LinearVariantDisplay

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Provided by the variants plugin. View source.

Example usage

A complete VariantTrack config to paste into tracks:

{
  type: 'VariantTrack',
  trackId: 'variants',
  name: 'Variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/variants.vcf.gz',
  },
  displays: [
    {
      type: 'LinearVariantDisplay',
      displayId: 'variants-LinearVariantDisplay',
      height: 150,
    },
  ],
}

GPU-accelerated variant display with custom feature widget on click.

The configuration slots for this model are documented on its config schema page.

Each section ends with the members a composed model contributes, linked to the page that documents them.

Properties

Member	Description
type `type: types.literal('LinearVariantDisplay')`

From LinearCanvasBaseDisplay: configuration, pinnedFeatureIds, soloFeatureIds, soloApplied, hiddenFeatureIds, expandedGeneIds, featureHighlights

From BaseDisplay: id

Volatiles

From LinearCanvasBaseDisplay: featureIdUnderMouse, subfeatureIdUnderMouse, mouseoverExtraInformation, sequenceHoverPosition, onScreenIdsMemo, incrementalLayout, incrementalLayoutLabelsOnly, incrementalLayoutBodiesOnly, incrementalLayoutDecimated, incrementalLayoutIsoforms, incrementalLayoutThinned, incrementalLayoutBare, packHeightsIsoforms, packHeightsThinned, packHeightsDecimated, morphFromTops, morphProgress, morphStartMs, morphFromMaxY

From BaseDisplay: error, statusMessage, statusProgress

From TrackHeightMixin: scrollTop

From MultiRegionDisplayMixin: loadedRegions

From RegionTooLargeMixin: forceLoadTrack, byteEstimate, gateMeasuredViewportKey

From RenderLifecycleMixin: canvasDrawn, paintCount, currentRenderingBackend, renderTick, autorunsInstalled, renderError, offScreen

From FetchMixin: activeSignal, fetchGeneration, reloadCounter, statusWindow, fetchCanceled, fetchRotation

From LegendMixin: dismissedLegendSections

From CanvasFeatureGateMixin: densityStatsPerRegion

From DensityBandMixin: densityHoverPx

From CoarseTierMixin: coarseTier, coarseTierRead, coarseTierLoading

From ContextMenuMixin: contextMenuInfo

From HiddenGroupsMixin: hiddenGroups

Getters

Member	Description
colorEncoding `string \| FieldColorEncoding \| undefined`	The canvas resolver, with the `impact` preset field resolved to the jexl color that computes it.
colorsBySvType `boolean`
colorByAttribute `string`	The attribute the Attribute dialog opens on, '' under a preset or the SV type, each of which has its own row.
featureNoun `string`	Names what the track holds in every menu row, chip and indicator, so a variant track says "Variant height" and "Showing 3 variants" rather than "feature". The context menu's per-hit noun still comes from the annotation's own type where it has one.
featureWidgetType `{ type: string; id: string; }`
colorsByConsequenceImpact `boolean`
featureColorScales `ColorScale[]`	The key while features draw: the impact tiers under that preset, or else the key a color by a field derives.

From LinearCanvasBaseDisplay: rpcDataMap, conf, colorSettings, workerColor, colorFieldName, colorField, paintedColorField, identityKeyEntries, colorKeyTitle, colorValueExtent, colorValueGaps, colorRamp, paintColorValue, fieldPalette, colorNotices, notices, showOutline, outlineColorSlot, featureColor, solidColor, colorByMode, geneGlyphNotice, facet, hiddenGroupFeatureIds, layoutReady, onScreenFeatureIds, labelDensityPerPx, onScreenWidthPx, geneLabelDensityPerPx, renderState, displayDirectionalChevrons, labelScrollBucket, displayMode, groupKeySpace, effectiveSubfeatureLabels, labelFontSize, showLabelsMode, showLabels, geneNamesOnly, showDescriptions, effectiveShowDescriptions, selectedFeatureId, colorByCDS, showAminoAcids, reversedRegions, pinnedFeatureIdSet, expandedGeneIdSet, soloFeatureIdSet, hiddenFeatureCount, soloFeatureCount, pinnedFeatureCount, canonicalFeatureHighlights, resolvedHighlights, highlightedFeatureIdSet, layoutPinnedFeatureIdSet, featureHighlightCount, layoutInputs, fitMeasureFeatureIds, canonicalTranscripts, showsEveryIsoform, effectiveGeneGlyphMode, reservesBelowLabelRows, fullReservation, labelsReservation, isoformsReservation, decimatedBaseInputs, decimatedHeightProbe, isoformsBaseInputs, isoformsHeightProbe, maxIsoformsOnScreen, fitIsoformCount, fitIsoformsSolved, thinnedBaseInputs, fitLabeledBodyFloor, fitBodyScale, fitThinnedSolved, baseLaidOutDataMap, fitLabelsOnlyLayout, fitDecimatedFactors, fitDecimatedSolved, fitDecimatedBodyScale, fitBodiesOnlyLayout, fitBareLayout, fitSmallestBoxPx, fitMinScale, fitStage, fitScale, laidOutDataMap, groupSections, showsGroupLabels, prefersOffset, renderedShowDescriptions, renderedShowLabels, renderedShowSubfeatureLabels, renderedLabelFontSize, fitDrops, fitNote, labelsFitHint, morphEased, animating, renderDataMap, settledMaxY, maxY, scrollExtentMaxY, hasOverflow, truncatedFeatureCount, contentHeight, scrollContentHeight, scrollViewportHeight, growTargetHeight, featureIdIndex, subfeatureIdIndex, hoveredFeature, hoveredSubfeature, hoverBoxFeature, hoverBoxSubfeature, regionInstanceIndexes, hoverInk, selectionInk, pinnedInk, soloInk, flatbushIndexes, derivedColorScales, colorScales, hasLegendKey

From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, plotKeys, plot, plotExamples, configDocsUrl

From TrackHeightMixin: height, resizing, scrollableHeight

From HeightModeMixin: heightMode, fitTargetHeight, growMaxHeight, autoHeight, fitHeightToDisplay, grownHeight

From MultiRegionDisplayMixin: host, canvasWidthPx, settledSubPixelBinBp, canRender, rendersCanvas, trackVisibleRegions, viewportWithinLoadedData, viewportEmpty, fetchSuspended, dataSuperseded, renderBlocks, fetchInputs, regionPayloads, hasRegionData, staleSettingsDrawn, dataCurrent, loadedAssembly, phaseViewportCurrent, svgReady, paintInert, paintSuperseded, displayPhase

From RegionTooLargeMixin: gateEnabled, byteGateAdapterConfig, configuredFetchSizeLimit, densityTooLarge, byteGateAdapterPath, adapterFetchSizeLimit, configForceLoad, gateViewportSpanBp, gateViewport, aboveForceLoadFloor, gateExempt, estimatedFetchBytes, gateMeasurementStale, gateByteLimit, gateActive, densityGateActive, tooLargeStatus, regionTooLarge, regionTooLargeReason, zoomCanReleaseGate, gateSkipsMeasuredViewport

From RenderLifecycleMixin: painted

From FetchMixin: isLoading, isLoadingOrCanceled, fetchInert, awaitingPrerequisite, awaitingDependentData, settingsFetchInputs

From LegendMixin: showLegend, legendTop, legendRight, legendSpec

From CanvasFeatureGateMixin: visibleFeatureDensityPerPx, maxFeatureDensity

From DensityBandMixin: densityBandLayer, densityHover, densityPeakReadout, densityReadout

From DensityTierMixin: coarseAdapterSlot, densityTierMode, densityTierThresholdBpPerPx, coarseTierMode, coarseTierPastThreshold, coarseReadKey

From CoarseTierMixin: coarseTierGated, coarseTierHasSomewhereToDraw, coarseSourceConfig, hasCoarseSource, coarseTierActive, coarseTierStandsIn, gateMeasuresCoarse, gateRefusesDetail, coarseTierIssueKey, drawsWhenTooLarge

From HiddenGroupsMixin: displayHiddenGroupKeys, ownGroupState, hiddenGroupKeys, groupStateKey

Methods

Member	Description
rpcProps `() => { displayConfig: {…}; colorByCDS: boolean; soloFeatureIds: (IMSTArray<…> & IStateTreeNode<…>) \| undefined; hiddenFeatureIds: (IMSTArray<…> & IStateTreeNode<…>) \| undefined; }`	The canvas payload with a preset field sent as the jexl color it resolves to, since the worker reads the raw `color` object.
contextMenuItems `() => MenuItem[]`	The shared feature menu plus, on a breakend record, the row that opens the split view for it, and beside a pileup the row that sorts its reads at the variant.
colorBySubMenuItems `() => ({ label: string; type: "radio"; checked: boolean; onClick: () => void; keepMenuOpen?: undefined; } \| { label: string; type: "radio"; checked: boolean; keepMenuOpen: boolean; onClick: () => void; })[]`	The Color by entries without the base's Strand radio, plus one-click consequence impact (SnpEff ANN / VEP CSQ) and SV type presets.