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LinearSNPCoverageDisplay

Note: this document is automatically generated from @jbrowse/mobx-state-tree objects in our source code. See Core concepts and intro to pluggable elements for more info

Also note: this document represents the state model API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag

Source code

GitHub page

Docs​

extends

LinearSNPCoverageDisplay - Properties​

property: type​

// type signature
ISimpleType<"LinearSNPCoverageDisplay">
// code
type: types.literal('LinearSNPCoverageDisplay')

property: showInterbaseCounts​

// type signature
IMaybe<ISimpleType<boolean>>
// code
showInterbaseCounts: types.maybe(types.boolean)

property: showInterbaseIndicators​

// type signature
IMaybe<ISimpleType<boolean>>
// code
showInterbaseIndicators: types.maybe(types.boolean)

property: showArcs​

// type signature
IMaybe<ISimpleType<boolean>>
// code
showArcs: types.maybe(types.boolean)

property: minArcScore​

// type signature
IOptionalIType<ISimpleType<number>, [undefined]>
// code
minArcScore: types.optional(types.number, 0)

property: filterBySetting​

// type signature
IType<FilterBy, FilterBy, FilterBy>
// code
filterBySetting: types.frozen<FilterBy | undefined>()

property: colorBySetting​

// type signature
IType<ColorBy, ColorBy, ColorBy>
// code
colorBySetting: types.frozen<ColorBy | undefined>()

property: jexlFilters​

// type signature
IOptionalIType<IArrayType<ISimpleType<string>>, [undefined]>
// code
jexlFilters: types.optional(types.array(types.string), [])

LinearSNPCoverageDisplay - Getters​

getter: colorBy​

// type
any

getter: filterBy​

// type
any

getter: modificationThreshold​

// type
any

getter: rendererConfig​

// type
any

getter: showArcsSetting​

// type
any

getter: skipFeatures​

Collect all skip features from rendered blocks for cross-region arc drawing Uses a Map to deduplicate features that appear in multiple blocks Only computed when showArcsSetting is true for performance Filters out arcs with score below minArcScore

// type
Feature[]

getter: showInterbaseCountsSetting​

// type
any

getter: showInterbaseIndicatorsSetting​

// type
any

getter: autorunReady​

// type
boolean

getter: renderReady​

// type
;() => boolean

getter: TooltipComponent​

// type
LazyExoticComponent<(props: { model: { featureUnderMouse?: Feature; mouseoverExtraInformation?: string; visibleModifications: Map<string, { color: string; base: string; strand: string; }>; simplexModifications?: Set<string>; }; height: number; offsetMouseCoord: [...]; clientMouseCoord: [...]; clientRect?: DOMRect; }...

getter: adapterConfig​

// type
{
  type: string
  subadapter: any
  sequenceAdapter: unknown
}

getter: rendererTypeName​

// type
string

getter: graphType​

// type
boolean

getter: filters​

// type
any

LinearSNPCoverageDisplay - Methods​

method: adapterProps​

// type signature
adapterProps: () => any

method: renderProps​

// type signature
renderProps: () => any

method: renderingProps​

// type signature
renderingProps: () => { displayModel: { [x: string]: any; heightPreConfig: number; userBpPerPxLimit: number; userByteSizeLimit: number; blockState: IMSTMap<IModelType<{ key: ISimpleType<string>; region: IType<...>; reloadFlag: IType<...>; isLeftEndOfDisplayedRegion: IType<...>; isRightEndOfDisplayedRegion: IType<...>; }, { ...; } &...

method: renderSvg​

Custom renderSvg that includes sashimi arcs

// type signature
renderSvg: (opts: ExportSvgDisplayOptions) => Promise<Element>

method: contextMenuItems​

// type signature
contextMenuItems: () => any[]

method: trackMenuItems​

// type signature
trackMenuItems: () => any[]

method: legendItems​

Returns legend items for SNP coverage display

// type signature
legendItems: (theme: Theme) => LegendItem[]

LinearSNPCoverageDisplay - Actions​

action: setConfig​

// type signature
setConfig: (configuration: AnyConfigurationModel) => void

action: setFilterBy​

// type signature
setFilterBy: (filter: FilterBy) => void

action: setColorScheme​

// type signature
setColorScheme: (colorBy?: ColorBy) => void

action: setJexlFilters​

// type signature
setJexlFilters: (filters: string[]) => void

action: setShowInterbaseIndicators​

// type signature
setShowInterbaseIndicators: (arg: boolean) => void

action: setShowInterbaseCounts​

// type signature
setShowInterbaseCounts: (arg: boolean) => void

action: setShowArcs​

// type signature
setShowArcs: (arg: boolean) => void

action: setMinArcScore​

// type signature
setMinArcScore: (arg: number) => void