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BaseChordDisplay

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Provided by the circular-view plugin. View source.

What the circular view's chord and ribbon displays share: the features and the per-assembly name tables that place them, 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.

Members a composed model contributes are listed here too, so these tables are the whole surface.

Properties

MemberDescriptionDefined by
bezierRadiusRatio
bezierRadiusRatio: types.stripDefault(types.number, 0.1)		how deep a chord bows toward the center, as a fraction of the radius; one straight across the circle reaches it, a shorter one bows in proportion to its spanBaseChordDisplay
id
id: ElementId		BaseDisplay
type
type: types.string		BaseDisplay

Volatiles

MemberDescriptionDefined by
features
features: undefined as Feature[] | undefined		BaseChordDisplay
adapterNames
adapterNames: undefined as Record<string, AdapterNames> | undefined
one entry per assembly of the track on the circle, keyed by canonical nameBaseChordDisplay
reloadCounter
reloadCounter: 0		the fetch's pure "go again" signalBaseChordDisplay
error
error: undefined as unknown		BaseDisplay
statusMessage
statusMessage: undefined as string | undefined		BaseDisplay
statusProgress
statusProgress: undefined as number | undefined		determinate progress fraction [0,1] for the current status, or undefined when the in-flight phase is indeterminate. Set alongside statusMessage by setStatusMessage; a display that never shows a bar simply leaves it undefined.BaseDisplay

Getters

MemberDescriptionDefined by
view
ModelInstanceTypeProps<_OverrideProps<Omit<Omit<…>, never>, { ...; }>> & ... 15 more ... & IStateTreeNode<...>
BaseChordDisplay
trackAssemblyNames
string[]		the track's assemblies that are on the circle, canonical and in the order the circle lays them outBaseChordDisplay
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 itBaseChordDisplay
loaded
boolean		both halves of a draw have arrived: the features and the name tables that place their endsBaseChordDisplay
ready
boolean		BaseChordDisplay
displayError
unknown		what the error ring showsBaseChordDisplay
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 messageBaseChordDisplay
displayPhase
DisplayStatusPhase		BaseChordDisplay
radiusPx
number		BaseChordDisplay
bezierRadius
number		BaseChordDisplay
sliceIndex
Record<string, Slice>		every slice of the circle, keyed by the assembly AND refName a feature off this display's adapter carries. Both halves are needed: two genomes on one circle can each carry a chr1. An elided slice answers to each refName it swallowed.BaseChordDisplay
selectedFeatureId
string | undefined		BaseChordDisplay
parentTrack
AbstractTrackModel		BaseDisplay
RenderingComponent
FC<…>		BaseDisplay
DisplayBlurb
FC<{ model: ModelInstanceTypeProps<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; type: ISimpleType<string>; }> & { ...; } & { ...; } & IStateTreeNode<...>; }> | null
BaseDisplay
adapterConfig
Record<string, unknown>		BaseDisplay
isMinimized
boolean		Returns true if the parent track is minimized. Used to skip expensive operations like autoruns when track is not visible.BaseDisplay
hoveredFeature
unknown		Overridable hook (default undefined): what the pointer is currently over, for readers outside the display. LinearGenomeViewContainer publishes it to session.hovered, the view-wide "what is the user pointing at" channel a plugin can subscribe to.

Declared here because a cross-display consumer can only read a name the base declares — the same reason FetchMixin.fetchInert is a hook rather than a getter each display invents. The container used to read featureUnderMouse, which only the wiggle, alignments and Manhattan families spelled that way — canvas said hoveredFeature, variants hoveredGenotype — so the channel carried a hover from a third of the display types and nothing said which. It also asked only displays[0] of each track.

unknown because the payload genuinely differs — a read, a wiggle bin, a SNP, a genotype cell — and session.hovered is typed to match ("can be anything; code that wants to deal with this should examine it"). Narrow it in the override.		BaseDisplay
featureNoun
string		Overridable hook (default 'feature'): the SINGULAR word for one of the things this display draws, as a menu row or a chip says it — "Hide this read", "Showing 3 variants".

Declared here for the same reason as hoveredFeature above: it is read across the display boundary, by chrome that has no idea which display it is drawing for (SoloSelectionChip, alignments' group-label overlay), and a name only the base declares is a name every such consumer can rely on. Two displays declared it independently and one of those declarations WAS this default.

A control keeps the generic word; content takes this one. "Variant height" reads as a different setting from "Feature height" when it is the same one, so the shared menus stay on "feature" however the display answers here, and the noun varies where it names what the user is looking at — "Showing 3 variants", "Hide this read". A display drawing something the generic word already fits is right to leave this alone.

Distinct from the per-hit noun a context menu takes off the clicked item's own type ("mRNA", "gene"); that names one annotation, this names what the track holds. The hit noun falls back to this.		BaseDisplay
featureWidgetType
{ type: string; id: string; }		The widget openFeatureWidget opens for one of this display's features. Displays may override it. The default is the generic feature widget, for displays drawing plain features.

Displays whose features are a specific kind (a read, a variant, a synteny block) override it, including the id: two displays naming one id share the drawer panel, which suits two displays showing the same kind of feature.		BaseDisplay

Methods

MemberDescriptionDefined by
sliceFor
(assemblyName: string | undefined, refName: string) => Slice		the slice one end of a feature lands on. A feature that names no assembly, as a VCF record does not, is on the track's first assembly.BaseChordDisplay
renderingProps
() => { displayModel: ModelInstanceTypeProps<{ id: IOptionalIType<…>; type: ISimpleType<string>; }> & { ...; } & { ...; } & { ...; } & IStateTreeNode<...>; }
props passed to the renderer's React "Rendering" component. these are client-side only and never sent to the worker. includes displayModel and callbacksBaseDisplay
trackMenuItems
() => MenuItem[]		BaseDisplay

Actions

MemberDescriptionDefined by
openErrorDialog
() => void		BaseChordDisplay
setFeatures
(features: Feature[] | undefined) => void		BaseChordDisplay
setAdapterNames
(names: Record<string, AdapterNames> | undefined) => void		BaseChordDisplay
reload
() => void		BaseChordDisplay
setStatusMessage
(status?: RpcStatus | undefined) => void		BaseDisplay
setError
(error?: unknown) => void		BaseDisplay
clearHoveredFeature
() => void		Overridable hook (default no-op): drop whatever hoveredFeature reports. The writing twin of that getter, and what installClearHoverOnViewportChange calls.

A display that STORES its hover owes an override; one that derives it from the live pointer (MAF, Hi-C, LD) owes nothing, and the default costs it nothing. Declared here so the clear can be installed for every display rather than remembered per display — forgetting it is the failure ARCHITECTURE.md's stored-hover section is about, and it used to be six closures at six call sites, which is six chances to omit one.		BaseDisplay
applyDisplaySettings
(settings: Record<string, unknown>, options?: { allowSetters?: boolean | undefined; } | undefined) => { applied: string[]; unapplied: UnappliedSetting[]; failed: { ...; }[]; }
Apply a set of display settings to the live display, and report which were applied. Each key runs through the display config schema's preProcessSnapshot (shorthand expansions and legacy-key migrations, as showTrackGeneric applies to a session spec's inline track keys), then writes the matching config slot. Keys that are not slots come back in unapplied as { key, reason }, so a caller can tell a misspelling from a key that has an action instead of a slot.

allowSetters also routes a non-slot key to a single-argument action named set<Key>. It is off by default because session specs, share links and embeds pass untyped JSON here, and a default fallback would let them call internal setters (setError, setScrollTop, ...) and call multi-argument setters with one argument. A caller that wants a specific action can call it directly.

A key whose write threw is reported in failed. Only failed means the caller passed a bad value. unapplied needs the caller's own context to read: showTrackGeneric spreads the same settings into the display's snapshot, so a declared prop (resolution) has already landed by the time it reports here, while the restyle path spreads nothing and every entry there did nothing.

A per-key error does not abort the remaining keys. A caller mid-showTrack has already pushed the track, and one rejected value should not leave it half-configured.		BaseDisplay