LinearReferenceSequenceDisplay

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

Draws a ReferenceSequenceTrack as rows of bases: the forward strand, the reverse complement and the translation frames.

The model composes BaseDisplay, TrackHeightMixin and MultiRegionDisplayMixin.

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('LinearReferenceSequenceDisplay')`
configuration `configuration: ConfigurationReference(configSchema)`

1 inherited property from one model

From BaseDisplay: id

Volatiles

22 inherited volatiles from 6 models

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

Getters

Member	Description
sequenceData `ReadonlyMap<number, SequenceRegionData>`	The fetched sequence, keyed by displayedRegionIndex — the foundation's per-region store, narrowed.
view ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & { rubberbandClickMenuItems(clickOffset: BpOffset): MenuItem[]; highlightMenuItems(_highlight: HighlightType): MenuItem[]; } & { flyTo: (centerBp: number, windowWidthBp: number) => void; flyToCenter(coord: number, refName: string, displayedRegionIndex?: number \| undefined): void; flyToFit(centerBp: number, fitWidthBp: number): void; } & { afterCreate(): void; afterAttach(): void; } & IStateTreeNode<…>
showForward `boolean`
showReverse `boolean`
showTranslation `boolean`
sequenceType `"dna" \| "pep"`
colorPalette `ColorPalette`	Theme-derived fill and text color for every cell this display paints
isDna `boolean`	the reverse-complement and translation rows are DNA-only
rowVisibility `RowVisibility`	Which rows the stack is showing, as the one value `rowLayout` takes
cellEncoding `CellEncoding`	What the cells' encode reads beyond the sequence itself
zoomedOut `boolean`	the view is too zoomed out to show individual bases
placeholderMessage `string \| undefined`	The message shown where the canvas would go: zoomed past base resolution, or every row toggled off (which would otherwise collapse the track to 0px). Undefined when the sequence paints.
fetchInert `boolean`	A shown message means no paint is coming. See FetchMixin.fetchInert.
numRows `number`
computedHeight `number`	fits the visible rows, or 50px while a message shows
height `number`	a manual resize if set, else `computedHeight`
rowHeight `number`	the track height split evenly across the shown rows
renderState `SequenceRenderState`	everything the marks and the letters need to paint a frame

68 inherited getters from 6 models

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

From TrackHeightMixin: configuredHeight, allottedHeight, resizing, scrollContentHeight, scrollViewportHeight, scrollableHeight

From MultiRegionDisplayMixin: host, canvasWidthPx, settledSubPixelBinBp, canRender, rendersCanvas, trackVisibleRegions, viewportWithinLoadedData, viewportEmpty, fetchSuspended, layoutReady, 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, awaitingPrerequisite, awaitingDependentData, settingsFetchInputs

Methods

Member	Description
colorPaletteIn `(palette: JBrowsePalette) => ColorPalette`	`colorPalette` in another palette: the SVG export's, whose theme need not be the session's.
hoverAt `(offsetX: number, offsetY: number) => SequenceHover \| undefined`	Resolve the genomic position, reference base, and codon/amino-acid under a cursor at track-relative pixel `(offsetX, offsetY)`. Drives the hover tooltip; returns undefined when no sequence is painted, off a fetched region, or between rows.
renderSvg `(opts?: ExportSvgDisplayOptions \| undefined) => Promise<ReactElement<unknown, string \| JSXElementConstructor<any>> \| Iterable<ReactNode> \| AwaitedReactNode>`
trackMenuItems `() => MenuItem[]`

8 inherited methods from 3 models

From BaseDisplay: renderingProps, liftPlot, plotProblems, plotWrites

From MultiRegionDisplayMixin: regionHasData, isCacheValid

From RegionTooLargeMixin: resolvedByteLimit, gateFetchState

Actions

Member	Description
toggleShowForward `() => void`
toggleShowReverse `() => void`
toggleShowTranslation `() => void`
startRenderingBackend `(backend: PerRegionRenderingBackend<SequenceCells, SequenceRenderState, RenderBlock, SequenceCells>) => void`
fetchNeeded `(needed: IndexedRegion[]) => Promise<void>`