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.

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',
    },
  ],
}

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

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)`

1 inherited property from one model

From BaseDisplay: id

Volatiles

37 inherited volatiles from 11 models

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

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 ScoreScaleMixin: unclippedQuantile

From LegendMixin: dismissedLegendSections

From ContextMenuMixin: contextMenuInfo

From LodTierInfoMixin: adapterHeaderRead

Getters

Member	Description
lodMode `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.
hideSelfAlignments `boolean`	Whether the view's own assembly lane is hidden — see the slot.
displayHiddenGroupKeys `ReadonlySet<string>`	The lane an all-vs-all track draws for the view's own assembly: its mate-assembly group key IS that assembly name. Hidden as a group key rather than filtered out of the fetch, so unchecking the option shows it again without a refetch. The display's own half of `hiddenGroupKeys`, which unions it with the lanes the user hid from a chip — overriding that would have dropped theirs. The key is the name the adapter resolved out of the track's `assemblyNames`, and the view may spell the same assembly another way, so every declared name that is this assembly goes in beside the view's own.
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`.

276 inherited getters from 14 models

From LinearAlignmentsDisplay: unit, showBezierConnections, showCoverage, showPileup, coverageHeight, coverageSnpMinFrequency, showMismatches, showInterbaseIndicators, showInterchrom, showOrdinaryPairs, minInterchromSupport, showLongRange, readConnections, readConnectionsDown, showSashimiArcs, sashimiArcsMode, minSashimiScore, sashimiArcsHeight, readConnectionsHeight, showSoftClipping, colorSetting, colorEncoding, colorLabels, colorTitle, colorKeyTitle, colorKeyDescending, colorNotices, facetNotices, pinnedInsertSizeBand, modificationSettings, colorBy, colorField, arcColorField, baseLayer, bodyColorScheme, readFilter, configuredFeatureHeight, maxHeight, showSashimiLabels, showNonCanonicalJunctions, fadeLowFrequencyMismatches, fadeLowQualityMismatches, layoutOrder, facet, readConnectionsLineWidth, rpcDataMap, view, showLinkedReadLines, bezierArcScope, selectedFeatureId, TooltipComponent, detectedModifications, modificationsReady, detectedModificationTypes, isFitting, featureHeight, featureSpacing, rowHeight, sortColumn, effectiveFacet, groupKeySpace, prefersOffset, collapseGroupRows, canCollapseGroupRows, sortReadsBlockedReason, canSortReads, canSizeGroupHeights, groupHeightOverrides, coverageScaleType, autoscaleRange, defaultScoreDomain, coverageDomain, coverageDepthDomain, coverageTicks, colorLegendCategories, presentTagValues, presentModifications, colorPalette, declaredReadLabels, arcLegendCategories, overlapLegendKind, keySectionOrder, arcLegendTitle, sashimiDownKeysByGroup, sashimiDownArcLanes, resizableBandBounds, bandHeights, belowCoverageBandsSettings, belowCoverageBandsInput, totalBandOverhead, groupRowCaps, fitDefaultCap, resolvedFitDefaultCap, fitRows, fitCeilingRows, laidOutByGroupUncolored, framesChainStrand, laidOutByGroupFramed, laidOutByGroupColored, laidOutByGroup, connectorsByGroup, groupLayoutContext, readColorContext, bakedColorExtent, tagValueExtent, baseQualitySpan, bakedColorScale, paintedRefNamePosition, readColorOpts, groupOrder, notices, showsGroupLabels, rawDataByGroup, chainAttachment, chainedByGroup, readIdsByChainName, loadedRegionInfos, displayedRegionInfos, canonicalRefName, arcsResult, arcsByGroup, crossRegionArcsByGroup, arcFeedsByGroup, modificationThreshold, showModifications, mismatchContrastMap, showPerBaseQuality, showPerBaseLetter, 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, sashimiFeedsByGroup, connectorFeedsByGroup, sourceSections, sashimiLegendStrands, colorScales, fittedFeatureHeight, sortTag, renderState, linkRegions, sashimiLabels, selectedSashimiHighlight, selectedConnectorHighlight, hoverInk, selectionInk, arcsYDomainBp, scoreRulesDrawn, valueScales, perBaseBinBp, livePerBaseBinBp, hoveredFeature, dataSuperseded, ownGroupState, gateEnabled

From BaseDisplay: parentTrack, RenderingComponent, DisplayBlurb, adapterConfig, isMinimized, 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, renderBlocks, fetchInputs, regionPayloads, hasRegionData, staleSettingsDrawn, dataCurrent, loadedAssembly, phaseViewportCurrent, svgReady, paintInert, paintSuperseded, displayPhase

From RegionTooLargeMixin: 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 ScoreScaleMixin: scaleType, scaleZero, domainQuantile, clipQuantile, symlogConstant, manualMinScore, manualMaxScore, valueScaleNotices, autoscaleGroup, scaleTitle, grid, minimalTicks, scoreRules

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

From LegendMixin: showLegend, legendTop, legendRight, legendSpec, hasLegendKey

From ColorWritesMixin: writtenColor

From HiddenGroupsMixin: hiddenGroups, hiddenGroupKeys, groupStateKey

From LodTierInfoMixin: adapterHeader, lodTierInfo

Methods

Member Description

groupChipLabel
(label: string) => string A mate-assembly chip reads the assembly's display name

contextMenuItems
() => MenuItem[]

Member	Description
groupChipLabel `(label: string) => string`	A mate-assembly chip reads the assembly's display name
contextMenuItems `() => MenuItem[]`
trackMenuItems `() => (MenuItem \| { label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; type: "subMenu"; subMenu: (MenuItem \| { label: string; onClick: () => void; })[]; })[]`

trackMenuItems

() => (MenuItem | { label: string; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; type: "subMenu"; subMenu: (MenuItem | { label: string; onClick: () => void; })[]; })[]

33 inherited methods from 5 models

From LinearAlignmentsDisplay: nonReferenceAt, colorPaletteIn, legendItems, arcLegendItems, arcFeedsByGroupIn, findFeatureInRpcData, laneFor, connectionLegendItems, groupPileupOffset, readIdsSharingChain, readIdsSharingChainWith, getFeatureInfoById, readLayoutRecord, connectorFeedsByGroupIn, sashimiFeedsByGroupIn, sourceSectionsIn, sourceSectionsWith, sashimiSupportingReadSlots, colorScalesIn, readInk, slotInk, rpcProps, zoomFetchArgs

From BaseDisplay: renderingProps, liftPlot, plotProblems, plotWrites

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

From LegendMixin: svgLegendWidth, legendSpecIn

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 own `assemblyNames` in a worker with no assembly manager — so a track declaring an alias fetched nothing. The comparative views do the same through `renameRegionsForAdapter`.
setHideSelfAlignments `(flag: boolean) => void`	Show/hide the view's own assembly lane of an all-vs-all track.
setLodMode `(arg: LodMode) => void`