@jbrowse/plugin-variants 3.7.0 → 4.0.0
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/esm/ChordVariantDisplay/components/ChordVariantDisplay.d.ts +11 -0
- package/esm/ChordVariantDisplay/components/ChordVariantDisplay.js +16 -0
- package/esm/ChordVariantDisplay/components/DisplayError.d.ts +9 -0
- package/esm/ChordVariantDisplay/components/DisplayError.js +7 -0
- package/esm/ChordVariantDisplay/components/Loading.d.ts +8 -0
- package/esm/ChordVariantDisplay/components/Loading.js +28 -0
- package/esm/ChordVariantDisplay/index.js +4 -4
- package/esm/ChordVariantDisplay/models/configSchema.d.ts +4 -5
- package/esm/ChordVariantDisplay/models/configSchema.js +10 -5
- package/esm/ChordVariantDisplay/models/renderReaction.d.ts +30 -0
- package/esm/ChordVariantDisplay/models/renderReaction.js +48 -0
- package/esm/ChordVariantDisplay/models/renderSvg.d.ts +6 -0
- package/esm/ChordVariantDisplay/models/renderSvg.js +12 -0
- package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +535 -46
- package/esm/ChordVariantDisplay/models/stateModelFactory.js +146 -8
- package/esm/LinearVariantDisplay/configSchema.d.ts +5 -5
- package/esm/LinearVariantDisplay/configSchema.js +2 -2
- package/esm/LinearVariantDisplay/index.js +6 -4
- package/esm/LinearVariantDisplay/model.d.ts +1086 -103
- package/esm/LinearVariantDisplay/model.js +10 -26
- package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +1 -1
- package/esm/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +8 -18
- package/esm/MultiLinearVariantDisplay/configSchema.d.ts +6 -44
- package/esm/MultiLinearVariantDisplay/configSchema.js +2 -2
- package/esm/MultiLinearVariantDisplay/index.js +4 -3
- package/esm/MultiLinearVariantDisplay/model.d.ts +1031 -125
- package/esm/MultiLinearVariantDisplay/model.js +3 -23
- package/esm/MultiLinearVariantDisplay/renderSvg.d.ts +1 -1
- package/esm/MultiLinearVariantDisplay/renderSvg.js +4 -4
- package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +8 -2
- package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +26 -23
- package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +1 -1
- package/esm/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +9 -20
- package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts +6 -6
- package/esm/MultiLinearVariantMatrixDisplay/configSchema.js +1 -1
- package/esm/MultiLinearVariantMatrixDisplay/index.js +5 -4
- package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +1110 -131
- package/esm/MultiLinearVariantMatrixDisplay/model.js +22 -48
- package/esm/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +1 -1
- package/esm/MultiLinearVariantMatrixDisplay/renderSvg.js +3 -3
- package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts +4 -35
- package/esm/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js +19 -33
- package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts +12 -1
- package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js +48 -22
- package/esm/MultiLinearVariantMatrixRenderer/configSchema.d.ts +1 -1
- package/esm/MultiLinearVariantMatrixRenderer/index.js +4 -4
- package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +10 -2
- package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js +155 -135
- package/esm/MultiLinearVariantMatrixRenderer/types.d.ts +2 -14
- package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts +3 -60
- package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js +9 -18
- package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.d.ts +7 -6
- package/esm/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.js +30 -26
- package/esm/MultiLinearVariantRenderer/configSchema.d.ts +1 -1
- package/esm/MultiLinearVariantRenderer/index.js +4 -4
- package/esm/MultiLinearVariantRenderer/makeImageData.d.ts +14 -11
- package/esm/MultiLinearVariantRenderer/makeImageData.js +127 -110
- package/esm/MultiLinearVariantRenderer/types.d.ts +3 -20
- package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js +1 -1
- package/esm/SplitVcfTabixAdapter/configSchema.d.ts +2 -2
- package/esm/SplitVcfTabixAdapter/index.d.ts +1 -1
- package/esm/SplitVcfTabixAdapter/index.js +3 -3
- package/esm/StructuralVariantChordRenderer/Chord.d.ts +1 -1
- package/esm/StructuralVariantChordRenderer/Chord.js +41 -58
- package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +3 -3
- package/esm/StructuralVariantChordRenderer/ReactComponent.js +3 -3
- package/esm/StructuralVariantChordRenderer/configSchema.d.ts +2 -2
- package/esm/StructuralVariantChordRenderer/index.js +3 -3
- package/esm/Tooltip.js +2 -2
- package/esm/VariantFeatureWidget/AltFormatter.js +1 -1
- package/esm/VariantFeatureWidget/Formatter.js +2 -2
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakpointSplitViewChoiceDialog.d.ts +1 -0
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakpointSplitViewChoiceDialog.js +1 -0
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.d.ts +1 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.js +8 -23
- package/esm/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGrid.js +1 -1
- package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +1 -1
- package/esm/VariantFeatureWidget/VariantFeatureWidget.js +16 -29
- package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.d.ts +5 -2
- package/esm/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js +68 -59
- package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleFilters.js +13 -2
- package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts +1 -1
- package/esm/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js +72 -30
- package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts +2 -2
- package/esm/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js +49 -26
- package/esm/VariantFeatureWidget/VariantSampleGrid/types.d.ts +3 -5
- package/esm/VariantFeatureWidget/configSchema.d.ts +1 -1
- package/esm/VariantFeatureWidget/index.js +3 -3
- package/esm/VariantFeatureWidget/stateModelFactory.d.ts +39 -39
- package/esm/VariantFeatureWidget/stateModelFactory.js +1 -1
- package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts +2 -7
- package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js +3 -14
- package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts +4 -2
- package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js +2 -5
- package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts +2 -2
- package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js +34 -19
- package/esm/VariantRPC/MultiVariantGetSources.js +2 -6
- package/esm/VariantRPC/executeClusterGenotypeMatrix.d.ts +22 -0
- package/esm/VariantRPC/executeClusterGenotypeMatrix.js +19 -0
- package/esm/VariantRPC/getGenotypeMatrix.d.ts +18 -3
- package/esm/VariantRPC/getGenotypeMatrix.js +23 -40
- package/esm/VariantRPC/types.d.ts +10 -24
- package/esm/VariantTrack/configSchema.d.ts +16 -11
- package/esm/VariantTrack/index.js +13 -2
- package/esm/VariantTrack/saveTrackFormats/vcf.d.ts +4 -0
- package/esm/VariantTrack/saveTrackFormats/vcf.js +15 -0
- package/esm/VcfAdapter/VcfAdapter.d.ts +6 -3
- package/esm/VcfAdapter/VcfAdapter.js +36 -24
- package/esm/VcfAdapter/configSchema.d.ts +2 -2
- package/esm/VcfAdapter/index.js +3 -2
- package/esm/VcfExtensionPoints/index.d.ts +2 -0
- package/esm/{extensionPoints.js → VcfExtensionPoints/index.js} +1 -1
- package/esm/VcfFeature/index.js +20 -8
- package/esm/VcfFeature/util.d.ts +0 -1
- package/esm/VcfFeature/util.js +70 -188
- package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts +2 -0
- package/esm/VcfTabixAdapter/VcfTabixAdapter.js +28 -3
- package/esm/VcfTabixAdapter/configSchema.d.ts +5 -5
- package/esm/VcfTabixAdapter/configSchema.js +1 -1
- package/esm/VcfTabixAdapter/index.d.ts +1 -1
- package/esm/VcfTabixAdapter/index.js +4 -3
- package/esm/d3-hierarchy2/accessors.d.ts +2 -0
- package/esm/d3-hierarchy2/accessors.js +8 -0
- package/esm/d3-hierarchy2/array.d.ts +2 -0
- package/esm/d3-hierarchy2/array.js +15 -0
- package/esm/d3-hierarchy2/cluster.d.ts +8 -0
- package/esm/d3-hierarchy2/cluster.js +63 -0
- package/esm/d3-hierarchy2/constant.d.ts +2 -0
- package/esm/d3-hierarchy2/constant.js +8 -0
- package/esm/d3-hierarchy2/hierarchy/ancestors.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/ancestors.js +7 -0
- package/esm/d3-hierarchy2/hierarchy/count.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/count.js +12 -0
- package/esm/d3-hierarchy2/hierarchy/descendants.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/descendants.js +3 -0
- package/esm/d3-hierarchy2/hierarchy/each.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/each.js +7 -0
- package/esm/d3-hierarchy2/hierarchy/eachAfter.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/eachAfter.js +15 -0
- package/esm/d3-hierarchy2/hierarchy/eachBefore.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/eachBefore.js +12 -0
- package/esm/d3-hierarchy2/hierarchy/find.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/find.js +8 -0
- package/esm/d3-hierarchy2/hierarchy/index.d.ts +3 -0
- package/esm/d3-hierarchy2/hierarchy/index.js +78 -0
- package/esm/d3-hierarchy2/hierarchy/iterator.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/iterator.js +14 -0
- package/esm/d3-hierarchy2/hierarchy/leaves.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/leaves.js +9 -0
- package/esm/d3-hierarchy2/hierarchy/links.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/links.js +9 -0
- package/esm/d3-hierarchy2/hierarchy/path.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/path.js +26 -0
- package/esm/d3-hierarchy2/hierarchy/sort.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/sort.js +7 -0
- package/esm/d3-hierarchy2/hierarchy/sum.d.ts +1 -0
- package/esm/d3-hierarchy2/hierarchy/sum.js +8 -0
- package/esm/d3-hierarchy2/index.d.ts +15 -0
- package/esm/d3-hierarchy2/index.js +15 -0
- package/esm/d3-hierarchy2/lcg.d.ts +1 -0
- package/esm/d3-hierarchy2/lcg.js +7 -0
- package/esm/d3-hierarchy2/pack/enclose.d.ts +10 -0
- package/esm/d3-hierarchy2/pack/enclose.js +84 -0
- package/esm/d3-hierarchy2/pack/index.d.ts +7 -0
- package/esm/d3-hierarchy2/pack/index.js +68 -0
- package/esm/d3-hierarchy2/pack/siblings.d.ts +2 -0
- package/esm/d3-hierarchy2/pack/siblings.js +94 -0
- package/esm/d3-hierarchy2/partition.d.ts +6 -0
- package/esm/d3-hierarchy2/partition.js +42 -0
- package/esm/d3-hierarchy2/stratify.d.ts +9 -0
- package/esm/d3-hierarchy2/stratify.js +115 -0
- package/esm/d3-hierarchy2/tree.d.ts +8 -0
- package/esm/d3-hierarchy2/tree.js +153 -0
- package/esm/d3-hierarchy2/treemap/binary.d.ts +1 -0
- package/esm/d3-hierarchy2/treemap/binary.js +36 -0
- package/esm/d3-hierarchy2/treemap/dice.d.ts +1 -0
- package/esm/d3-hierarchy2/treemap/dice.js +7 -0
- package/esm/d3-hierarchy2/treemap/index.d.ts +17 -0
- package/esm/d3-hierarchy2/treemap/index.js +72 -0
- package/esm/d3-hierarchy2/treemap/resquarify.d.ts +5 -0
- package/esm/d3-hierarchy2/treemap/resquarify.js +28 -0
- package/esm/d3-hierarchy2/treemap/round.d.ts +1 -0
- package/esm/d3-hierarchy2/treemap/round.js +6 -0
- package/esm/d3-hierarchy2/treemap/slice.d.ts +1 -0
- package/esm/d3-hierarchy2/treemap/slice.js +7 -0
- package/esm/d3-hierarchy2/treemap/sliceDice.d.ts +1 -0
- package/esm/d3-hierarchy2/treemap/sliceDice.js +5 -0
- package/esm/d3-hierarchy2/treemap/squarify.d.ts +11 -0
- package/esm/d3-hierarchy2/treemap/squarify.js +46 -0
- package/esm/index.d.ts +1 -1
- package/esm/index.js +19 -22
- package/esm/shared/MultiVariantBaseModel.d.ts +1103 -117
- package/esm/shared/MultiVariantBaseModel.js +231 -65
- package/esm/shared/SharedVariantConfigSchema.d.ts +2 -40
- package/esm/shared/SharedVariantConfigSchema.js +1 -46
- package/esm/shared/components/AddFiltersDialog.d.ts +2 -3
- package/esm/shared/components/AddFiltersDialog.js +20 -28
- package/esm/shared/components/{ui/SetColorDialog.d.ts → BaseSetColorDialog.d.ts} +2 -1
- package/esm/shared/components/BaseSetColorDialog.js +61 -0
- package/esm/shared/components/ClearTreeWarningDialog.d.ts +4 -0
- package/esm/shared/components/ClearTreeWarningDialog.js +9 -0
- package/esm/shared/components/MAFFilterDialog.d.ts +2 -3
- package/esm/shared/components/MAFFilterDialog.js +4 -8
- package/esm/shared/components/MultiVariantBaseDisplayComponent.d.ts +1 -1
- package/esm/shared/components/MultiVariantBaseDisplayComponent.js +8 -17
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialog.d.ts +1 -1
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialog.js +3 -3
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.d.ts +1 -1
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.js +9 -14
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogManual.d.ts +1 -1
- package/esm/shared/components/MultiVariantClusterDialog/ClusterDialogManual.js +11 -15
- package/esm/shared/components/MultiVariantClusterDialog/types.d.ts +3 -2
- package/esm/shared/components/MultiVariantColorLegend.d.ts +1 -1
- package/esm/shared/components/MultiVariantColorLegend.js +22 -12
- package/esm/shared/components/MultiVariantCrosshairs.d.ts +4 -2
- package/esm/shared/components/MultiVariantCrosshairs.js +31 -23
- package/esm/shared/components/MultiVariantLegendBar.d.ts +4 -4
- package/esm/shared/components/MultiVariantLegendBar.js +24 -22
- package/esm/shared/components/MultiVariantLegendBarWrapper.d.ts +7 -0
- package/esm/shared/components/MultiVariantLegendBarWrapper.js +18 -0
- package/esm/shared/components/MultiVariantTooltip.d.ts +5 -6
- package/esm/shared/components/MultiVariantTooltip.js +35 -17
- package/esm/shared/components/ScrollableVariantContainer.d.ts +8 -0
- package/esm/shared/components/ScrollableVariantContainer.js +23 -0
- package/esm/shared/components/SetColorDialog.d.ts +3 -2
- package/esm/shared/components/SetColorDialog.js +2 -2
- package/esm/shared/components/SetColorDialogBulkEditPanel.d.ts +7 -8
- package/esm/shared/components/SetColorDialogBulkEditPanel.js +24 -54
- package/esm/shared/components/SetColorDialogRowPalettizer.js +13 -23
- package/esm/shared/components/SetRowHeightDialog.d.ts +2 -3
- package/esm/shared/components/SourcesDataGrid.d.ts +1 -1
- package/esm/shared/components/SourcesDataGrid.js +1 -1
- package/esm/shared/components/SourcesGrid.d.ts +1 -1
- package/esm/shared/components/SourcesGrid.js +2 -2
- package/esm/shared/components/SourcesGridHeader.d.ts +1 -1
- package/esm/shared/components/SourcesGridHeader.js +1 -1
- package/esm/shared/components/SvgTree.d.ts +5 -0
- package/esm/shared/components/SvgTree.js +19 -0
- package/esm/shared/components/TreeSidebar.d.ts +5 -0
- package/esm/shared/components/TreeSidebar.js +121 -0
- package/esm/shared/components/types.d.ts +43 -0
- package/esm/shared/components/types.js +1 -0
- package/esm/shared/constants.d.ts +8 -2
- package/esm/shared/constants.js +11 -2
- package/esm/shared/drawAlleleCount.d.ts +2 -1
- package/esm/shared/drawAlleleCount.js +50 -16
- package/esm/shared/drawPhased.js +11 -12
- package/{dist → esm/shared}/getMultiVariantFeaturesAutorun.d.ts +5 -4
- package/esm/{getMultiVariantFeaturesAutorun.js → shared/getMultiVariantFeaturesAutorun.js} +9 -2
- package/esm/{getMultiVariantSourcesAutorun.d.ts → shared/getMultiVariantSourcesAutorun.d.ts} +4 -3
- package/esm/{getMultiVariantSourcesAutorun.js → shared/getMultiVariantSourcesAutorun.js} +10 -2
- package/esm/shared/getSources.d.ts +1 -1
- package/esm/shared/getSources.js +2 -2
- package/esm/shared/hooks/useMouseTracking.d.ts +6 -0
- package/esm/shared/hooks/useMouseTracking.js +34 -0
- package/esm/shared/makeSidebarSvg.d.ts +9 -0
- package/esm/shared/makeSidebarSvg.js +9 -0
- package/esm/shared/minorAlleleFrequencyUtils.d.ts +6 -5
- package/esm/shared/minorAlleleFrequencyUtils.js +37 -38
- package/esm/shared/setupMultiVariantAutoruns.d.ts +2 -0
- package/esm/shared/setupMultiVariantAutoruns.js +8 -0
- package/esm/shared/treeDrawingAutorun.d.ts +16 -0
- package/esm/shared/treeDrawingAutorun.js +71 -0
- package/esm/shared/types.d.ts +15 -0
- package/package.json +38 -39
- package/dist/ChordVariantDisplay/index.d.ts +0 -2
- package/dist/ChordVariantDisplay/index.js +0 -25
- package/dist/ChordVariantDisplay/models/configSchema.d.ts +0 -12
- package/dist/ChordVariantDisplay/models/configSchema.js +0 -15
- package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +0 -115
- package/dist/ChordVariantDisplay/models/stateModelFactory.js +0 -35
- package/dist/LinearVariantDisplay/configSchema.d.ts +0 -34
- package/dist/LinearVariantDisplay/configSchema.js +0 -12
- package/dist/LinearVariantDisplay/index.d.ts +0 -2
- package/dist/LinearVariantDisplay/index.js +0 -24
- package/dist/LinearVariantDisplay/model.d.ts +0 -278
- package/dist/LinearVariantDisplay/model.js +0 -37
- package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.d.ts +0 -5
- package/dist/MultiLinearVariantDisplay/components/VariantDisplayComponent.js +0 -29
- package/dist/MultiLinearVariantDisplay/configSchema.d.ts +0 -80
- package/dist/MultiLinearVariantDisplay/configSchema.js +0 -30
- package/dist/MultiLinearVariantDisplay/index.d.ts +0 -2
- package/dist/MultiLinearVariantDisplay/index.js +0 -57
- package/dist/MultiLinearVariantDisplay/model.d.ts +0 -422
- package/dist/MultiLinearVariantDisplay/model.js +0 -82
- package/dist/MultiLinearVariantDisplay/renderSvg.d.ts +0 -3
- package/dist/MultiLinearVariantDisplay/renderSvg.js +0 -15
- package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.d.ts +0 -6
- package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js +0 -83
- package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.d.ts +0 -5
- package/dist/MultiLinearVariantMatrixDisplay/components/VariantDisplayComponent.js +0 -31
- package/dist/MultiLinearVariantMatrixDisplay/configSchema.d.ts +0 -37
- package/dist/MultiLinearVariantMatrixDisplay/configSchema.js +0 -22
- package/dist/MultiLinearVariantMatrixDisplay/index.d.ts +0 -2
- package/dist/MultiLinearVariantMatrixDisplay/index.js +0 -24
- package/dist/MultiLinearVariantMatrixDisplay/model.d.ts +0 -431
- package/dist/MultiLinearVariantMatrixDisplay/model.js +0 -125
- package/dist/MultiLinearVariantMatrixDisplay/renderSvg.d.ts +0 -3
- package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js +0 -17
- package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts +0 -37
- package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js +0 -87
- package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.d.ts +0 -8
- package/dist/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js +0 -41
- package/dist/MultiLinearVariantMatrixRenderer/configSchema.d.ts +0 -2
- package/dist/MultiLinearVariantMatrixRenderer/configSchema.js +0 -6
- package/dist/MultiLinearVariantMatrixRenderer/index.d.ts +0 -2
- package/dist/MultiLinearVariantMatrixRenderer/index.js +0 -20
- package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts +0 -14
- package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js +0 -154
- package/dist/MultiLinearVariantMatrixRenderer/types.d.ts +0 -14
- package/dist/MultiLinearVariantMatrixRenderer/types.js +0 -2
- package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts +0 -63
- package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.js +0 -79
- package/dist/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.d.ts +0 -33
- package/dist/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.js +0 -67
- package/dist/MultiLinearVariantRenderer/components/util.d.ts +0 -1
- package/dist/MultiLinearVariantRenderer/components/util.js +0 -15
- package/dist/MultiLinearVariantRenderer/configSchema.d.ts +0 -2
- package/dist/MultiLinearVariantRenderer/configSchema.js +0 -8
- package/dist/MultiLinearVariantRenderer/index.d.ts +0 -2
- package/dist/MultiLinearVariantRenderer/index.js +0 -19
- package/dist/MultiLinearVariantRenderer/makeImageData.d.ts +0 -14
- package/dist/MultiLinearVariantRenderer/makeImageData.js +0 -140
- package/dist/MultiLinearVariantRenderer/types.d.ts +0 -21
- package/dist/MultiLinearVariantRenderer/types.js +0 -2
- package/dist/MultiVariantBaseRenderer.d.ts +0 -46
- package/dist/MultiVariantBaseRenderer.js +0 -39
- package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts +0 -18
- package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js +0 -92
- package/dist/SplitVcfTabixAdapter/configSchema.d.ts +0 -23
- package/dist/SplitVcfTabixAdapter/configSchema.js +0 -29
- package/dist/SplitVcfTabixAdapter/index.d.ts +0 -3
- package/dist/SplitVcfTabixAdapter/index.js +0 -52
- package/dist/StructuralVariantChordRenderer/Chord.d.ts +0 -13
- package/dist/StructuralVariantChordRenderer/Chord.js +0 -82
- package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +0 -16
- package/dist/StructuralVariantChordRenderer/ReactComponent.js +0 -30
- package/dist/StructuralVariantChordRenderer/configSchema.d.ts +0 -21
- package/dist/StructuralVariantChordRenderer/configSchema.js +0 -25
- package/dist/StructuralVariantChordRenderer/index.d.ts +0 -2
- package/dist/StructuralVariantChordRenderer/index.js +0 -18
- package/dist/StructuralVariantChordRenderer/types.d.ts +0 -17
- package/dist/StructuralVariantChordRenderer/types.js +0 -2
- package/dist/Tooltip.d.ts +0 -19
- package/dist/Tooltip.js +0 -32
- package/dist/VariantFeatureWidget/AltFormatter.d.ts +0 -4
- package/dist/VariantFeatureWidget/AltFormatter.js +0 -13
- package/dist/VariantFeatureWidget/Checkbox2.d.ts +0 -6
- package/dist/VariantFeatureWidget/Checkbox2.js +0 -8
- package/dist/VariantFeatureWidget/Formatter.d.ts +0 -3
- package/dist/VariantFeatureWidget/Formatter.js +0 -23
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/BreakendMultiLevelOptionDialog.d.ts +0 -1
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/BreakendMultiLevelOptionDialog.js +0 -5
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/BreakendSingleLevelOptionDialog.d.ts +0 -1
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/BreakendSingleLevelOptionDialog.js +0 -5
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.d.ts +0 -7
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendPanel.js +0 -111
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendWidgetArea.d.ts +0 -4
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendWidgetArea.js +0 -60
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/index.d.ts +0 -1
- package/dist/VariantFeatureWidget/LaunchBreakendPanel/index.js +0 -8
- package/dist/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGrid.d.ts +0 -5
- package/dist/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGrid.js +0 -15
- package/dist/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGridWrapper.d.ts +0 -5
- package/dist/VariantFeatureWidget/VariantConsequence/VariantConsequenceDataGridWrapper.js +0 -18
- package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +0 -5
- package/dist/VariantFeatureWidget/VariantFeatureWidget.js +0 -103
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.d.ts +0 -4
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantGenotypeFrequencyTable.js +0 -80
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleFilters.d.ts +0 -9
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleFilters.js +0 -10
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.d.ts +0 -6
- package/dist/VariantFeatureWidget/VariantSampleGrid/VariantSampleGrid.js +0 -54
- package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.d.ts +0 -5
- package/dist/VariantFeatureWidget/VariantSampleGrid/getSampleGridRows.js +0 -51
- package/dist/VariantFeatureWidget/VariantSampleGrid/index.d.ts +0 -1
- package/dist/VariantFeatureWidget/VariantSampleGrid/index.js +0 -8
- package/dist/VariantFeatureWidget/VariantSampleGrid/types.d.ts +0 -21
- package/dist/VariantFeatureWidget/VariantSampleGrid/types.js +0 -2
- package/dist/VariantFeatureWidget/VariantSampleGrid/util.d.ts +0 -1
- package/dist/VariantFeatureWidget/VariantSampleGrid/util.js +0 -14
- package/dist/VariantFeatureWidget/configSchema.d.ts +0 -1
- package/dist/VariantFeatureWidget/configSchema.js +0 -5
- package/dist/VariantFeatureWidget/index.d.ts +0 -2
- package/dist/VariantFeatureWidget/index.js +0 -52
- package/dist/VariantFeatureWidget/stateModelFactory.d.ts +0 -104
- package/dist/VariantFeatureWidget/stateModelFactory.js +0 -12
- package/dist/VariantFeatureWidget/types.d.ts +0 -16
- package/dist/VariantFeatureWidget/types.js +0 -2
- package/dist/VariantFeatureWidget/variantFieldDescriptions.d.ts +0 -9
- package/dist/VariantFeatureWidget/variantFieldDescriptions.js +0 -12
- package/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts +0 -14
- package/dist/VariantRPC/MultiVariantClusterGenotypeMatrix.js +0 -30
- package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts +0 -6
- package/dist/VariantRPC/MultiVariantGetGenotypeMatrix.js +0 -21
- package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts +0 -19
- package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js +0 -58
- package/dist/VariantRPC/MultiVariantGetSources.d.ts +0 -14
- package/dist/VariantRPC/MultiVariantGetSources.js +0 -22
- package/dist/VariantRPC/getGenotypeMatrix.d.ts +0 -6
- package/dist/VariantRPC/getGenotypeMatrix.js +0 -68
- package/dist/VariantRPC/types.d.ts +0 -36
- package/dist/VariantRPC/types.js +0 -2
- package/dist/VariantTrack/configSchema.d.ts +0 -79
- package/dist/VariantTrack/configSchema.js +0 -10
- package/dist/VariantTrack/index.d.ts +0 -2
- package/dist/VariantTrack/index.js +0 -20
- package/dist/VcfAdapter/VcfAdapter.d.ts +0 -35
- package/dist/VcfAdapter/VcfAdapter.js +0 -119
- package/dist/VcfAdapter/configSchema.d.ts +0 -18
- package/dist/VcfAdapter/configSchema.js +0 -35
- package/dist/VcfAdapter/index.d.ts +0 -2
- package/dist/VcfAdapter/index.js +0 -49
- package/dist/VcfAdapter/vcfParser.d.ts +0 -7
- package/dist/VcfAdapter/vcfParser.js +0 -26
- package/dist/VcfFeature/index.d.ts +0 -19
- package/dist/VcfFeature/index.js +0 -80
- package/dist/VcfFeature/util.d.ts +0 -6
- package/dist/VcfFeature/util.js +0 -227
- package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts +0 -25
- package/dist/VcfTabixAdapter/VcfTabixAdapter.js +0 -117
- package/dist/VcfTabixAdapter/configSchema.d.ts +0 -32
- package/dist/VcfTabixAdapter/configSchema.js +0 -56
- package/dist/VcfTabixAdapter/index.d.ts +0 -3
- package/dist/VcfTabixAdapter/index.js +0 -52
- package/dist/extensionPoints.d.ts +0 -2
- package/dist/extensionPoints.js +0 -39
- package/dist/getMultiVariantFeaturesAutorun.js +0 -48
- package/dist/getMultiVariantSourcesAutorun.d.ts +0 -11
- package/dist/getMultiVariantSourcesAutorun.js +0 -38
- package/dist/index.d.ts +0 -7
- package/dist/index.js +0 -52
- package/dist/shared/MultiVariantBaseModel.d.ts +0 -413
- package/dist/shared/MultiVariantBaseModel.js +0 -373
- package/dist/shared/SharedVariantConfigSchema.d.ts +0 -66
- package/dist/shared/SharedVariantConfigSchema.js +0 -56
- package/dist/shared/SharedVariantMixin.d.ts +0 -325
- package/dist/shared/SharedVariantMixin.js +0 -58
- package/dist/shared/components/AddFiltersDialog.d.ts +0 -9
- package/dist/shared/components/AddFiltersDialog.js +0 -61
- package/dist/shared/components/MAFFilterDialog.d.ts +0 -8
- package/dist/shared/components/MAFFilterDialog.js +0 -28
- package/dist/shared/components/MultiVariantBaseDisplayComponent.d.ts +0 -5
- package/dist/shared/components/MultiVariantBaseDisplayComponent.js +0 -29
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialog.d.ts +0 -6
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialog.js +0 -29
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.d.ts +0 -7
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogAuto.js +0 -74
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogManual.d.ts +0 -7
- package/dist/shared/components/MultiVariantClusterDialog/ClusterDialogManual.js +0 -145
- package/dist/shared/components/MultiVariantClusterDialog/types.d.ts +0 -10
- package/dist/shared/components/MultiVariantClusterDialog/types.js +0 -2
- package/dist/shared/components/MultiVariantColorLegend.d.ts +0 -10
- package/dist/shared/components/MultiVariantColorLegend.js +0 -24
- package/dist/shared/components/MultiVariantCrosshairs.d.ts +0 -7
- package/dist/shared/components/MultiVariantCrosshairs.js +0 -40
- package/dist/shared/components/MultiVariantLegendBar.d.ts +0 -7
- package/dist/shared/components/MultiVariantLegendBar.js +0 -32
- package/dist/shared/components/MultiVariantTooltip.d.ts +0 -10
- package/dist/shared/components/MultiVariantTooltip.js +0 -24
- package/dist/shared/components/RectBg.d.ts +0 -8
- package/dist/shared/components/RectBg.js +0 -10
- package/dist/shared/components/SetColorDialog.d.ts +0 -11
- package/dist/shared/components/SetColorDialog.js +0 -12
- package/dist/shared/components/SetColorDialogBulkEditPanel.d.ts +0 -10
- package/dist/shared/components/SetColorDialogBulkEditPanel.js +0 -84
- package/dist/shared/components/SetColorDialogHelpfulTips.d.ts +0 -1
- package/dist/shared/components/SetColorDialogHelpfulTips.js +0 -7
- package/dist/shared/components/SetColorDialogRowPalettizer.d.ts +0 -10
- package/dist/shared/components/SetColorDialogRowPalettizer.js +0 -41
- package/dist/shared/components/SetMinMaxDialog.d.ts +0 -10
- package/dist/shared/components/SetMinMaxDialog.js +0 -26
- package/dist/shared/components/SetRowHeightDialog.d.ts +0 -8
- package/dist/shared/components/SetRowHeightDialog.js +0 -18
- package/dist/shared/components/SourcesDataGrid.d.ts +0 -7
- package/dist/shared/components/SourcesDataGrid.js +0 -68
- package/dist/shared/components/SourcesGrid.d.ts +0 -7
- package/dist/shared/components/SourcesGrid.js +0 -14
- package/dist/shared/components/SourcesGridHeader.d.ts +0 -8
- package/dist/shared/components/SourcesGridHeader.js +0 -41
- package/dist/shared/components/ui/SetColorDialog.d.ts +0 -31
- package/dist/shared/components/ui/SetColorDialog.js +0 -51
- package/dist/shared/components/ui/SetColorDialogBulkEditPanel.d.ts +0 -10
- package/dist/shared/components/ui/SetColorDialogBulkEditPanel.js +0 -84
- package/dist/shared/components/ui/SetColorDialogHelpfulTips.d.ts +0 -1
- package/dist/shared/components/ui/SetColorDialogHelpfulTips.js +0 -7
- package/dist/shared/components/ui/SetColorDialogRowPalettizer.d.ts +0 -10
- package/dist/shared/components/ui/SetColorDialogRowPalettizer.js +0 -41
- package/dist/shared/constants.d.ts +0 -2
- package/dist/shared/constants.js +0 -5
- package/dist/shared/drawAlleleCount.d.ts +0 -2
- package/dist/shared/drawAlleleCount.js +0 -50
- package/dist/shared/drawPhased.d.ts +0 -1
- package/dist/shared/drawPhased.js +0 -25
- package/dist/shared/findSecondLargestNumber.d.ts +0 -0
- package/dist/shared/findSecondLargestNumber.js +0 -1
- package/dist/shared/getSources.d.ts +0 -15
- package/dist/shared/getSources.js +0 -34
- package/dist/shared/minorAlleleFrequencyUtils.d.ts +0 -14
- package/dist/shared/minorAlleleFrequencyUtils.js +0 -72
- package/dist/shared/sourcesGridUtils.d.ts +0 -11
- package/dist/shared/sourcesGridUtils.js +0 -32
- package/dist/shared/types.d.ts +0 -14
- package/dist/shared/types.js +0 -2
- package/dist/shared/util.d.ts +0 -2
- package/dist/shared/util.js +0 -21
- package/dist/util.d.ts +0 -0
- package/dist/util.js +0 -1
- package/esm/MultiVariantBaseRenderer.d.ts +0 -46
- package/esm/MultiVariantBaseRenderer.js +0 -33
- package/esm/VariantFeatureWidget/Checkbox2.d.ts +0 -6
- package/esm/VariantFeatureWidget/Checkbox2.js +0 -5
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakendMultiLevelOptionDialog.d.ts +0 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakendMultiLevelOptionDialog.js +0 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakendSingleLevelOptionDialog.d.ts +0 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/BreakendSingleLevelOptionDialog.js +0 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendWidgetArea.d.ts +0 -4
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/LaunchBreakendWidgetArea.js +0 -24
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/index.d.ts +0 -1
- package/esm/VariantFeatureWidget/LaunchBreakendPanel/index.js +0 -1
- package/esm/VariantFeatureWidget/VariantSampleGrid/index.d.ts +0 -1
- package/esm/VariantFeatureWidget/VariantSampleGrid/index.js +0 -1
- package/esm/VariantFeatureWidget/VariantSampleGrid/util.d.ts +0 -1
- package/esm/VariantFeatureWidget/VariantSampleGrid/util.js +0 -11
- package/esm/extensionPoints.d.ts +0 -2
- package/esm/getMultiVariantFeaturesAutorun.d.ts +0 -18
- package/esm/shared/SharedVariantMixin.d.ts +0 -325
- package/esm/shared/SharedVariantMixin.js +0 -55
- package/esm/shared/components/ui/SetColorDialog.js +0 -45
- package/esm/shared/components/ui/SetColorDialogBulkEditPanel.d.ts +0 -10
- package/esm/shared/components/ui/SetColorDialogBulkEditPanel.js +0 -81
- package/esm/shared/components/ui/SetColorDialogHelpfulTips.d.ts +0 -1
- package/esm/shared/components/ui/SetColorDialogHelpfulTips.js +0 -4
- package/esm/shared/components/ui/SetColorDialogRowPalettizer.d.ts +0 -10
- package/esm/shared/components/ui/SetColorDialogRowPalettizer.js +0 -38
- package/esm/shared/findSecondLargestNumber.d.ts +0 -0
- package/esm/shared/findSecondLargestNumber.js +0 -1
- package/esm/shared/util.d.ts +0 -2
- package/esm/shared/util.js +0 -17
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configuration: AnyConfigurationModel;
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function getMultiVariantSourcesAutorun(self) {
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name: string;
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const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
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const ChordVariantDisplay_1 = __importDefault(require("./ChordVariantDisplay"));
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const MultiLinearVariantRenderer_1 = __importDefault(require("./MultiLinearVariantRenderer"));
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const SplitVcfTabixAdapter_1 = __importDefault(require("./SplitVcfTabixAdapter"));
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const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
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const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
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const MultiVariantClusterGenotypeMatrix_1 = require("./VariantRPC/MultiVariantClusterGenotypeMatrix");
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const MultiVariantGetGenotypeMatrix_1 = require("./VariantRPC/MultiVariantGetGenotypeMatrix");
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const MultiVariantGetSimplifiedFeatures_1 = require("./VariantRPC/MultiVariantGetSimplifiedFeatures");
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const MultiVariantGetSources_1 = require("./VariantRPC/MultiVariantGetSources");
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const VariantTrack_1 = __importDefault(require("./VariantTrack"));
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const VcfAdapter_1 = __importDefault(require("./VcfAdapter"));
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const VcfTabixAdapter_1 = __importDefault(require("./VcfTabixAdapter"));
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const extensionPoints_1 = __importDefault(require("./extensionPoints"));
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class VariantsPlugin extends Plugin_1.default {
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constructor() {
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}
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install(pluginManager) {
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(0, VcfAdapter_1.default)(pluginManager);
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(0, VcfTabixAdapter_1.default)(pluginManager);
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(0, SplitVcfTabixAdapter_1.default)(pluginManager);
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(0, VariantFeatureWidget_1.default)(pluginManager);
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(0, VariantTrack_1.default)(pluginManager);
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(0, extensionPoints_1.default)(pluginManager);
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(0, LinearVariantDisplay_1.default)(pluginManager);
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(0, MultiLinearVariantMatrixDisplay_1.default)(pluginManager);
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(0, MultiLinearVariantDisplay_1.default)(pluginManager);
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(0, MultiLinearVariantRenderer_1.default)(pluginManager);
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(0, MultiLinearVariantMatrixRenderer_1.default)(pluginManager);
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(0, StructuralVariantChordRenderer_1.default)(pluginManager);
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(0, ChordVariantDisplay_1.default)(pluginManager);
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pluginManager.addRpcMethod(() => new MultiVariantGetSources_1.MultiVariantGetSources(pluginManager));
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pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix_1.MultiVariantGetGenotypeMatrix(pluginManager));
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pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix_1.MultiVariantClusterGenotypeMatrix(pluginManager));
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pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures_1.MultiVariantGetSimplifiedFeatures(pluginManager));
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}
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}
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exports.default = VariantsPlugin;
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var VcfFeature_1 = require("./VcfFeature");
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Object.defineProperty(exports, "VcfFeature", { enumerable: true, get: function () { return __importDefault(VcfFeature_1).default; } });
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@@ -1,413 +0,0 @@
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import type { SampleInfo, Source } from './types';
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import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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import type { Feature } from '@jbrowse/core/util';
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import type { Instance } from 'mobx-state-tree';
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export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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} & {
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heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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} & {
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userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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} & {
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blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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key: import("mobx-state-tree").ISimpleType<string>;
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region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
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reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
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isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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}, {
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stopToken: string | undefined;
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filled: boolean;
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reactElement: React.ReactElement | undefined;
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features: Map<string, Feature> | undefined;
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reload: () => void;
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message: React.ReactNode;
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filled?: boolean;
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};
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}) => import("react/jsx-runtime").JSX.Element | undefined;
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renderProps: any;
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} & {
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doReload(): void;
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afterAttach(): void;
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setStatus(message: string): void;
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setLoading(newStopToken: string): void;
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setMessage(messageText: string): void;
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setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
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setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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maxFeatureScreenDensity: {
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type: string;
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description: string;
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defaultValue: number;
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};
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fetchSizeLimit: {
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type: string;
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defaultValue: number;
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description: string;
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};
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height: {
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type: string;
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defaultValue: number;
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description: string;
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};
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mouseover: {
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type: string;
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description: string;
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defaultValue: string;
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contextVariable: string[];
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};
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jexlFilters: {
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type: string;
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description: string;
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defaultValue: never[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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|
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} & {
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|
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type: import("mobx-state-tree").ISimpleType<"LinearBareDisplay">;
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|
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configuration: AnyConfigurationSchemaType;
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|
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} & {
|
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|
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type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
|
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|
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layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
|
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|
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configuration: AnyConfigurationSchemaType;
|
|
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|
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minorAlleleFrequencyFilter: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
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|
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showSidebarLabelsSetting: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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|
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renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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|
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rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
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|
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autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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|
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lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
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|
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jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
|
|
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|
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referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
|
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|
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}, {
|
|
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|
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rendererTypeName: string;
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|
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|
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error: unknown;
|
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|
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message: string | undefined;
|
|
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|
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} & {
|
|
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|
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readonly RenderingComponent: React.FC<{
|
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|
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model: {
|
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|
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id: string;
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|
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type: string;
|
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|
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rpcDriverName: string | undefined;
|
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|
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
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|
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rendererTypeName: string;
|
|
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|
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error: unknown;
|
|
109
|
-
message: string | undefined;
|
|
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|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
111
|
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
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|
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type: import("mobx-state-tree").ISimpleType<string>;
|
|
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|
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
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|
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}, {
|
|
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|
-
rendererTypeName: string;
|
|
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|
-
error: unknown;
|
|
117
|
-
message: string | undefined;
|
|
118
|
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
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|
-
onHorizontalScroll?: () => void;
|
|
120
|
-
blockState?: Record<string, any>;
|
|
121
|
-
}>;
|
|
122
|
-
readonly DisplayBlurb: React.FC<{
|
|
123
|
-
model: {
|
|
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|
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id: string;
|
|
125
|
-
type: string;
|
|
126
|
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rpcDriverName: string | undefined;
|
|
127
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
128
|
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rendererTypeName: string;
|
|
129
|
-
error: unknown;
|
|
130
|
-
message: string | undefined;
|
|
131
|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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|
132
|
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
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|
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type: import("mobx-state-tree").ISimpleType<string>;
|
|
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|
-
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
135
|
-
}, {
|
|
136
|
-
rendererTypeName: string;
|
|
137
|
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error: unknown;
|
|
138
|
-
message: string | undefined;
|
|
139
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
140
|
-
}> | null;
|
|
141
|
-
readonly adapterConfig: any;
|
|
142
|
-
readonly parentTrack: any;
|
|
143
|
-
renderProps(): any;
|
|
144
|
-
readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
|
|
145
|
-
readonly DisplayMessageComponent: undefined | React.FC<any>;
|
|
146
|
-
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
147
|
-
readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
|
|
148
|
-
regionCannotBeRendered(): null;
|
|
149
|
-
} & {
|
|
150
|
-
setMessage(arg?: string): void;
|
|
151
|
-
setError(error?: unknown): void;
|
|
152
|
-
setRpcDriverName(rpcDriverName: string): void;
|
|
153
|
-
reload(): void;
|
|
154
|
-
} & {
|
|
155
|
-
scrollTop: number;
|
|
156
|
-
} & {
|
|
157
|
-
readonly height: number;
|
|
158
|
-
} & {
|
|
159
|
-
setScrollTop(scrollTop: number): void;
|
|
160
|
-
setHeight(displayHeight: number): number;
|
|
161
|
-
resizeHeight(distance: number): number;
|
|
162
|
-
} & {
|
|
163
|
-
featureDensityStatsP: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
164
|
-
featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
|
|
165
|
-
currStatsBpPerPx: number;
|
|
166
|
-
} & {
|
|
167
|
-
readonly currentBytesRequested: number;
|
|
168
|
-
readonly currentFeatureScreenDensity: number;
|
|
169
|
-
readonly maxFeatureScreenDensity: any;
|
|
170
|
-
readonly featureDensityStatsReady: boolean;
|
|
171
|
-
readonly maxAllowableBytes: number;
|
|
172
|
-
} & {
|
|
173
|
-
afterAttach(): void;
|
|
174
|
-
} & {
|
|
175
|
-
setCurrStatsBpPerPx(n: number): void;
|
|
176
|
-
setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
|
|
177
|
-
getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
|
|
178
|
-
setFeatureDensityStatsP(arg: any): void;
|
|
179
|
-
setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
|
|
180
|
-
clearFeatureDensityStats(): void;
|
|
181
|
-
} & {
|
|
182
|
-
readonly regionTooLarge: boolean;
|
|
183
|
-
readonly regionTooLargeReason: string;
|
|
184
|
-
} & {
|
|
185
|
-
readonly statsReadyAndRegionNotTooLarge: boolean;
|
|
186
|
-
regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
|
|
187
|
-
regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
|
|
188
|
-
} & {
|
|
189
|
-
mouseoverExtraInformation: string | undefined;
|
|
190
|
-
featureIdUnderMouse: undefined | string;
|
|
191
|
-
contextMenuFeature: undefined | Feature;
|
|
192
|
-
} & {
|
|
193
|
-
readonly DisplayMessageComponent: undefined | React.FC<any>;
|
|
194
|
-
readonly blockType: "staticBlocks" | "dynamicBlocks";
|
|
195
|
-
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
196
|
-
} & {
|
|
197
|
-
readonly renderDelay: number;
|
|
198
|
-
readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
|
|
199
|
-
readonly selectedFeatureId: string | undefined;
|
|
200
|
-
copyInfoToClipboard(feature: Feature): void;
|
|
201
|
-
} & {
|
|
202
|
-
readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
|
|
203
|
-
readonly featureUnderMouse: Feature | undefined;
|
|
204
|
-
readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
|
|
205
|
-
label?: string;
|
|
206
|
-
description?: string;
|
|
207
|
-
refName: string;
|
|
208
|
-
}]>;
|
|
209
|
-
getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
|
|
210
|
-
getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
|
|
211
|
-
label?: string;
|
|
212
|
-
description?: string;
|
|
213
|
-
refName: string;
|
|
214
|
-
}]) | undefined;
|
|
215
|
-
searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
|
|
216
|
-
label?: string;
|
|
217
|
-
description?: string;
|
|
218
|
-
refName: string;
|
|
219
|
-
}]) | undefined;
|
|
220
|
-
} & {
|
|
221
|
-
addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
|
|
222
|
-
deleteBlock(key: string): void;
|
|
223
|
-
selectFeature(feature: Feature): void;
|
|
224
|
-
navToFeature(feature: Feature): void;
|
|
225
|
-
clearFeatureSelection(): void;
|
|
226
|
-
setFeatureIdUnderMouse(feature?: string): void;
|
|
227
|
-
setContextMenuFeature(feature?: Feature): void;
|
|
228
|
-
setMouseoverExtraInformation(extra?: string): void;
|
|
229
|
-
} & {
|
|
230
|
-
reload(): Promise<void>;
|
|
231
|
-
} & {
|
|
232
|
-
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
233
|
-
contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
234
|
-
renderProps(): any;
|
|
235
|
-
} & {
|
|
236
|
-
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
|
|
237
|
-
afterAttach(): void;
|
|
238
|
-
} & {
|
|
239
|
-
readonly rendererConfig: {
|
|
240
|
-
[x: string]: any;
|
|
241
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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242
|
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setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
|
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243
|
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[x: string]: any;
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244
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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245
|
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setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
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246
|
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[x: string]: any;
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247
|
-
} & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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248
|
-
} & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
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249
|
-
} & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
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250
|
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readonly rendererTypeName: any;
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251
|
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} & {
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252
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renderProps(): any;
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253
|
-
} & {
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254
|
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sourcesLoadingStopToken: string | undefined;
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255
|
-
simplifiedFeaturesStopToken: string | undefined;
|
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256
|
-
featureUnderMouseVolatile: Feature | undefined;
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257
|
-
sourcesVolatile: Source[] | undefined;
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258
|
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featuresVolatile: Feature[] | undefined;
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259
|
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hasPhased: boolean;
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260
|
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sampleInfo: undefined | Record<string, SampleInfo>;
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261
|
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hoveredGenotype: {
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262
|
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genotype: string;
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263
|
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name: string;
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264
|
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} | undefined;
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265
|
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} & {
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266
|
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setJexlFilters(f?: string[]): void;
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267
|
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setRowHeight(arg: number): void;
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268
|
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setHoveredGenotype(arg?: {
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269
|
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genotype: string;
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270
|
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name: string;
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271
|
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}): void;
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272
|
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setFeatures(f: Feature[]): void;
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273
|
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setLayout(layout: Source[]): void;
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274
|
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clearLayout(): void;
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275
|
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setSourcesLoading(str: string): void;
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276
|
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setSimplifiedFeaturesLoading(str: string): void;
|
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277
|
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setSources(sources: Source[]): void;
|
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278
|
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setMafFilter(arg: number): void;
|
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279
|
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setShowSidebarLabels(arg: boolean): void;
|
|
280
|
-
setPhasedMode(arg: string): void;
|
|
281
|
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setAutoHeight(arg: boolean): void;
|
|
282
|
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setHasPhased(arg: boolean): void;
|
|
283
|
-
setSampleInfo(arg: Record<string, SampleInfo>): void;
|
|
284
|
-
setReferenceDrawingMode(arg: string): void;
|
|
285
|
-
} & {
|
|
286
|
-
readonly activeFilters: any;
|
|
287
|
-
readonly preSources: Source[] | undefined;
|
|
288
|
-
readonly sourcesWithoutLayout: {
|
|
289
|
-
label: string;
|
|
290
|
-
id: string;
|
|
291
|
-
baseUri?: string;
|
|
292
|
-
name: string;
|
|
293
|
-
color?: string;
|
|
294
|
-
group?: string;
|
|
295
|
-
HP?: number;
|
|
296
|
-
}[] | undefined;
|
|
297
|
-
readonly sources: {
|
|
298
|
-
label: string;
|
|
299
|
-
id: string;
|
|
300
|
-
baseUri?: string;
|
|
301
|
-
name: string;
|
|
302
|
-
color?: string;
|
|
303
|
-
group?: string;
|
|
304
|
-
HP?: number;
|
|
305
|
-
}[] | undefined;
|
|
306
|
-
} & {
|
|
307
|
-
readonly sourceMap: {
|
|
308
|
-
[k: string]: {
|
|
309
|
-
label: string;
|
|
310
|
-
id: string;
|
|
311
|
-
baseUri?: string;
|
|
312
|
-
name: string;
|
|
313
|
-
color?: string;
|
|
314
|
-
group?: string;
|
|
315
|
-
HP?: number;
|
|
316
|
-
};
|
|
317
|
-
} | undefined;
|
|
318
|
-
readonly rowHeight: number;
|
|
319
|
-
adapterProps(): any;
|
|
320
|
-
trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
|
|
321
|
-
label: string;
|
|
322
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
323
|
-
muiName: string;
|
|
324
|
-
};
|
|
325
|
-
type: string;
|
|
326
|
-
checked: boolean;
|
|
327
|
-
onClick: () => void;
|
|
328
|
-
subMenu?: undefined;
|
|
329
|
-
} | {
|
|
330
|
-
label: string;
|
|
331
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
332
|
-
muiName: string;
|
|
333
|
-
};
|
|
334
|
-
subMenu: ({
|
|
335
|
-
label: string;
|
|
336
|
-
disabled: boolean;
|
|
337
|
-
onClick: () => void;
|
|
338
|
-
type?: undefined;
|
|
339
|
-
checked?: undefined;
|
|
340
|
-
} | {
|
|
341
|
-
label: string;
|
|
342
|
-
type: string;
|
|
343
|
-
checked: boolean;
|
|
344
|
-
onClick: () => void;
|
|
345
|
-
disabled?: undefined;
|
|
346
|
-
})[];
|
|
347
|
-
type?: undefined;
|
|
348
|
-
checked?: undefined;
|
|
349
|
-
onClick?: undefined;
|
|
350
|
-
} | {
|
|
351
|
-
label: string;
|
|
352
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
353
|
-
muiName: string;
|
|
354
|
-
};
|
|
355
|
-
subMenu: ({
|
|
356
|
-
label: string;
|
|
357
|
-
type: string;
|
|
358
|
-
checked: boolean;
|
|
359
|
-
onClick: () => void;
|
|
360
|
-
disabled?: undefined;
|
|
361
|
-
} | {
|
|
362
|
-
label: string;
|
|
363
|
-
disabled: boolean;
|
|
364
|
-
checked: boolean;
|
|
365
|
-
type: string;
|
|
366
|
-
onClick: () => void;
|
|
367
|
-
})[];
|
|
368
|
-
type?: undefined;
|
|
369
|
-
checked?: undefined;
|
|
370
|
-
onClick?: undefined;
|
|
371
|
-
} | {
|
|
372
|
-
label: string;
|
|
373
|
-
type: string;
|
|
374
|
-
subMenu: {
|
|
375
|
-
label: string;
|
|
376
|
-
type: string;
|
|
377
|
-
checked: boolean;
|
|
378
|
-
onClick: () => void;
|
|
379
|
-
}[];
|
|
380
|
-
icon?: undefined;
|
|
381
|
-
checked?: undefined;
|
|
382
|
-
onClick?: undefined;
|
|
383
|
-
} | {
|
|
384
|
-
label: string;
|
|
385
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
386
|
-
muiName: string;
|
|
387
|
-
};
|
|
388
|
-
subMenu: {
|
|
389
|
-
label: string;
|
|
390
|
-
onClick: () => void;
|
|
391
|
-
}[];
|
|
392
|
-
type?: undefined;
|
|
393
|
-
checked?: undefined;
|
|
394
|
-
onClick?: undefined;
|
|
395
|
-
} | {
|
|
396
|
-
label: string;
|
|
397
|
-
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
398
|
-
muiName: string;
|
|
399
|
-
};
|
|
400
|
-
onClick: () => void;
|
|
401
|
-
type?: undefined;
|
|
402
|
-
checked?: undefined;
|
|
403
|
-
subMenu?: undefined;
|
|
404
|
-
})[];
|
|
405
|
-
} & {
|
|
406
|
-
readonly canDisplayLabels: boolean;
|
|
407
|
-
readonly totalHeight: number;
|
|
408
|
-
readonly featuresReady: boolean;
|
|
409
|
-
} & {
|
|
410
|
-
renderProps(): any;
|
|
411
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
412
|
-
export type MultiVariantBaseStateModel = ReturnType<typeof MultiVariantBaseModelF>;
|
|
413
|
-
export type MultiVariantBaseModel = Instance<MultiVariantBaseStateModel>;
|