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.

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

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,
    },
  ],
}

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')`

9 inherited properties from 3 models

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

From ParkedColorMixin: parkedColors

From BaseDisplay: id

Volatiles

44 inherited volatiles from 9 models

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

From ContextMenuMixin: contextMenuInfo

From CanvasFeatureGateMixin: densityStatsPerRegion

From LegendMixin: dismissedLegendSections

From MultiRegionDisplayMixin: loadedRegions

From FetchMixin: activeSignal, fetchGeneration, reloadCounter, statusWindow, error, statusMessage, statusProgress, fetchCanceled, fetchRotation

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

From RegionTooLargeMixin: forceLoadTrack, byteEstimate, gateMeasuredViewportKey

From TrackHeightMixin: scrollTop, hostHeight

Getters

Member	Description
colorsByConsequenceImpact `boolean`
colorsBySvType `boolean`
colorByAttribute `string`	The attribute the Attribute dialog opens on, '' under the impact or SV type preset, each of which has a separate row.
featureNoun `string`	The noun for what the track holds, used in every menu row, chip and indicator, so a variant track shows "Variant height" and "Showing 3 variants" rather than "feature". The context menu's per-hit noun still comes from the annotation's type where it has one.
colorFieldNoun `string`	What Color by calls a record's named value: a VCF has fields, as the multi-sample display's menu says, where a GFF has attributes.
featureWidgetType `{ type: string; id: string; }`

215 inherited getters from 14 models

From LinearCanvasBaseDisplay: rpcDataMap, conf, colorSetting, workerColor, colorEncoding, colorField, solidColor, colorByMode, categoricalColorField, paintedColorField, identityKeyEntries, colorKeyTitle, colorValueExtent, colorValueGaps, colorRamp, paintColorValue, fieldPalette, showOutline, outlineColor, featureColor, proteinFeaturesArg, domainPalette, liveNotices, geneGlyphNotice, facet, hiddenGroupFeatureIds, layoutReady, onScreenFeatureIds, labelDensityPerPx, onScreenWidthPx, geneLabelDensityPerPx, renderState, showChevrons, labelScrollBucket, displayMode, groupKeySpace, effectiveSubfeatureLabels, labelFontSize, showLabelsMode, labelVisibility, showLabels, geneNamesOnly, showDescriptions, effectiveShowDescriptions, selectedFeatureId, colorByFrame, 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, namedFeatures, hoverInk, shownTooltipRows, selectionInk, pinnedInk, soloInk, flatbushIndexes, derivedColorScales, colorScales

From HiddenGroupsMixin: ownGroupState, hiddenGroups, hiddenGroupKeys, groupStateKey

From CanvasFeatureGateMixin: gateEnabled, visibleFeatureDensityPerPx, maxFeatureDensity, densityTooLarge

From FacetWritesMixin: writtenFacet

From ColorWritesMixin: writtenColor

From ParkedColorMixin: parkedColor

From LegendMixin: showLegend, legendRight, legendSpec, hasLegendKey

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

From RenderLifecycleMixin: painted

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

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

From TrackHeightMixin: configuredHeight, allottedHeight, resizing, scrollableHeight

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

Methods

Member	Description
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 `() => MenuItem[]`	The Color by entries without the base's Strand radio, plus one-click consequence impact (SnpEff ANN / VEP CSQ) and SV type presets.

39 inherited methods from 7 models

From LinearCanvasBaseDisplay: configuredFilters, baseFilters, rampColorScales, domainColorScales, renderStateIn, rpcProps, gpuProps, fitLayoutAt, decimatedLayoutInputs, solveLabelRoomFactors, bodyScaleHeightProbe, floatingLabels, searchFeatureByID, renderSvg, featureNarrowings, featureMarks, zoomFetchArgs, groupByPlot, scanGroupByCandidates, configProblemsOf, showSubmenuCheckboxItems, showSubmenuRadioGroups, filterSubMenuItems, showSubmenuMenuItems, colorMenuItems, featureHeightMenuItems, trackMenuItems