ChordSyntenyDisplay

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.

Example usage#

The circular-view display for a SyntenyTrack: each alignment is drawn as a ribbon between its span on one side and its mate's span on the other, so an inversion reads as a twist. The track config below is what creates it; its colors are the config slots on ChordSyntenyDisplay:

{
  type: 'SyntenyTrack',
  trackId: 'volvox_self',
  name: 'Volvox self-alignment',
  assemblyNames: ['volvox', 'volvox'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/volvox_self.paf',
    queryAssembly: 'volvox',
    targetAssembly: 'volvox',
  },
  displays: [
    {
      type: 'ChordSyntenyDisplay',
      displayId: 'volvox_self-ChordSyntenyDisplay',
    },
  ],
}

A track aligning two assemblies needs both of them on the circle, which is the view's assembly: ['hg38', 'mm39'] — see the synteny track guide.

The configuration slots for this model are documented on its config schema page.

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

Properties#

Volatiles#

adapterNames: undefined as Record<string, AdapterNames> | undefined

Getters#

ModelInstanceTypeProps<_OverrideProps<Omit<…>, { ...; }>> & ... 13 more ... & IStateTreeNode<...>

FC<{ model: ModelInstanceTypeProps<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; type: ISimpleType<string>; }> & { ...; } & { ...; } & IStateTreeNode<...>; }> | null

Methods#

(assemblyName: string | undefined, refName: string) => Slice | undefined

(_opts: ViewExportSvgOptions & { theme?: ThemeOptions | undefined; }) => Promise<Element | null>

() => { displayModel: ModelInstanceTypeProps<{ id: IOptionalIType<…>; type: ISimpleType<string>; }> & { ...; } & { ...; } & { ...; } & IStateTreeNode<...>; }

Actions#

(settings: Record<…>, options?: { allowSetters?: boolean | undefined; } | undefined) => { applied: string[]; unapplied: string[]; failed: { key: string; error: string; }[]; }