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
512
|
+
* bar simply leaves it undefined.
|
|
513
|
+
*/
|
|
514
|
+
statusProgress: number | undefined;
|
|
515
|
+
} & {
|
|
516
|
+
/**
|
|
517
|
+
* #getter
|
|
518
|
+
*/
|
|
519
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
141
520
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
142
|
-
onHorizontalScroll?: () => void;
|
|
143
|
-
blockState?: Record<string,
|
|
521
|
+
onHorizontalScroll?: (distance: number) => void;
|
|
522
|
+
blockState?: Record<string, unknown>;
|
|
144
523
|
}>;
|
|
524
|
+
/**
|
|
525
|
+
* #getter
|
|
526
|
+
*/
|
|
145
527
|
readonly DisplayBlurb: React.FC<{
|
|
146
|
-
model: {
|
|
147
|
-
|
|
148
|
-
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
|
|
528
|
+
model: import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<{
|
|
529
|
+
/**
|
|
530
|
+
* #property
|
|
531
|
+
*/
|
|
532
|
+
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
533
|
+
/**
|
|
534
|
+
* #property
|
|
535
|
+
*/
|
|
536
|
+
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
537
|
+
}> & {
|
|
152
538
|
error: unknown;
|
|
153
539
|
statusMessage: string | undefined;
|
|
540
|
+
/**
|
|
541
|
+
* #volatile
|
|
542
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
543
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
544
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
545
|
+
* bar simply leaves it undefined.
|
|
546
|
+
*/
|
|
547
|
+
statusProgress: number | undefined;
|
|
548
|
+
} & {
|
|
549
|
+
/**
|
|
550
|
+
* #getter
|
|
551
|
+
*/
|
|
552
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
154
553
|
} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
|
|
554
|
+
/**
|
|
555
|
+
* #property
|
|
556
|
+
*/
|
|
155
557
|
id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
558
|
+
/**
|
|
559
|
+
* #property
|
|
560
|
+
*/
|
|
156
561
|
type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
|
|
157
|
-
rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
|
|
158
562
|
}, {
|
|
159
|
-
rendererTypeName: string;
|
|
160
563
|
error: unknown;
|
|
161
564
|
statusMessage: string | undefined;
|
|
565
|
+
/**
|
|
566
|
+
* #volatile
|
|
567
|
+
* determinate progress fraction [0,1] for the current status, or
|
|
568
|
+
* undefined when the in-flight phase is indeterminate. Set alongside
|
|
569
|
+
* `statusMessage` by `setStatusMessage`; a display that never shows a
|
|
570
|
+
* bar simply leaves it undefined.
|
|
571
|
+
*/
|
|
572
|
+
statusProgress: number | undefined;
|
|
573
|
+
} & {
|
|
574
|
+
/**
|
|
575
|
+
* #getter
|
|
576
|
+
*/
|
|
577
|
+
readonly parentTrack: import("../../util/index.ts").AbstractTrackModel;
|
|
162
578
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
163
579
|
}> | null;
|
|
164
|
-
|
|
165
|
-
|
|
580
|
+
/**
|
|
581
|
+
* #getter
|
|
582
|
+
*/
|
|
583
|
+
readonly adapterConfig: Record<string, unknown>;
|
|
584
|
+
/**
|
|
585
|
+
* #getter
|
|
586
|
+
* Returns true if the parent track is minimized. Used to skip
|
|
587
|
+
* expensive operations like autoruns when track is not visible.
|
|
588
|
+
*/
|
|
166
589
|
readonly isMinimized: boolean;
|
|
167
|
-
|
|
168
|
-
|
|
590
|
+
/**
|
|
591
|
+
* #getter
|
|
592
|
+
* Overridable hook (default `undefined`): what the pointer is currently
|
|
593
|
+
* over, for readers **outside** the display. `LinearGenomeViewContainer`
|
|
594
|
+
* publishes it to `session.hovered`, the view-wide "what is the user
|
|
595
|
+
* pointing at" channel a plugin can subscribe to.
|
|
596
|
+
*
|
|
597
|
+
* Declared here because a cross-display consumer can only read a name the
|
|
598
|
+
* base declares — the same reason `SyntenyFetchStateMixin.fetchInert` is a
|
|
599
|
+
* hook rather than a getter each display invents. The container used to
|
|
600
|
+
* read `featureUnderMouse`, which only the wiggle, alignments and
|
|
601
|
+
* Manhattan families spelled that way — canvas said `hoveredFeature`,
|
|
602
|
+
* variants `hoveredGenotype` — so the channel carried a hover from a third
|
|
603
|
+
* of the display types and nothing said which. It also asked only
|
|
604
|
+
* `displays[0]` of each track.
|
|
605
|
+
*
|
|
606
|
+
* `unknown` because the payload genuinely differs — a read, a wiggle bin,
|
|
607
|
+
* a SNP, a genotype cell — and `session.hovered` is typed to match ("can
|
|
608
|
+
* be anything; code that wants to deal with this should examine it").
|
|
609
|
+
* Narrow it in the override.
|
|
610
|
+
*/
|
|
611
|
+
readonly hoveredFeature: unknown;
|
|
612
|
+
/**
|
|
613
|
+
* #getter
|
|
614
|
+
* Overridable hook (default `'feature'`): the SINGULAR word for one of
|
|
615
|
+
* the things this display draws, as a menu row or a chip says it —
|
|
616
|
+
* "Hide this read", "Showing 3 variants".
|
|
617
|
+
*
|
|
618
|
+
* Declared here for the same reason as `hoveredFeature` above: it is read
|
|
619
|
+
* across the display boundary, by chrome that has no idea which display
|
|
620
|
+
* it is drawing for (`SoloSelectionChip`, alignments' group-label
|
|
621
|
+
* overlay), and a name only the base declares is a name every such
|
|
622
|
+
* consumer can rely on. Two displays declared it independently and one of
|
|
623
|
+
* those declarations WAS this default.
|
|
624
|
+
*
|
|
625
|
+
* **A control keeps the generic word; content takes this one.** "Variant
|
|
626
|
+
* height" reads as a different setting from "Feature height" when it is
|
|
627
|
+
* the same one, so the shared menus stay on "feature" however the display
|
|
628
|
+
* answers here, and the noun varies where it names what the user is
|
|
629
|
+
* looking at — "Showing 3 variants", "Hide this read". A display drawing
|
|
630
|
+
* something the generic word already fits is right to leave this alone.
|
|
631
|
+
*
|
|
632
|
+
* Distinct from the per-hit noun a context menu takes off the clicked
|
|
633
|
+
* item's own `type` ("mRNA", "gene"); that names one annotation, this
|
|
634
|
+
* names what the track holds. The hit noun falls back to this.
|
|
635
|
+
*/
|
|
636
|
+
readonly featureNoun: string;
|
|
637
|
+
/**
|
|
638
|
+
* #getter
|
|
639
|
+
* Overridable hook: which widget `openFeatureWidget` opens for one of
|
|
640
|
+
* this display's features. The default is the generic one, which is what
|
|
641
|
+
* a display drawing plain features wants and what the canvas base spelled
|
|
642
|
+
* out by hand.
|
|
643
|
+
*
|
|
644
|
+
* An override is a display whose features have a vocabulary of their own —
|
|
645
|
+
* a read, a variant, a synteny block — and the `id` is deliberately part
|
|
646
|
+
* of it: two displays naming one id share the drawer panel, which is the
|
|
647
|
+
* behaviour when the two are showing the same kind of thing.
|
|
648
|
+
*/
|
|
649
|
+
readonly featureWidgetType: {
|
|
650
|
+
type: string;
|
|
651
|
+
id: string;
|
|
652
|
+
};
|
|
169
653
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
|
|
170
654
|
};
|
|
171
|
-
|
|
172
|
-
|
|
655
|
+
/**
|
|
656
|
+
* #method
|
|
657
|
+
*/
|
|
173
658
|
trackMenuItems(): MenuItem[];
|
|
174
|
-
readonly viewMenuActions: MenuItem[];
|
|
175
|
-
regionCannotBeRendered(): null;
|
|
176
659
|
} & {
|
|
177
|
-
|
|
660
|
+
/**
|
|
661
|
+
* #action
|
|
662
|
+
*/
|
|
663
|
+
setStatusMessage(status?: RpcStatus): void;
|
|
664
|
+
/**
|
|
665
|
+
* #action
|
|
666
|
+
*/
|
|
178
667
|
setError(error?: unknown): void;
|
|
179
|
-
|
|
668
|
+
/**
|
|
669
|
+
* #action
|
|
670
|
+
* Overridable hook (default no-op): drop whatever `hoveredFeature`
|
|
671
|
+
* reports. The writing twin of that getter, and what
|
|
672
|
+
* `installClearHoverOnViewportChange` calls.
|
|
673
|
+
*
|
|
674
|
+
* A display that STORES its hover owes an override; one that derives it
|
|
675
|
+
* from the live pointer (MAF, Hi-C, LD) owes nothing, and the default
|
|
676
|
+
* costs it nothing. Declared here so the clear can be installed for every
|
|
677
|
+
* display rather than remembered per display — forgetting it is the
|
|
678
|
+
* failure ARCHITECTURE.md's stored-hover section is about, and it used to
|
|
679
|
+
* be six closures at six call sites, which is six chances to omit one.
|
|
680
|
+
*/
|
|
681
|
+
clearHoveredFeature(): void;
|
|
682
|
+
/**
|
|
683
|
+
* #action
|
|
684
|
+
* base display reload does nothing, see specialized displays for details
|
|
685
|
+
*/
|
|
180
686
|
reload(): void;
|
|
181
687
|
}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
|
|
182
688
|
export type BaseDisplayStateModel = typeof BaseDisplay;
|
|
183
689
|
export type BaseDisplayModel = Instance<BaseDisplayStateModel>;
|
|
690
|
+
/**
|
|
691
|
+
* The shape every display instance held in a track's `displays` array
|
|
692
|
+
* satisfies: the composed `BaseDisplay` state model (RenderingComponent,
|
|
693
|
+
* DisplayBlurb, trackMenuItems, ...) plus the `configuration`
|
|
694
|
+
* reference every display gains at instantiation. `getPortableSettings` is
|
|
695
|
+
* optional — only display types that support switching type via the track menu
|
|
696
|
+
* implement it. This is the concrete element type behind
|
|
697
|
+
* `BaseTrackModel.displays`, which the runtime plugin union erases to `any`.
|
|
698
|
+
*/
|
|
699
|
+
export interface DisplayModel extends BaseDisplayModel {
|
|
700
|
+
configuration: AnyConfigurationModel & {
|
|
701
|
+
displayId: string;
|
|
702
|
+
};
|
|
703
|
+
getPortableSettings?: (newDisplayId?: string) => Record<string, unknown> | undefined;
|
|
704
|
+
}
|