@jbrowse/core 4.2.1 → 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 +196 -55
- 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
package/esm/util/index.d.ts
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regions?: Region[];
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stopToken?: string;
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adapterConfig: Record<string, unknown>;
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sessionId: string;
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statusCallback?: (arg: string) => void;
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}>(assemblyManager: AssemblyManager, args: ARGTYPE): Promise<ARGTYPE & {
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regions: (Region & {
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originalRefName?: string;
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})[];
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}>;
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export declare function minmax(a: number, b: number): readonly [number, number];
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export declare function shorten(name: string, max?: number, short?: number): string;
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export declare function shorten2(name: string, max?: number): string;
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export declare function stringify({ refName, coord, assemblyName, oob, }: {
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assemblyName?: string;
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coord: number;
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oob?: boolean;
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}, useAssemblyName?: boolean): string;
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export declare const isElectron: boolean;
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export declare const complementTable: Record<string, string>;
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export declare function revcom(str: string): string;
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export declare function reverse(str: string): string;
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export declare function complement(str: string): string;
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export declare const rIC: (((callback: IdleRequestCallback, options?: IdleRequestOptions) => number) & typeof requestIdleCallback) | ((cb: () => void) => void);
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export declare function measureText(str: unknown, fontSize?: number): number;
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export type Frame = 1 | 2 | 3 | -1 | -2 | -3;
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export declare function getFrame(start: number, end: number, strand: 1 | -1, phase: 0 | 1 | 2): Frame;
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export declare const defaultStarts: string[];
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export declare const defaultStops: string[];
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export declare const defaultCodonTable: {
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TCA: string;
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TCC: string;
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TCG: string;
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TCT: string;
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TTC: string;
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TTT: string;
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TTA: string;
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TTG: string;
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TAC: string;
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TAT: string;
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TAA: string;
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TAG: string;
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TGC: string;
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TGT: string;
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TGA: string;
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TGG: string;
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CTA: string;
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CTC: string;
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CTG: string;
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CTT: string;
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CCA: string;
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CCC: string;
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CCG: string;
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CCT: string;
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CAC: string;
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CAT: string;
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CAA: string;
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CAG: string;
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CGA: string;
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CGC: string;
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CGG: string;
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CGT: string;
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ATA: string;
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ATC: string;
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ATT: string;
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ATG: string;
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ACA: string;
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ACC: string;
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ACG: string;
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ACT: string;
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AAC: string;
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AAT: string;
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AAA: string;
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AAG: string;
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AGC: string;
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AGT: string;
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AGA: string;
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AGG: string;
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GTA: string;
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GTC: string;
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GTG: string;
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GTT: string;
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GCA: string;
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GCC: string;
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GCG: string;
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GCT: string;
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GAC: string;
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GAT: string;
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GAA: string;
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GAG: string;
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GGA: string;
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GGC: string;
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GGG: string;
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GGT: string;
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};
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export declare function generateCodonTable(table: any): Record<string, string>;
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export declare function updateStatus<U>(msg: string, cb: ((arg: string) => void) | undefined, fn: () => U | Promise<U>): Promise<U>;
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export declare function updateStatus2<U>(msg: string, cb: (arg: string) => void, stopToken: StopToken | undefined, fn: () => U | Promise<U>): Promise<U>;
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export declare function hashCode(str: string): number;
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export declare function objectHash(obj: Record<string, any>): string;
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interface VirtualOffset {
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blockPosition: number;
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}
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interface Block {
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minv: VirtualOffset;
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maxv: VirtualOffset;
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}
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export declare function bytesForRegions(regions: Region[], index: {
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blocksForRange: (ref: string, start: number, end: number) => Promise<Block[]>;
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}): Promise<number>;
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export interface ViewSnap {
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bpPerPx: number;
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interRegionPaddingWidth: number;
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minimumBlockWidth: number;
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width: number;
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offsetPx: number;
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staticBlocks: {
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contentBlocks: BaseBlock[];
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blocks: BaseBlock[];
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};
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displayedRegions: (IStateTreeNode & {
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start: number;
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end: number;
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refName: string;
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reversed?: boolean;
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assemblyName: string;
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})[];
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}
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1
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import type { FileLocation } from './types/data.ts';
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2
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export { capitalizeFirst, pluralize, shorten, shorten2, truncateMiddle, } from './stringUtils.ts';
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3
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export { formatBytes } from './formatBytes.ts';
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export { getFillProps, getStrokeProps, stripAlpha } from './svgColorProps.ts';
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export { fetchAndMaybeUnzip, fetchAndMaybeUnzipText, isGzip, } from './fetchAndMaybeUnzip.ts';
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export { type AbstractDisplayModel, type AbstractMenuManager, type AbstractRootModel, type AbstractSessionModel, type AbstractTrackModel, type AbstractViewContainer, type AbstractViewModel, type AnimationMode, type AnyReactComponentType, type AppRootModel, type AssemblyHost, type AssemblyManager, type AugmentedRegion, AuthNeededError, type BasePlugin, type BlobLocation, type ClassReturnedBy, type ConnectionInstance, type DialogComponentType, type DialogHost, type DrawerPosition, type FileHandleLocation, type FileLocation, type InstanceTypeRestrictive, type JBrowsePlugin, type JBrowsePluginVersion, type LocalPathLocation, type NoAssemblyRegion, type NotificationLevel, type NotificationSink, type PaletteHost, type PreBlobLocation, type PreFileHandleLocation, type PreFileLocation, type PreLocalPathLocation, type PreUriLocation, type Region, type RenderingServices, type RpcCaller, type RpcHost, type RootModelWithInternetAccounts, type SelectionContainer, type SessionServices, type SessionWithAddAssembly, type SessionWithAddSessionTrack, type SessionWithPublishTrackConf, type SessionWithConfigEditing, type SessionWithConnectionEditing, type SessionWithConnections, type SessionWithDeleteTrackConf, type SessionWithDrawerWidgets, type SessionWithFocusedViewAndDrawerWidgets, type SessionWithPermanentPlugins, type SessionWithSessionPlugins, type SessionWithShareURL, type SessionWithViewReplacement, type SessionWithWidgets, type SnackAction, type TrackActionView, type TrackCatalog, type TrackContainer, type TrackViewModel, type TypeTestedByPredicate, type UriLocation, type Widget, type WidgetMap, addOrReplaceView, canReplaceView, isAbstractMenuManager, isAppRootModel, isAuthNeededException, isBlobLocation, isDisplayModel, isFileHandleLocation, isLocalPathLocation, isRootModelWithInternetAccounts, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithPermanentPlugins, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isTrackModel, isTrackViewModel, isUriLocation, isViewContainer, isViewModel, } from './types/index.ts';
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7
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export { type PluginUpdate, type ResolvedPlugin, type StorePluginFailure, type StorePluginResolution, getPluginUpdate, installablePlugins, installedVersionFromUrl, isPluginInstalled, resolvePlugin, resolveStorePluginRefs, resolveStoreRefs, } from './pluginStore.ts';
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8
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export { type PhaseFailure, type ProgressReporter, type RpcStatus, type StatusCallback, type StatusPhase, type StatusStream, type StatusWindow, type StatusWithProgress, createProgressReporter, createStatusFanOut, createStatusWindow, downloadStatus, progressLabel, statusFraction, statusMessageText, statusProgressLabel, statusReading, statusSource, throttleStatusEmits, updateStatus, withProgress, } from './progress.ts';
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9
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export { calculateRedispatchRange, doesIntersect2, intersection2, } from './range.ts';
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10
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export { dedupe } from './dedupe.ts';
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11
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export { MAX_GLOB_REGIONS, matchRefNames, parseRegionNames, resolveNamedRegions, selectNamedRegions, } from './selectNamedRegions.ts';
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12
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export type { RefNameMatchSource } from './selectNamedRegions.ts';
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13
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export { isValidTag, tagRegex } from './tags.ts';
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14
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export { formatRelativeTime } from './formatRelativeTime.ts';
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15
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export { fetchJson } from './fetchJson.ts';
|
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16
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export { type EncodedSessionParam, type SessionShareMode, ENCODED_PREFIX, JSON_PREFIX, SHARE_PREFIX, b64PadSuffix, encodeSessionParam, fromUrlSafeB64, readSessionFromDynamo, shareEndpoint, toUrlSafeB64, } from './sessionSharing.ts';
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17
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export { coarseStripHTML } from './coarseStripHTML.ts';
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18
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export { measureText, measuredFont } from './measureText.ts';
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19
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export type { MeasuredFont } from './measureText.ts';
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20
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export { createScrollLatch } from './scrollLatch.ts';
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21
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export { MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, applyZoomAccum, getZoomNormalizer, isActivelyZooming, normalizeWheelDelta, wheelFrameElapsedMs, wheelZoomAccum, } from './wheelZoom.ts';
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22
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export { avg, clamp, getDisplayStr, getNumberGrouping, max, maxFinite, min, minmax, polarToCartesian, radToDeg, reducePrecision, setNumberGrouping, sum, toLocale, } from './numericUtils.ts';
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23
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export { type MinimalRegion, bpSpanPx, bpToPx, bytesForRegions, featureSpanPx, getBpDisplayStr, getTickDisplayStr, parseBpString, } from './bpUtils.ts';
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24
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export { type BasicFeature, gatherOverlaps, mergeIntervals, } from './intervals.ts';
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25
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export { clampToContig } from './clampToContig.ts';
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26
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export { animationAllowed } from './animationAllowed.ts';
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27
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export { springAnimate } from './springAnimate.ts';
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28
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export { localStorageAvailable, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageGetStringArray, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, notifyLocalStorageKey, subscribeToLocalStorageKey, } from './localStorage.ts';
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29
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export { renameRegionIfNeeded, renameRegionsIfNeeded } from './renameRegions.ts';
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30
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export { addAndShowTrack } from './addAndShowTrack.ts';
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31
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export { addTrackFromWidget, containerDisplaysAssembly, finishAddTrack, type AddTrackWidgetSelf, type AddTrackWorkflowModel, } from './addTrackFromWidget.ts';
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32
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export { namesTemporaryAssembly } from './temporaryAssembly.ts';
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33
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export { makeTrackId } from './makeTrackId.ts';
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34
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export { matchTrackId } from './matchTrackId.ts';
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35
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export { drawImageOntoCanvasContext } from './offscreenCanvasPonyfill.ts';
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36
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export { indexedDBAvailable, isElectron, isNode, rIC } from './environment.ts';
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37
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export { isWebWorker } from './isWebWorker.ts';
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38
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export { sessionStorageAvailable, sessionStorageGetItem, sessionStorageRemoveItem, sessionStorageSetItem, } from './sessionStorage.ts';
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39
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export { isObject } from './objectUtils.ts';
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40
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export { openPromotableDisplays } from './openDisplays.ts';
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41
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export { type ReorderDirection, applyOrderWithin, reorder, reorderWithin, } from './reorder.ts';
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42
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export { getStr } from './getStr.ts';
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43
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export { downloadPhase, getLocationUri, resolveUri } from './getLocationUri.ts';
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44
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export { measureGridWidth, resolveSelectedIds } from './dataGridUtils.ts';
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45
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export { isRpcResult } from './rpc.ts';
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export { aesDecrypt, aesEncrypt, sha256, sha256Base64, sha256Base64Url, toBase64, toBase64Url, } from './crypto.ts';
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export { type FeatureWidgetTypeRef, notifyFeatureDetailsMiss, openFeatureWidget, } from './openFeatureWidget.ts';
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48
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export { withFeatureDetails } from './withFeatureDetails.ts';
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export { canonicalizeViewRefName, findParentThat, findParentThatIs, getAssemblyHost, getContainingDisplay, getContainingTrack, getContainingView, getEnv, getRenderingServices, getSession, hashCode, objectHash, } from './mstUtils.ts';
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export { getDialogHost, getNotificationSink, getPaletteHost, getRpcHost, getSessionServices, } from './sessionServices.ts';
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/**
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* Convert a browser File (from a drop zone or file input) into a FileLocation:
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* a native local path under electron, or an in-memory blob location otherwise.
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*/
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export declare function fileToLocation(file: File): FileLocation;
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export { type Frame, complement, complementTable, defaultStarts, getFrame, revcom, reverse, stitch, } from './seqUtils.ts';
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export { revlist } from './revlist.ts';
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export { useCreateOnce, useDebounce, useFinalUnmount, useLocalStorage, useWidthSetter, } from './hooks.ts';
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export { renderToStaticMarkup } from './renderToStaticMarkup.ts';
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export { codonTable, defaultCodonTable, generateCodonTable, } from './geneticCodes.ts';
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export { IUPAC_MOTIF_REGEX, isPalindromic, iupacToRegex, reverseComplementIupac, } from './iupac.ts';
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export { type MotifListParse, type MotifParseError, type ParsedMotif, parseMotifList, } from './parseMotifList.ts';
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192
63
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export declare function isSupportedIndexingAdapter(type?: string): boolean;
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193
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export declare function getBpDisplayStr(total: number): string;
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194
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export declare function reducePrecision(s: number, n?: number): string;
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195
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export declare function getProgressDisplayStr(current: number, total: number): string;
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export declare function toLocale(n: number): string;
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export declare function getTickDisplayStr(totalBp: number, bpPerPx: number): string;
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198
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export declare function getLayoutId({ sessionId, trackInstanceId, }: {
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sessionId: string;
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trackInstanceId: string;
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}): string;
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export declare function getStatsId({ sessionId, trackInstanceId, }: {
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203
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sessionId: string;
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trackInstanceId: string;
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}): string;
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export declare function useLocalStorage<T>(key: string, initialValue: T, enabled?: boolean): readonly [T, (value: T | ((val: T) => T)) => void];
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207
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export declare function getUriLink(value: {
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208
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uri: string;
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baseUri?: string;
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}): string;
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export declare function getStr(obj: unknown): string;
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212
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export declare function linkify(s: string): string;
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export declare function measureGridWidth(elements: unknown[], args?: {
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214
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minWidth?: number;
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215
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fontSize?: number;
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maxWidth?: number;
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padding?: number;
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218
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stripHTML?: boolean;
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}): number;
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220
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export declare function getEnv(obj: any): {
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pluginManager: PluginManager;
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};
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223
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export declare function localStorageGetItem(item: string): string | null | undefined;
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224
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export declare function localStorageSetItem(str: string, item: string): void;
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export declare function max(arr: Iterable<number>, init?: number): number;
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export declare function min(arr: Iterable<number>, init?: number): number;
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export declare function sum(arr: Iterable<number>): number;
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228
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export declare function avg(arr: number[]): number;
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64
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export declare function groupBy<T>(array: Iterable<T>, predicate: (v: T) => string): Record<string, T[]>;
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230
65
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export declare function notEmpty<T>(value: T | null | undefined): value is T;
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231
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export declare function mergeIntervals<T extends {
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232
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start: number;
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233
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end: number;
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234
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}>(intervals: T[], w?: number): T[];
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235
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export interface BasicFeature {
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236
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end: number;
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237
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start: number;
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238
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refName: string;
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239
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}
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240
|
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export declare function gatherOverlaps<T extends BasicFeature>(regions: T[], w?: number): T[];
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241
|
-
export declare function stripAlpha(str: string): string;
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|
242
|
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export declare function getStrokeProps(str: string): {
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243
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strokeOpacity: number;
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244
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stroke: string;
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245
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} | {
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246
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strokeOpacity?: undefined;
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247
|
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stroke?: undefined;
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248
|
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};
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249
|
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export declare function getFillProps(str: string): {
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250
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fillOpacity: number;
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251
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fill: string;
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252
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} | {
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fillOpacity?: undefined;
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254
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fill?: undefined;
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255
|
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};
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256
|
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export declare function renderToStaticMarkup(node: React.ReactElement): string;
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257
|
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export declare function isGzip(buf: Uint8Array): boolean;
|
|
258
|
-
export declare function fetchAndMaybeUnzip(loc: GenericFilehandle, opts?: BaseOptions): Promise<any>;
|
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259
|
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export declare function fetchAndMaybeUnzipText(loc: GenericFilehandle, opts?: BaseOptions): Promise<string>;
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260
|
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export declare function isObject(x: unknown): x is Record<string | symbol | number, unknown>;
|
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261
|
-
export declare function localStorageGetNumber(key: string, defaultVal: number): number;
|
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262
|
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export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
|
|
263
|
-
export declare function localStorageSetBoolean(key: string, value: boolean): void;
|
|
264
66
|
export declare function testAdapter(fileName: string, regex: RegExp, adapterHint: string | undefined, expected: string): boolean;
|
|
265
67
|
export { type Feature, type SimpleFeatureSerialized, type SimpleFeatureSerializedNoId, default as SimpleFeature, isFeature, } from './simpleFeature.ts';
|
|
266
|
-
export {
|
|
267
|
-
export {
|
|
268
|
-
export
|
|
269
|
-
export
|
|
270
|
-
export
|
|
271
|
-
export
|
|
272
|
-
export
|
|
273
|
-
export
|
|
68
|
+
export { saveAs } from './FileSaver/index.ts';
|
|
69
|
+
export { type SaveSvgAsImageOptions, saveSvgAsImage, svgHtmlToPngBlob, } from '../svg/saveSvgAsImage.ts';
|
|
70
|
+
export { type ActiveFetch, type StatusChannel, type StatusReporter, createStatusChannel, createStopTokenRotation, } from './createStopTokenRotation.ts';
|
|
71
|
+
export { createSharedSetup } from './cachedSetup.ts';
|
|
72
|
+
export { isDataCurrent } from './isDataCurrent.ts';
|
|
73
|
+
export { handleFetchError, isAbortException, makeAbortError, } from './aborting.ts';
|
|
74
|
+
export { linkify } from './linkify.ts';
|
|
75
|
+
export { locStringsToRegions } from './locStringsToRegions.ts';
|
|
76
|
+
export type { RefNameSource } from './locStringsToRegions.ts';
|
|
77
|
+
export { type ParsedLocString, UnknownRefNameError, assembleLocString, assembleLocStringRaw, assembleLocStrings, compareLocStrings, compareLocs, parseLocString, parseLocStringOneBased, stringify, } from './locString.ts';
|
|
78
|
+
export { type LastStopTokenCheck, type StopToken, type StopTokenChecker, type StopTokenSignal, checkStopToken, checkStopTokenThrottled, createStopToken, createStopTokenChecker, hasSharedArrayBuffer, isStopToken, isStopped, markStopTokenStopped, registerStopTokenBroadcaster, stopStopToken, stopTokenSignal, withStopTokenCheck, withStopTokenSignal, } from './stopToken.ts';
|
|
79
|
+
export { type AddTrackComponentModel, type AddTrackComponentProps, adapterNeedsAddTrackComponent, addAddTrackComponent, } from './addTrackComponent.ts';
|
|
80
|
+
export { adapterConfigFromSpec } from './formatGuessers.ts';
|
|
81
|
+
export { type AdapterConfig, type AdapterGuesser, type LooseTrackInput, type TrackTypeGuesser, UNKNOWN, UNSUPPORTED, addAdapterGuesser, addTrackTypeGuesser, clearFileFromCache, ensureFileHandleReady, expandLooseTrackConfig, findFileHandleIds, generateUnknownTrackConf, generateUnsupportedTrackConf, getBlob, getBlobMap, getConfAssemblyNames, getFileFromCache, getFileName, getRpcSessionId, getTrackAssemblyNames, getTrackName, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hideTrackGeneric, isLooseTrackConfig, makeIndex, makeIndexType, restoreFileHandles, restoreFileHandlesFromSnapshot, setBlobMap, setFileInCache, showTrackGeneric, storeBlobLocation, storeFileHandleLocation, stripFileExtension, stripTrackIds, toggleTrackGeneric, } from './tracks.ts';
|
|
82
|
+
export { getFileHandle, isFileSystemAccessSupported, storeFileHandle, verifyPermission, } from './fileHandleStore.ts';
|
|
274
83
|
export { IntervalTree } from './IntervalTree.ts';
|
|
84
|
+
export { cmpStr } from './cmpStr.ts';
|
|
85
|
+
export { diffTrackConfig, flattenTrackConfigDelta, mergeTrackConfig, } from './trackConfigDelta.ts';
|
|
86
|
+
export type { TrackConfigChange } from './trackConfigDelta.ts';
|
|
87
|
+
export { BEZIER_CONNECTOR_MAX_REACH_PX, bezierConnectorPath, } from './bezierConnector.ts';
|
|
88
|
+
export { type AlignmentData, type DiagonalizationResult, diagonalizeRegions, } from './diagonalizeRegions.ts';
|