LinearBasicDisplay

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

Example usage

A complete FeatureTrack config (e.g. genes from a GFF3) to paste into tracks. displayMode sets the feature height preset (normal, compact, or superCompact), or collapsed for a single-row overview:

{
  type: 'FeatureTrack',
  trackId: 'genes',
  name: 'Genes',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'Gff3TabixAdapter',
    uri: 'https://example.com/genes.gff3.gz',
  },
  displays: [
    {
      type: 'LinearBasicDisplay',
      displayId: 'genes-LinearBasicDisplay',
      height: 200,
      displayMode: 'compact',
    },
  ],
}

GPU-accelerated feature display with gene-specific UI on top of the shared canvas base display (LinearCanvasBaseDisplay).

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

9 inherited properties from 2 models

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

From BaseDisplay: id, type

Volatiles

Member	Description
geneGlyphNoticeDismissed `boolean`

44 inherited volatiles from 10 models

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, hostHeight

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 ContextMenuMixin: contextMenuInfo

Getters

Member	Description
conf `ConfigNodeProps<…> & ConfigNodeActions & ConfigNodeBrand<ConfigurationSchemaType<…>>`	The config typed off this display's own schema, reclaiming its slots for direct reads the way `configuration` above does for `getConf`.
subfeatureLabels `"below" \| "none" \| "overlay"`
effectiveSubfeatureLabels `"below" \| "none" \| "overlay"`
displayDirectionalChevrons `boolean`
utrColor `string`
geneGlyphMode `"all" \| "auto" \| "longestCoding"`
showOnlyGenes `boolean`
effectiveGeneGlyphMode `"all" \| "auto" \| "longestCoding"`
showsEveryIsoform `boolean`
showGeneGlyphNotice `boolean`
geneGlyphIsoformPicks `IsoformPicks`	What picked the transcript each collapsed gene in the loaded view is showing, summed over its regions: the chip names the commonest rule (`RefSeq Select`) instead of only saying that transcripts are hidden.
geneGlyphTrimmedGenes `ReadonlyMap<string, IsoformTrim>`
geneGlyphIsoformCap `number \| undefined`	The isoform count the fit ladder trimmed to, or undefined when nothing on screen was trimmed.
geneGlyphCollapsed `boolean`
isGeneLike `boolean`	whether the right-clicked feature is a gene, transcript or RNA
geneGlyphNotice `{ collapsed: boolean; maxIsoforms: number \| undefined; picks: IsoformPicks; dismissed: boolean; mode: "all" \| "auto" \| "longestCoding"; setMode: (value: "all" \| "auto" \| "longestCoding") => void; dismiss: () => void; } \| undefined`	This display's answer to the base's isoform-collapse chrome hook (see `geneGlyphNotice` on the canvas base): absent unless the loaded data has a multi-isoform gene, so switching modes is meaningful.

206 inherited getters from 12 models

From LinearCanvasBaseDisplay: rpcDataMap, colorSetting, workerColor, colorEncoding, colorField, categoricalColorField, paintedColorField, identityKeyEntries, colorKeyTitle, colorValueExtent, colorValueGaps, colorRamp, paintColorValue, fieldPalette, colorNotices, notices, showOutline, outlineColor, featureColor, solidColor, colorByMode, colorByAttribute, facet, hiddenGroupFeatureIds, layoutReady, onScreenFeatureIds, labelDensityPerPx, onScreenWidthPx, geneLabelDensityPerPx, renderState, labelScrollBucket, displayMode, groupKeySpace, labelFontSize, showLabelsMode, labelVisibility, showLabels, geneNamesOnly, showDescriptions, effectiveShowDescriptions, selectedFeatureId, colorByCDS, showAminoAcids, reversedRegions, pinnedFeatureIdSet, expandedGeneIdSet, soloFeatureIdSet, hiddenFeatureCount, soloFeatureCount, pinnedFeatureCount, canonicalFeatureHighlights, resolvedHighlights, highlightedFeatureIdSet, layoutPinnedFeatureIdSet, featureHighlightCount, layoutInputs, fitMeasureFeatureIds, canonicalTranscripts, 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

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

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

From TrackHeightMixin: configuredHeight, allottedHeight, resizing, scrollableHeight

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, hasLegendKey

From ColorWritesMixin: writtenColor

From CanvasFeatureGateMixin: visibleFeatureDensityPerPx, maxFeatureDensity

From HiddenGroupsMixin: displayHiddenGroupKeys, ownGroupState, hiddenGroups, hiddenGroupKeys, groupStateKey

Methods

Member	Description
rpcProps `() => { showOnlyGenes: boolean; displayConfig: {…}; colorByCDS: boolean; soloFeatureIds: (IMSTArray<…> & IStateTreeNode<…>) \| undefined; hiddenFeatureIds: (IMSTArray<…> & IStateTreeNode<…>) \| undefined; }`
featureNarrowings `() => { showOnlyGenes: { count: number; clear: () => void; }; }`
showSubmenuCheckboxItems `() => MenuItem[]`
showSubmenuRadioGroups `() => MenuItem[]`
trackMenuItems `() => (MenuDivider \| MenuSubHeader \| NormalMenuItem \| CheckboxMenuItem \| RadioMenuItem \| SubMenuItem \| CustomMenuItem \| { label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; subMenu: (RadioMenuItem \| { type: "divider"; label?: undefined; icon?: undefined; onClick?: undefined; } \| { label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; onClick: () => void; type?: undefined; })[]; })[]`
contextMenuItems `() => MenuItem[]`

32 inherited methods from 6 models

From LinearCanvasBaseDisplay: configuredFilters, baseFilters, rampColorScales, renderStateIn, gpuProps, fitLayoutAt, decimatedLayoutInputs, solveLabelRoomFactors, bodyScaleHeightProbe, floatingLabels, searchFeatureByID, renderSvg, featureMarks, zoomFetchArgs, groupByPlot, scanGroupByCandidates, plotProblems, showSubmenuMenuItems, colorBySubMenuItems, colorMenuItems, featureHeightMenuItems

From BaseDisplay: renderingProps, liftPlot, plotWrites

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

From LegendMixin: svgLegendWidth, colorScalesIn, legendSpecIn

From CanvasFeatureGateMixin: observedMaxDensity

Actions

Member	Description
setSubfeatureLabels `(value: "below" \| "none" \| "overlay") => void`
setGeneGlyphMode `(value: "all" \| "auto" \| "longestCoding") => void`
dismissGeneGlyphNotice `() => void`
setShowOnlyGenes `(value: boolean) => void`
setDisplayDirectionalChevrons `(value: boolean) => void`
setUtrColor `(color?: string \| undefined) => void`