@jbrowse/plugin-alignments 2.17.0 → 3.0.0
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/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -3
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +25 -24
- package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js +0 -1
- package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js +0 -1
- package/dist/AlignmentsFeatureDetail/Flags.d.ts +1 -2
- package/dist/AlignmentsFeatureDetail/Flags.js +8 -10
- package/dist/AlignmentsFeatureDetail/Formatter.d.ts +1 -2
- package/dist/AlignmentsFeatureDetail/Formatter.js +11 -39
- package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts +4 -7
- package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js +46 -54
- package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts +4 -7
- package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js +58 -61
- package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts +3 -4
- package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js +4 -5
- package/dist/AlignmentsFeatureDetail/PairLink.d.ts +2 -3
- package/dist/AlignmentsFeatureDetail/PairLink.js +3 -7
- package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts +3 -4
- package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js +6 -9
- package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts +2 -3
- package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js +21 -31
- package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts +2 -2
- package/dist/AlignmentsFeatureDetail/getSAFeatures.js +0 -4
- package/dist/AlignmentsFeatureDetail/index.d.ts +1 -1
- package/dist/AlignmentsFeatureDetail/index.js +17 -7
- package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +2 -2
- package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts +2 -2
- package/dist/AlignmentsFeatureDetail/stateModelFactory.js +1 -1
- package/dist/AlignmentsFeatureDetail/tagInfo.js +1 -1
- package/dist/AlignmentsFeatureDetail/util.d.ts +1 -1
- package/dist/AlignmentsTrack/configSchemaF.d.ts +1 -1
- package/dist/AlignmentsTrack/configSchemaF.js +1 -8
- package/dist/AlignmentsTrack/index.d.ts +1 -1
- package/dist/AlignmentsTrack/index.js +0 -3
- package/dist/BamAdapter/BamAdapter.d.ts +6 -5
- package/dist/BamAdapter/BamAdapter.js +21 -39
- package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -3
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +0 -3
- package/dist/BamAdapter/configSchema.d.ts +0 -17
- package/dist/BamAdapter/configSchema.js +1 -22
- package/dist/BamAdapter/index.d.ts +1 -1
- package/dist/BamAdapter/index.js +17 -7
- package/dist/CramAdapter/CramAdapter.d.ts +6 -9
- package/dist/CramAdapter/CramAdapter.js +25 -43
- package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +3 -3
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +0 -17
- package/dist/CramAdapter/CramTestAdapters.d.ts +3 -3
- package/dist/CramAdapter/CramTestAdapters.js +6 -6
- package/dist/CramAdapter/configSchema.d.ts +0 -14
- package/dist/CramAdapter/configSchema.js +1 -19
- package/dist/CramAdapter/index.d.ts +1 -1
- package/dist/CramAdapter/index.js +17 -8
- package/dist/CramAdapter/util.d.ts +2 -2
- package/dist/CramAdapter/util.js +1 -24
- package/dist/GuessAlignmentsTypes/index.d.ts +1 -1
- package/dist/GuessAlignmentsTypes/index.js +19 -34
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +2 -2
- package/dist/HtsgetBamAdapter/configSchema.d.ts +0 -9
- package/dist/HtsgetBamAdapter/configSchema.js +1 -14
- package/dist/HtsgetBamAdapter/index.d.ts +1 -1
- package/dist/HtsgetBamAdapter/index.js +18 -8
- package/dist/LinearAlignmentsDisplay/alignmentsModel.d.ts +2 -5
- package/dist/LinearAlignmentsDisplay/alignmentsModel.js +1 -31
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -3
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -18
- package/dist/LinearAlignmentsDisplay/configSchema.d.ts +2 -16
- package/dist/LinearAlignmentsDisplay/configSchema.js +3 -20
- package/dist/LinearAlignmentsDisplay/index.d.ts +1 -1
- package/dist/LinearAlignmentsDisplay/index.js +1 -2
- package/dist/LinearAlignmentsDisplay/model.d.ts +7 -77
- package/dist/LinearAlignmentsDisplay/model.js +10 -85
- package/dist/LinearAlignmentsDisplay/util.d.ts +1 -1
- package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +52 -164
- package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +71 -145
- package/dist/LinearPileupDisplay/components/ColorByTagDialog.d.ts +1 -2
- package/dist/LinearPileupDisplay/components/ColorByTagDialog.js +12 -41
- package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts +3 -4
- package/dist/LinearPileupDisplay/components/GroupByDialog.js +106 -92
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +3 -8
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +3 -7
- package/dist/LinearPileupDisplay/components/SetFeatureHeightDialog.d.ts +1 -2
- package/dist/LinearPileupDisplay/components/SetFeatureHeightDialog.js +15 -44
- package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts +1 -2
- package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.js +12 -40
- package/dist/LinearPileupDisplay/components/SortByTagDialog.d.ts +1 -2
- package/dist/LinearPileupDisplay/components/SortByTagDialog.js +17 -46
- package/dist/LinearPileupDisplay/configSchema.d.ts +13 -16
- package/dist/LinearPileupDisplay/configSchema.js +12 -30
- package/dist/LinearPileupDisplay/index.d.ts +1 -1
- package/dist/LinearPileupDisplay/index.js +2 -2
- package/dist/LinearPileupDisplay/model.d.ts +123 -111
- package/dist/LinearPileupDisplay/model.js +29 -109
- package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +2 -3
- package/dist/LinearReadArcsDisplay/components/ReactComponent.js +6 -33
- package/dist/LinearReadArcsDisplay/configSchema.d.ts +12 -20
- package/dist/LinearReadArcsDisplay/configSchema.js +8 -31
- package/dist/LinearReadArcsDisplay/drawFeats.d.ts +1 -1
- package/dist/LinearReadArcsDisplay/drawFeats.js +1 -9
- package/dist/LinearReadArcsDisplay/index.d.ts +1 -1
- package/dist/LinearReadArcsDisplay/index.js +18 -9
- package/dist/LinearReadArcsDisplay/model.d.ts +16 -94
- package/dist/LinearReadArcsDisplay/model.js +34 -111
- package/dist/LinearReadArcsDisplay/util.d.ts +1 -1
- package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +2 -3
- package/dist/LinearReadCloudDisplay/components/ReactComponent.js +6 -33
- package/dist/LinearReadCloudDisplay/configSchema.d.ts +5 -17
- package/dist/LinearReadCloudDisplay/configSchema.js +3 -28
- package/dist/LinearReadCloudDisplay/drawFeats.d.ts +1 -1
- package/dist/LinearReadCloudDisplay/drawFeats.js +2 -2
- package/dist/LinearReadCloudDisplay/drawLongReadChains.d.ts +4 -4
- package/dist/LinearReadCloudDisplay/drawLongReadChains.js +1 -4
- package/dist/LinearReadCloudDisplay/drawPairChains.d.ts +4 -4
- package/dist/LinearReadCloudDisplay/drawPairChains.js +0 -3
- package/dist/LinearReadCloudDisplay/index.d.ts +1 -1
- package/dist/LinearReadCloudDisplay/index.js +18 -9
- package/dist/LinearReadCloudDisplay/model.d.ts +14 -56
- package/dist/LinearReadCloudDisplay/model.js +34 -75
- package/dist/LinearReadCloudDisplay/util.js +0 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +2 -3
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +16 -55
- package/dist/LinearSNPCoverageDisplay/configSchema.d.ts +17 -22
- package/dist/LinearSNPCoverageDisplay/configSchema.js +16 -32
- package/dist/LinearSNPCoverageDisplay/index.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/index.js +1 -2
- package/dist/LinearSNPCoverageDisplay/model.d.ts +13 -54
- package/dist/LinearSNPCoverageDisplay/model.js +69 -159
- package/dist/MismatchParser/cigarToMismatches.d.ts +2 -3
- package/dist/MismatchParser/cigarToMismatches.js +4 -7
- package/dist/MismatchParser/getNextRefPos.js +0 -2
- package/dist/MismatchParser/index.d.ts +3 -4
- package/dist/MismatchParser/index.js +1 -9
- package/dist/MismatchParser/mdToMismatches.d.ts +2 -3
- package/dist/MismatchParser/mdToMismatches.js +0 -6
- package/dist/ModificationParser/index.d.ts +1 -1
- package/dist/ModificationParser/index.js +1 -18
- package/dist/PileupRPC/base.d.ts +2 -2
- package/dist/PileupRPC/base.js +0 -1
- package/dist/PileupRPC/index.d.ts +1 -1
- package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts +2 -3
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js +1 -2
- package/dist/PileupRPC/methods/GetReducedFeatures.d.ts +2 -3
- package/dist/PileupRPC/methods/GetReducedFeatures.js +3 -5
- package/dist/PileupRPC/methods/GetVisibleModifications.d.ts +3 -4
- package/dist/PileupRPC/methods/GetVisibleModifications.js +1 -1
- package/dist/PileupRPC/util.d.ts +1 -1
- package/dist/PileupRenderer/PileupLayoutSession.d.ts +5 -5
- package/dist/PileupRenderer/PileupLayoutSession.js +2 -5
- package/dist/PileupRenderer/PileupRenderer.d.ts +14 -24
- package/dist/PileupRenderer/PileupRenderer.js +28 -23
- package/dist/PileupRenderer/colorBy.d.ts +2 -2
- package/dist/PileupRenderer/colorBy.js +0 -6
- package/dist/PileupRenderer/components/PileupRendering.d.ts +2 -3
- package/dist/PileupRenderer/components/PileupRendering.js +15 -43
- package/dist/PileupRenderer/configSchema.d.ts +5 -31
- package/dist/PileupRenderer/configSchema.js +6 -35
- package/dist/PileupRenderer/getAlignmentShapeColor.d.ts +2 -2
- package/dist/PileupRenderer/getAlignmentShapeColor.js +1 -6
- package/dist/PileupRenderer/index.d.ts +1 -1
- package/dist/PileupRenderer/index.js +1 -1
- package/dist/PileupRenderer/layoutFeature.d.ts +2 -2
- package/dist/PileupRenderer/layoutFeature.js +0 -1
- package/dist/PileupRenderer/layoutFeatures.d.ts +5 -2
- package/dist/PileupRenderer/layoutFeatures.js +6 -4
- package/dist/PileupRenderer/makeImageData.d.ts +3 -4
- package/dist/PileupRenderer/makeImageData.js +10 -2
- package/dist/PileupRenderer/renderAlignment.d.ts +3 -3
- package/dist/PileupRenderer/renderAlignment.js +3 -5
- package/dist/PileupRenderer/renderAlignmentShape.d.ts +3 -3
- package/dist/PileupRenderer/renderAlignmentShape.js +1 -1
- package/dist/PileupRenderer/renderMethylation.d.ts +4 -4
- package/dist/PileupRenderer/renderMethylation.js +0 -4
- package/dist/PileupRenderer/renderMismatches.d.ts +5 -4
- package/dist/PileupRenderer/renderMismatches.js +19 -25
- package/dist/PileupRenderer/renderModifications.d.ts +3 -3
- package/dist/PileupRenderer/renderModifications.js +1 -3
- package/dist/PileupRenderer/renderPerBaseLettering.d.ts +2 -2
- package/dist/PileupRenderer/renderPerBaseLettering.js +0 -1
- package/dist/PileupRenderer/renderPerBaseQuality.d.ts +2 -2
- package/dist/PileupRenderer/renderPerBaseQuality.js +2 -2
- package/dist/PileupRenderer/renderSoftClipping.d.ts +5 -5
- package/dist/PileupRenderer/renderSoftClipping.js +0 -4
- package/dist/PileupRenderer/sortUtil.d.ts +2 -2
- package/dist/PileupRenderer/sortUtil.js +1 -4
- package/dist/PileupRenderer/types.d.ts +26 -0
- package/dist/PileupRenderer/types.js +2 -0
- package/dist/PileupRenderer/util.d.ts +2 -2
- package/dist/PileupRenderer/util.js +1 -3
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +4 -3
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -6
- package/dist/SNPCoverageAdapter/configSchema.d.ts +0 -4
- package/dist/SNPCoverageAdapter/configSchema.js +1 -8
- package/dist/SNPCoverageAdapter/generateCoverageBins.d.ts +4 -8
- package/dist/SNPCoverageAdapter/generateCoverageBins.js +25 -247
- package/dist/SNPCoverageAdapter/index.d.ts +1 -1
- package/dist/SNPCoverageAdapter/index.js +17 -7
- package/dist/SNPCoverageAdapter/processDepth.d.ts +8 -0
- package/dist/SNPCoverageAdapter/processDepth.js +38 -0
- package/dist/SNPCoverageAdapter/processMismatches.d.ts +9 -0
- package/dist/SNPCoverageAdapter/processMismatches.js +58 -0
- package/dist/SNPCoverageAdapter/processModifications.d.ts +10 -0
- package/dist/SNPCoverageAdapter/processModifications.js +49 -0
- package/dist/SNPCoverageAdapter/processReferenceCpGs.d.ts +9 -0
- package/dist/SNPCoverageAdapter/processReferenceCpGs.js +63 -0
- package/dist/SNPCoverageAdapter/util.d.ts +10 -0
- package/dist/SNPCoverageAdapter/util.js +41 -0
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -18
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +35 -288
- package/dist/SNPCoverageRenderer/configSchema.d.ts +3 -18
- package/dist/SNPCoverageRenderer/configSchema.js +4 -22
- package/dist/SNPCoverageRenderer/index.d.ts +1 -1
- package/dist/SNPCoverageRenderer/index.js +2 -2
- package/dist/SNPCoverageRenderer/makeImage.d.ts +2 -0
- package/dist/SNPCoverageRenderer/makeImage.js +270 -0
- package/dist/SNPCoverageRenderer/types.d.ts +19 -0
- package/dist/SNPCoverageRenderer/types.js +2 -0
- package/dist/index.d.ts +2 -2
- package/dist/index.js +29 -19
- package/dist/shared/afterAttach.d.ts +1 -1
- package/dist/shared/afterAttach.js +0 -2
- package/dist/shared/color.d.ts +1 -1
- package/dist/shared/color.js +0 -8
- package/dist/shared/components/BaseDisplayComponent.d.ts +3 -4
- package/dist/shared/components/BaseDisplayComponent.js +13 -19
- package/dist/shared/components/FilterByTagDialog.d.ts +2 -3
- package/dist/shared/components/FilterByTagDialog.js +44 -94
- package/dist/shared/fetchChains.d.ts +2 -2
- package/dist/shared/fetchChains.js +1 -2
- package/dist/shared/getMaximumModificationAtEachPosition.d.ts +1 -1
- package/dist/shared/getMaximumModificationAtEachPosition.js +1 -2
- package/dist/shared/getUniqueModifications.d.ts +5 -5
- package/dist/shared/getUniqueTags.d.ts +4 -4
- package/dist/shared/renderSvgUtil.d.ts +1 -2
- package/dist/shared/renderSvgUtil.js +20 -19
- package/dist/shared/util.d.ts +11 -1
- package/dist/shared/util.js +27 -1
- package/dist/util.d.ts +4 -4
- package/dist/util.js +3 -9
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +2 -3
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +8 -17
- package/esm/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js +0 -1
- package/esm/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js +0 -1
- package/esm/AlignmentsFeatureDetail/Flags.d.ts +1 -2
- package/esm/AlignmentsFeatureDetail/Flags.js +8 -10
- package/esm/AlignmentsFeatureDetail/Formatter.d.ts +1 -2
- package/esm/AlignmentsFeatureDetail/Formatter.js +11 -16
- package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts +4 -7
- package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js +30 -48
- package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts +4 -7
- package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js +41 -54
- package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts +3 -4
- package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js +4 -5
- package/esm/AlignmentsFeatureDetail/PairLink.d.ts +2 -3
- package/esm/AlignmentsFeatureDetail/PairLink.js +3 -4
- package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts +3 -4
- package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js +6 -9
- package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts +2 -3
- package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js +22 -29
- package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts +2 -2
- package/esm/AlignmentsFeatureDetail/getSAFeatures.js +0 -4
- package/esm/AlignmentsFeatureDetail/index.d.ts +1 -1
- package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts +2 -2
- package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +2 -2
- package/esm/AlignmentsFeatureDetail/stateModelFactory.js +1 -1
- package/esm/AlignmentsFeatureDetail/tagInfo.js +1 -1
- package/esm/AlignmentsFeatureDetail/util.d.ts +1 -1
- package/esm/AlignmentsTrack/configSchemaF.d.ts +1 -1
- package/esm/AlignmentsTrack/configSchemaF.js +1 -8
- package/esm/AlignmentsTrack/index.d.ts +1 -1
- package/esm/AlignmentsTrack/index.js +0 -3
- package/esm/BamAdapter/BamAdapter.d.ts +6 -5
- package/esm/BamAdapter/BamAdapter.js +19 -37
- package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +3 -3
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +0 -3
- package/esm/BamAdapter/configSchema.d.ts +0 -17
- package/esm/BamAdapter/configSchema.js +1 -22
- package/esm/BamAdapter/index.d.ts +1 -1
- package/esm/CramAdapter/CramAdapter.d.ts +6 -9
- package/esm/CramAdapter/CramAdapter.js +24 -42
- package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +3 -3
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +0 -17
- package/esm/CramAdapter/CramTestAdapters.d.ts +3 -3
- package/esm/CramAdapter/CramTestAdapters.js +6 -6
- package/esm/CramAdapter/configSchema.d.ts +0 -14
- package/esm/CramAdapter/configSchema.js +1 -19
- package/esm/CramAdapter/index.d.ts +1 -1
- package/esm/CramAdapter/index.js +0 -1
- package/esm/CramAdapter/util.d.ts +2 -2
- package/esm/CramAdapter/util.js +1 -24
- package/esm/GuessAlignmentsTypes/index.d.ts +1 -1
- package/esm/GuessAlignmentsTypes/index.js +20 -35
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +2 -2
- package/esm/HtsgetBamAdapter/configSchema.d.ts +0 -9
- package/esm/HtsgetBamAdapter/configSchema.js +1 -14
- package/esm/HtsgetBamAdapter/index.d.ts +1 -1
- package/esm/HtsgetBamAdapter/index.js +1 -1
- package/esm/LinearAlignmentsDisplay/alignmentsModel.d.ts +2 -5
- package/esm/LinearAlignmentsDisplay/alignmentsModel.js +1 -31
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -3
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +10 -15
- package/esm/LinearAlignmentsDisplay/configSchema.d.ts +2 -16
- package/esm/LinearAlignmentsDisplay/configSchema.js +3 -20
- package/esm/LinearAlignmentsDisplay/index.d.ts +1 -1
- package/esm/LinearAlignmentsDisplay/index.js +1 -2
- package/esm/LinearAlignmentsDisplay/model.d.ts +7 -77
- package/esm/LinearAlignmentsDisplay/model.js +11 -86
- package/esm/LinearAlignmentsDisplay/util.d.ts +1 -1
- package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +52 -164
- package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +56 -140
- package/esm/LinearPileupDisplay/components/ColorByTagDialog.d.ts +1 -2
- package/esm/LinearPileupDisplay/components/ColorByTagDialog.js +12 -18
- package/esm/LinearPileupDisplay/components/GroupByDialog.d.ts +3 -4
- package/esm/LinearPileupDisplay/components/GroupByDialog.js +106 -69
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +3 -8
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +3 -4
- package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.d.ts +1 -2
- package/esm/LinearPileupDisplay/components/SetFeatureHeightDialog.js +15 -21
- package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts +1 -2
- package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.js +12 -17
- package/esm/LinearPileupDisplay/components/SortByTagDialog.d.ts +1 -2
- package/esm/LinearPileupDisplay/components/SortByTagDialog.js +17 -23
- package/esm/LinearPileupDisplay/configSchema.d.ts +13 -16
- package/esm/LinearPileupDisplay/configSchema.js +12 -30
- package/esm/LinearPileupDisplay/index.d.ts +1 -1
- package/esm/LinearPileupDisplay/index.js +2 -2
- package/esm/LinearPileupDisplay/model.d.ts +123 -111
- package/esm/LinearPileupDisplay/model.js +13 -103
- package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +2 -3
- package/esm/LinearReadArcsDisplay/components/ReactComponent.js +6 -10
- package/esm/LinearReadArcsDisplay/configSchema.d.ts +12 -20
- package/esm/LinearReadArcsDisplay/configSchema.js +8 -31
- package/esm/LinearReadArcsDisplay/drawFeats.d.ts +1 -1
- package/esm/LinearReadArcsDisplay/drawFeats.js +1 -9
- package/esm/LinearReadArcsDisplay/index.d.ts +1 -1
- package/esm/LinearReadArcsDisplay/index.js +1 -2
- package/esm/LinearReadArcsDisplay/model.d.ts +16 -94
- package/esm/LinearReadArcsDisplay/model.js +18 -105
- package/esm/LinearReadArcsDisplay/util.d.ts +1 -1
- package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +2 -3
- package/esm/LinearReadCloudDisplay/components/ReactComponent.js +6 -10
- package/esm/LinearReadCloudDisplay/configSchema.d.ts +5 -17
- package/esm/LinearReadCloudDisplay/configSchema.js +3 -28
- package/esm/LinearReadCloudDisplay/drawFeats.d.ts +1 -1
- package/esm/LinearReadCloudDisplay/drawFeats.js +2 -2
- package/esm/LinearReadCloudDisplay/drawLongReadChains.d.ts +4 -4
- package/esm/LinearReadCloudDisplay/drawLongReadChains.js +1 -4
- package/esm/LinearReadCloudDisplay/drawPairChains.d.ts +4 -4
- package/esm/LinearReadCloudDisplay/drawPairChains.js +0 -3
- package/esm/LinearReadCloudDisplay/index.d.ts +1 -1
- package/esm/LinearReadCloudDisplay/index.js +1 -2
- package/esm/LinearReadCloudDisplay/model.d.ts +14 -56
- package/esm/LinearReadCloudDisplay/model.js +17 -68
- package/esm/LinearReadCloudDisplay/util.js +0 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +2 -3
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +16 -52
- package/esm/LinearSNPCoverageDisplay/configSchema.d.ts +17 -22
- package/esm/LinearSNPCoverageDisplay/configSchema.js +16 -32
- package/esm/LinearSNPCoverageDisplay/index.d.ts +1 -1
- package/esm/LinearSNPCoverageDisplay/index.js +1 -2
- package/esm/LinearSNPCoverageDisplay/model.d.ts +13 -54
- package/esm/LinearSNPCoverageDisplay/model.js +53 -153
- package/esm/MismatchParser/cigarToMismatches.d.ts +2 -3
- package/esm/MismatchParser/cigarToMismatches.js +4 -7
- package/esm/MismatchParser/getNextRefPos.js +0 -2
- package/esm/MismatchParser/index.d.ts +3 -4
- package/esm/MismatchParser/index.js +1 -9
- package/esm/MismatchParser/mdToMismatches.d.ts +2 -3
- package/esm/MismatchParser/mdToMismatches.js +0 -6
- package/esm/ModificationParser/index.d.ts +1 -1
- package/esm/ModificationParser/index.js +1 -18
- package/esm/PileupRPC/base.d.ts +2 -2
- package/esm/PileupRPC/base.js +0 -1
- package/esm/PileupRPC/index.d.ts +1 -1
- package/esm/PileupRPC/index.js +1 -1
- package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +2 -3
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js +1 -2
- package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +2 -3
- package/esm/PileupRPC/methods/GetReducedFeatures.js +3 -5
- package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +3 -4
- package/esm/PileupRPC/methods/GetVisibleModifications.js +1 -1
- package/esm/PileupRPC/util.d.ts +1 -1
- package/esm/PileupRenderer/PileupLayoutSession.d.ts +5 -5
- package/esm/PileupRenderer/PileupLayoutSession.js +2 -5
- package/esm/PileupRenderer/PileupRenderer.d.ts +14 -24
- package/esm/PileupRenderer/PileupRenderer.js +12 -17
- package/esm/PileupRenderer/colorBy.d.ts +2 -2
- package/esm/PileupRenderer/colorBy.js +1 -7
- package/esm/PileupRenderer/components/PileupRendering.d.ts +2 -3
- package/esm/PileupRenderer/components/PileupRendering.js +15 -20
- package/esm/PileupRenderer/configSchema.d.ts +5 -31
- package/esm/PileupRenderer/configSchema.js +6 -35
- package/esm/PileupRenderer/getAlignmentShapeColor.d.ts +2 -2
- package/esm/PileupRenderer/getAlignmentShapeColor.js +2 -7
- package/esm/PileupRenderer/index.d.ts +1 -1
- package/esm/PileupRenderer/index.js +1 -1
- package/esm/PileupRenderer/layoutFeature.d.ts +2 -2
- package/esm/PileupRenderer/layoutFeature.js +0 -1
- package/esm/PileupRenderer/layoutFeatures.d.ts +5 -2
- package/esm/PileupRenderer/layoutFeatures.js +7 -5
- package/esm/PileupRenderer/makeImageData.d.ts +3 -4
- package/esm/PileupRenderer/makeImageData.js +10 -2
- package/esm/PileupRenderer/renderAlignment.d.ts +3 -3
- package/esm/PileupRenderer/renderAlignment.js +3 -5
- package/esm/PileupRenderer/renderAlignmentShape.d.ts +3 -3
- package/esm/PileupRenderer/renderAlignmentShape.js +1 -1
- package/esm/PileupRenderer/renderMethylation.d.ts +4 -4
- package/esm/PileupRenderer/renderMethylation.js +0 -4
- package/esm/PileupRenderer/renderMismatches.d.ts +5 -4
- package/esm/PileupRenderer/renderMismatches.js +19 -25
- package/esm/PileupRenderer/renderModifications.d.ts +3 -3
- package/esm/PileupRenderer/renderModifications.js +1 -3
- package/esm/PileupRenderer/renderPerBaseLettering.d.ts +2 -2
- package/esm/PileupRenderer/renderPerBaseLettering.js +0 -1
- package/esm/PileupRenderer/renderPerBaseQuality.d.ts +2 -2
- package/esm/PileupRenderer/renderPerBaseQuality.js +2 -2
- package/esm/PileupRenderer/renderSoftClipping.d.ts +5 -5
- package/esm/PileupRenderer/renderSoftClipping.js +1 -5
- package/esm/PileupRenderer/sortUtil.d.ts +2 -2
- package/esm/PileupRenderer/sortUtil.js +1 -4
- package/esm/PileupRenderer/types.d.ts +26 -0
- package/esm/PileupRenderer/types.js +1 -0
- package/esm/PileupRenderer/util.d.ts +2 -2
- package/esm/PileupRenderer/util.js +1 -3
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +4 -3
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +5 -7
- package/esm/SNPCoverageAdapter/configSchema.d.ts +0 -4
- package/esm/SNPCoverageAdapter/configSchema.js +1 -8
- package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts +4 -8
- package/esm/SNPCoverageAdapter/generateCoverageBins.js +24 -246
- package/esm/SNPCoverageAdapter/index.d.ts +1 -1
- package/esm/SNPCoverageAdapter/processDepth.d.ts +8 -0
- package/esm/SNPCoverageAdapter/processDepth.js +35 -0
- package/esm/SNPCoverageAdapter/processMismatches.d.ts +9 -0
- package/esm/SNPCoverageAdapter/processMismatches.js +55 -0
- package/esm/SNPCoverageAdapter/processModifications.d.ts +10 -0
- package/esm/SNPCoverageAdapter/processModifications.js +46 -0
- package/esm/SNPCoverageAdapter/processReferenceCpGs.d.ts +9 -0
- package/esm/SNPCoverageAdapter/processReferenceCpGs.js +60 -0
- package/esm/SNPCoverageAdapter/util.d.ts +10 -0
- package/esm/SNPCoverageAdapter/util.js +35 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -18
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +3 -289
- package/esm/SNPCoverageRenderer/configSchema.d.ts +3 -18
- package/esm/SNPCoverageRenderer/configSchema.js +4 -22
- package/esm/SNPCoverageRenderer/index.d.ts +1 -1
- package/esm/SNPCoverageRenderer/index.js +2 -2
- package/esm/SNPCoverageRenderer/makeImage.d.ts +2 -0
- package/esm/SNPCoverageRenderer/makeImage.js +267 -0
- package/esm/SNPCoverageRenderer/types.d.ts +19 -0
- package/esm/SNPCoverageRenderer/types.js +1 -0
- package/esm/index.d.ts +2 -2
- package/esm/index.js +10 -10
- package/esm/shared/afterAttach.d.ts +1 -1
- package/esm/shared/afterAttach.js +0 -2
- package/esm/shared/color.d.ts +1 -1
- package/esm/shared/color.js +0 -8
- package/esm/shared/components/BaseDisplayComponent.d.ts +3 -4
- package/esm/shared/components/BaseDisplayComponent.js +13 -16
- package/esm/shared/components/FilterByTagDialog.d.ts +2 -3
- package/esm/shared/components/FilterByTagDialog.js +44 -71
- package/esm/shared/fetchChains.d.ts +2 -2
- package/esm/shared/fetchChains.js +1 -2
- package/esm/shared/getMaximumModificationAtEachPosition.d.ts +1 -1
- package/esm/shared/getMaximumModificationAtEachPosition.js +1 -2
- package/esm/shared/getUniqueModifications.d.ts +5 -5
- package/esm/shared/getUniqueTags.d.ts +4 -4
- package/esm/shared/renderSvgUtil.d.ts +1 -2
- package/esm/shared/renderSvgUtil.js +3 -9
- package/esm/shared/util.d.ts +11 -1
- package/esm/shared/util.js +24 -0
- package/esm/util.d.ts +4 -4
- package/esm/util.js +3 -9
- package/package.json +6 -7
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import PluginManager from '@jbrowse/core/PluginManager';
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import type PluginManager from '@jbrowse/core/PluginManager';
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import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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import { Feature } from '@jbrowse/core/util';
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readonly renderDelay: number;
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@@ -255,68 +213,33 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
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tagsReady: boolean;
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} & {
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readonly autorunReady: boolean;
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readonly hideSmallIndels: boolean | undefined;
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copyFeatureToClipboard(feature: Feature): void;
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|
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readonly rendererConfig: {
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[x: string]: any;
|
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} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
|
|
@@ -329,34 +252,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
|
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252
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} & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
|
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} & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
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*/
|
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readonly maxHeight: any;
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/**
|
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*/
|
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256
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readonly featureHeightSetting: any;
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|
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|
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257
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readonly featureUnderMouse: Feature | undefined;
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*/
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renderReady(): boolean;
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/**
|
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|
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*/
|
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259
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readonly filters: SerializableFilterChain;
|
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/**
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|
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*/
|
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261
|
readonly rendererTypeName: string;
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|
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/**
|
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|
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|
|
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|
-
*/
|
|
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262
|
contextMenuItems(): ({
|
|
361
263
|
label: string;
|
|
362
264
|
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
@@ -368,47 +270,38 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
|
|
|
368
270
|
icon: typeof ContentCopyIcon;
|
|
369
271
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onClick: () => void;
|
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})[];
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|
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/**
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* #getter
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*/
|
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273
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readonly DisplayBlurb: ({ model, }: {
|
|
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274
|
model: {
|
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376
|
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sortedBy?:
|
|
377
|
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pos: number;
|
|
378
|
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refName: number;
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|
-
type: string;
|
|
380
|
-
tag?: string;
|
|
381
|
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};
|
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sortedBy?: import("../shared/types").SortedBy;
|
|
382
276
|
};
|
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|
-
}) => import("react").JSX.Element | null;
|
|
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|
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/**
|
|
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|
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* #method
|
|
386
|
-
*/
|
|
277
|
+
}) => import("react/jsx-runtime").JSX.Element | null;
|
|
387
278
|
renderPropsPre(): any;
|
|
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|
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/**
|
|
389
|
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* #method
|
|
390
|
-
*/
|
|
391
279
|
colorSchemeSubMenuItems(): {
|
|
392
280
|
label: string;
|
|
393
281
|
onClick: () => void;
|
|
394
282
|
}[];
|
|
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|
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/**
|
|
396
|
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* #method
|
|
397
|
-
*/
|
|
398
283
|
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 | {
|
|
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|
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label: string;
|
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+
priority: number;
|
|
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|
+
type: string;
|
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287
|
+
checked: boolean | undefined;
|
|
288
|
+
onClick: () => void;
|
|
289
|
+
icon?: undefined;
|
|
290
|
+
} | {
|
|
399
291
|
label: string;
|
|
400
292
|
icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
|
|
401
293
|
muiName: string;
|
|
402
294
|
};
|
|
403
295
|
onClick: () => void;
|
|
296
|
+
priority?: undefined;
|
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|
+
type?: undefined;
|
|
298
|
+
checked?: undefined;
|
|
404
299
|
})[];
|
|
405
300
|
} & {
|
|
406
301
|
renderProps(): any;
|
|
407
302
|
} & {
|
|
408
303
|
afterAttach(): void;
|
|
409
|
-
}, {
|
|
410
|
-
type: string;
|
|
411
|
-
} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
304
|
+
}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
|
|
412
305
|
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
413
306
|
type: import("mobx-state-tree").ISimpleType<string>;
|
|
414
307
|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
@@ -420,21 +313,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
|
|
|
420
313
|
} & {
|
|
421
314
|
blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
|
|
422
315
|
key: import("mobx-state-tree").ISimpleType<string>;
|
|
423
|
-
region: import("mobx-state-tree").
|
|
424
|
-
refName: import("mobx-state-tree").ISimpleType<string>;
|
|
425
|
-
start: import("mobx-state-tree").ISimpleType<number>;
|
|
426
|
-
end: import("mobx-state-tree").ISimpleType<number>;
|
|
427
|
-
reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
|
|
428
|
-
} & {
|
|
429
|
-
assemblyName: import("mobx-state-tree").ISimpleType<string>;
|
|
430
|
-
}, {
|
|
431
|
-
setRefName(newRefName: string): void;
|
|
432
|
-
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
316
|
+
region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
|
|
433
317
|
reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
434
318
|
isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
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435
319
|
isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
|
|
436
320
|
}, {
|
|
437
|
-
|
|
321
|
+
stopToken: string | undefined;
|
|
438
322
|
filled: boolean;
|
|
439
323
|
reactElement: React.ReactElement | undefined;
|
|
440
324
|
features: Map<string, Feature> | undefined;
|
|
@@ -452,21 +336,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
|
|
|
452
336
|
status?: string;
|
|
453
337
|
reactElement?: React.ReactElement;
|
|
454
338
|
};
|
|
455
|
-
}) => import("react").JSX.Element | undefined;
|
|
339
|
+
}) => import("react/jsx-runtime").JSX.Element | undefined;
|
|
456
340
|
renderProps: any;
|
|
457
341
|
} & {
|
|
458
342
|
doReload(): void;
|
|
459
343
|
afterAttach(): void;
|
|
460
344
|
setStatus(message: string): void;
|
|
461
|
-
setLoading(
|
|
345
|
+
setLoading(newStopToken: string): void;
|
|
462
346
|
setMessage(messageText: string): void;
|
|
463
|
-
setRendered(props:
|
|
464
|
-
reactElement: React.ReactElement;
|
|
465
|
-
features: Map<string, Feature>;
|
|
466
|
-
layout: any;
|
|
467
|
-
maxHeightReached: boolean;
|
|
468
|
-
renderProps: any;
|
|
469
|
-
} | undefined): void;
|
|
347
|
+
setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
|
|
470
348
|
setError(error: unknown): void;
|
|
471
349
|
reload(): void;
|
|
472
350
|
beforeDestroy(): void;
|
|
@@ -499,12 +377,22 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
|
|
|
499
377
|
defaultValue: never[];
|
|
500
378
|
};
|
|
501
379
|
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
|
|
502
|
-
}
|
|
503
|
-
|
|
380
|
+
} & {
|
|
381
|
+
configuration: AnyConfigurationSchemaType;
|
|
382
|
+
featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
383
|
+
noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
384
|
+
fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
385
|
+
trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
386
|
+
colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
|
|
387
|
+
filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
|
|
388
|
+
jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
|
|
389
|
+
hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
390
|
+
}>>, {
|
|
504
391
|
id: string;
|
|
392
|
+
type: string;
|
|
505
393
|
configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
|
|
506
|
-
heightPreConfig: number | undefined;
|
|
507
394
|
rpcDriverName: string | undefined;
|
|
395
|
+
heightPreConfig: number | undefined;
|
|
508
396
|
userBpPerPxLimit: number | undefined;
|
|
509
397
|
userByteSizeLimit: number | undefined;
|
|
510
398
|
} & import("mobx-state-tree")._NotCustomized>;
|