LGVSyntenyDisplay

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

Draws where a SyntenyTrack's alignments fall in a plain linear genome view, with menu items that open them in a synteny view.

Example usage

Shows a SyntenyTrack's alignments in a plain linear view (rather than the two-row synteny view). Same track config as a synteny track — just pick this display type:

{
  type: 'SyntenyTrack',
  trackId: 'hg38_vs_mm10',
  name: 'hg38 vs mm10',
  assemblyNames: ['hg38', 'mm10'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/hg38_vs_mm10.paf',
    queryAssembly: 'hg38',
    targetAssembly: 'mm10',
  },
  displays: [
    {
      type: 'LGVSyntenyDisplay',
      displayId: 'hg38_vs_mm10-LGVSyntenyDisplay',
    },
  ],
}

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('LGVSyntenyDisplay')`
configuration `configuration: ConfigurationReference(schema)`

2 inherited properties from 2 models

From ParkedColorMixin: parkedColors

From BaseDisplay: id

Volatiles

38 inherited volatiles from 10 models

From LodTierInfoMixin: adapterHeaderRead

From LinearAlignmentsDisplay: featureIdUnderMouse, mouseoverExtraInformation, contextMenuFeature, collapsedGroups, groupMaxHeightOverrides, expandedGroups, fittedHeightPx, highlightedChainReadIds, hoveredJunction, overCigarItem, hoverCoverageBand, hoveredArcHighlight

From ContextMenuMixin: contextMenuInfo

From LegendMixin: dismissedLegendSections

From ScoreScaleMixin: unclippedFenceQuantile

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
resolution `LodMode`	the level-of-detail tier the reader pinned, or 'auto' for the adapter's own bpPerPx threshold. `lodTier` is what resolves it
featureWidgetType `{ type: string; id: string; }`	synteny features open the SyntenyFeatureWidget; the inherited `selectFeature` action reads this getter, so no override is needed.
featureNoun `string`	A row here is a PAF block, not a read — the group-label chips say "Show all features". The ONE place that word is chosen: the two menu builders below that take a `noun` read it from here rather than spelling it again, so the chips and the menus cannot end up naming the same row two different things.
selfLaneKeys `string[]`	The mate-assembly keys of the lane an all-vs-all track draws for the view's own assembly: the view's name, and every name the track declares for the same assembly, since the adapter keys a lane by the track's spelling.
selfLaneHidden `boolean`	Whether `facet.hidden` holds the self lane, the "Hide self-alignment lane" box.
hasLodCapableAdapter `boolean`	Whether this track's adapter has tiered storage to switch between — gates the "Level of detail" menu.
lodTier `LodTier`	The tier this display's fetch asks for: the alignments base's hook, resolved here on the main thread off the SETTLED zoom. It is the base's `zoomFetchArgs` term and rides the RPC at the call site, so a tier flip refetches the regions on screen while they keep drawing — and, being settled, a gesture travelling through the threshold does not hand `FetchVisibleRegions` a tier of a zoom it never stops at, on the pipeline whose extract is the expensive one. The tier the adapter will serve once `lodTierInfo` has landed: a file with no coarse tier is 'fine' at any zoom, and the threshold is clamped up to the file's `--coarse` bound.
liveLodTier `LodTier`	The same tier off the live zoom, for the base's `dataSuperseded`.

284 inherited getters from 16 models

From LodTierInfoMixin: adapterHeader, lodTierInfo

From LinearAlignmentsDisplay: unit, showCoverage, coverageHeight, showInterbaseIndicators, showCoverageAlleles, coverageMinAlleleFraction, interbaseIndicatorRule, showPileup, configuredReadHeight, pileupMaxLayoutHeight, showMismatches, showSoftClipping, showConnectors, mismatchOpacityField, mismatchQualityOpacity, fadeLowFrequency, hasSashimi, showSashimi, sashimiHeight, sashimiPlacement, effectiveSashimiPlacement, showSashimiCounts, writtenFilter, filterPredicates, configProblems, junctionFilter, showReadConnections, readConnectionsMark, drawnReadConnections, readConnectionsHeight, readConnectionsPlacement, readConnectionsStrokeScale, readConnectionsLineWidth, showOrdinaryPairs, connectionFilter, colorSetting, colorEncoding, colorLabels, colorTitle, colorKeyTitle, colorKeyDescending, pinnedInsertSizeBand, basesFilter, colorField, readConnectionsColorField, baseLayer, bodyColorKind, readPredicates, layoutOrder, facet, rpcDataMap, view, showLinkedReadLines, bezierArcScope, selectedFeatureId, TooltipComponent, detectedModifications, modificationsReady, detectedModificationTypes, isFitting, featureHeight, featureSpacing, rowHeight, sortColumn, effectiveFacet, groupKeySpace, prefersOffset, collapseSections, canCollapseSections, sortReadsBlockedReason, collapseSortBlockedReason, canSortReads, canSizeGroupHeights, groupHeightOverrides, expandedGroupKeys, coverageScaleType, autoscaleRange, defaultScoreDomain, coverageDomain, coverageDepthDomain, coverageTicks, colorLegendCategories, presentTagValues, presentModifications, declaredReadLabels, arcLegendCategories, overlapLegendKind, keySectionOrder, arcLegendTitle, sashimiDownKeysByGroup, sashimiDownArcLanes, resizableBandBounds, bandHeights, belowCoverageBandsSettings, belowCoverageBandsInput, totalBandOverhead, groupRowCaps, fitDefaultCap, resolvedFitDefaultCap, fitRows, fitCeilingRows, laidOutByGroupUncolored, framesChainStrand, laidOutByGroupFramed, laidOutByGroupColored, laidOutByGroup, connectorsByGroup, connectorFilter, groupLayoutContext, readColorContext, bakedColorExtent, linearFieldExtent, baseQualitySpan, bakedColorScale, paintedRefNamePosition, readColorOpts, groupOrder, liveNotices, showsGroupLabels, rawDataByGroup, chainAttachment, chainedByGroup, readIdsByChainName, loadedRegionInfos, displayedRegionInfos, canonicalRefName, arcsResult, arcCollection, arcsByGroup, crossRegionArcsByGroup, showModifications, mismatchContrastMap, showPerBaseQuality, showPerBaseLetter, readIdIndex, readIdIndexMap, layoutReady, belowCoverageBands, coverageDisplayHeight, lanes, drawnLanes, sections, renderSections, bezierPairSections, connectionColorTypes, legendMaxWidth, contextMenuHit, contextMenuFeatureId, isGrouped, scrollModel, stickyBandHeight, scrollViewportHeight, scrollContentHeight, growTargetHeight, showOutline, visibleLabels, selectedChainReadIds, readCategoryLabel, arcCategoryLabel, readArraysByGroup, sashimiJunctionSections, drawsSashimi, sashimiLegendStrands, sashimiLegendSplitClasses, themed, colorScales, fittedFeatureHeight, sortTag, renderState, linkRegions, sashimiLabels, selectedSashimiHighlight, selectedConnectorHighlight, hoverInk, selectionInk, arcsYDomainBp, scoreRulesDrawn, valueScales, perBaseBinBp, livePerBaseBinBp, hoveredFeature, dataSuperseded, ownGroupState, gateEnabled

From HiddenGroupsMixin: hiddenGroups, hiddenGroupKeys, groupStateKey

From FacetWritesMixin: writtenFacet

From ColorWritesMixin: writtenColor

From ParkedColorMixin: parkedColor

From LegendMixin: showLegend, legendRight, legendSpec, hasLegendKey

From ScoreScaleMixin: scaleType, scaleZero, fenceQuantile, clipFenceQuantile, symlogConstant, manualMinScore, manualMaxScore, autoscaleGroup, scaleTitle, grid, scoreRules

From ScoreAxisMixin: axisReachesZero, autoscaledDomain, minScoreBound, maxScoreBound, hasManualScoreBounds, axes

From MultiRegionDisplayMixin: host, canvasWidthPx, settledSubPixelBinBp, canRender, rendersCanvas, trackVisibleRegions, viewportWithinLoadedData, viewportEmpty, fetchSuspended, 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, densityTooLarge, 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
groupChipLabel `(label: string) => string`	A mate-assembly chip reads the assembly's display name
contextMenuItems `() => MenuItem[]`
trackMenuItems `() => (MenuItem \| { subMenu: MenuItem[]; label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; type: "subMenu"; })[]`

31 inherited methods from 6 models

From LinearAlignmentsDisplay: filterNarrowing, nonReferenceAt, legendItems, arcLegendItems, configProblemsOf, findFeatureInRpcData, laneFor, connectionLegendItems, groupPileupOffset, readIdsSharingChain, readIdsSharingChainWith, getFeatureInfoById, readLayoutRecord, sashimiSupportingReadSlots, themedIn, connectorStylerIn, colorScalesIn, readInk, slotInk, rpcProps, zoomFetchArgs

From ParkedColorMixin: parkedColorOf

From LegendMixin: legendSpecIn

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

From BaseDisplay: renderingProps, liftPlot, plotProblems, plotWrites

Actions

Member	Description
fetchNeeded `(needed: IndexedRegion[]) => void`	The inherited fetch, with each region's assembly respelled the way the track declares it. The view names its assembly canonically and the adapter answers a region by comparing that text against its configured `assemblyNames` in a worker with no assembly manager, so a track declaring an alias would fetch nothing. The comparative views do the same through `renameRegionsForAdapter`.
setSelfLaneHidden `(flag: boolean) => void`	Write the self lane into `facet.hidden`, or take it out.
setResolution `(arg: LodMode) => void`