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BaseChordDisplay

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

What the circular view's chord and ribbon displays share: the features, the slice index a feature end is looked up in, and the lifecycle getters ChordDisplayFrame publishes. A track draws on the arcs of its own assemblies, so a one-genome variant track on a two-genome circle fetches and places only that genome's chords.

Each section ends with the members a composed model contributes, linked to the page that documents them.

Properties

From BaseDisplay: id, type

Volatiles

MemberDescription
features
Feature[] | undefined
reloadCounter
number		the fetch's pure "go again" signal

From BaseDisplay: error, statusMessage, statusProgress

Getters

MemberDescription
view
ModelInstanceTypeProps<…> & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & {…} & { resizeHeight(distance: number): number; resizeWidth(distance: number): number; } & { afterCreate(): void; beforeDestroy(): void; afterAttach(): void; } & { tracksMenuItem(): MenuItem; } & { readonly legendSpec: LegendSpec; legendSpecIn(palette?: JBrowsePalette | undefined): LegendSpec; menuItems(): MenuItem[]; } & IStateTreeNode<…>
trackAssemblyNames
string[]		the track's assemblies that are on the circle, canonical and in the order the circle lays them out
fetchInert
boolean		nothing of this track's is on the circle, so the fetch never runs; the SVG export's wait and the retry contract check both read it
loaded
boolean
ready
boolean
displayError
unknown		what the error ring shows
svgReady
boolean		the off-screen export gate, on the shared computeSvgReady policy. A radial display has no box to draw an error in, so the export fails rather than exporting a message
displayPhase
DisplayStatusPhase
radiusPx
number
bezierRadiusRatio
number		how far from the center a chord across the circle passes, as a fraction of the radius; a shorter chord bows less, in proportion to its span
bezierRadius
number
sliceIndex
Record<string, Slice>		every slice of the circle, keyed by canonical assembly AND refName: two genomes on one circle can each carry a chr1. An elided slice answers to each refName it swallowed.
drawnFeatures
Feature[] | undefined		what the chord components draw
selectedFeatureId
string | undefined
hoveredFeatureId
string | undefined		the feature under the pointer, which the view hit-tests for every chord display at once
chordStage
ChordStage		the polar stage as the canvas and the pointer see it, rotation in
figureStage
ChordStage		the polar stage on the unrotated figure, which the view's SVG turns: what the export and the highlight paths are placed on

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

Methods

MemberDescription
assemblyOf
(assemblyName: string | undefined) => string | undefined		the assembly on the circle a feature names, in whatever spelling the adapter wrote. A feature that names none, as a VCF record does not, is on the track's first assembly.
canonicalRefName
(assemblyName: string, refName: string) => string		a refName as the adapter wrote it, in the assembly's canonical spelling
sliceFor
(assemblyName: string | undefined, refName: string) => Slice | undefined
the slice one end of a feature lands on
axisSlice
(assemblyName: string | undefined, refName: string) => AxisSlice | undefined
the slice of the unrolled axis one end of a feature lands on

From BaseDisplay: renderingProps, trackMenuItems, liftPlot, plotProblems, plotWrites

Actions

MemberDescription
openErrorDialog
() => void
setFeatures
(features: Feature[] | undefined) => void
reload
() => void

From BaseDisplay: setStatusMessage, setError, clearHoveredFeature, applyDisplaySettings, applyPlot