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MultiVariantBaseModel

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

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Docs​

extends

MultiVariantBaseModel - Properties​

property: type​

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

property: layout​

// type signature
IOptionalIType<IType<Source[], Source[], Source[]>, [undefined]>
// code
layout: types.optional(types.frozen<Source[]>(), [])

property: configuration​

// type signature
any
// code
configuration: ConfigurationReference(configSchema)

property: minorAlleleFrequencyFilterSetting​

When undefined, falls back to config value

// type signature
IMaybe<ISimpleType<number>>
// code
minorAlleleFrequencyFilterSetting: types.maybe(types.number)

property: showSidebarLabelsSetting​

When undefined, falls back to config value

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

property: showTreeSetting​

When undefined, falls back to config value

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

property: renderingModeSetting​

When undefined, falls back to config value

// type signature
IMaybe<ISimpleType<string>>
// code
renderingModeSetting: types.maybe(types.string)

property: rowHeightMode​

Controls row height: 'auto' calculates from available height, or a number specifies manual pixel height per row

// type signature
IOptionalIType<ITypeUnion<number | "auto", number | "auto", number | "auto">, [undefined]>
// code
rowHeightMode: types.optional(
          types.union(types.literal('auto'), types.number),
          'auto',
        )

property: lengthCutoffFilter​

// type signature
IOptionalIType<ISimpleType<number>, [undefined]>
// code
lengthCutoffFilter: types.optional(
          types.number,
          Number.MAX_SAFE_INTEGER,
        )

property: jexlFilters​

// type signature
IMaybe<IArrayType<ISimpleType<string>>>
// code
jexlFilters: types.maybe(types.array(types.string))

property: referenceDrawingModeSetting​

When undefined, falls back to config value (showReferenceAlleles)

// type signature
IMaybe<ISimpleType<string>>
// code
referenceDrawingModeSetting: types.maybe(types.string)

property: clusterTree​

// type signature
IMaybe<ISimpleType<string>>
// code
clusterTree: types.maybe(types.string)

property: treeAreaWidth​

// type signature
IOptionalIType<ISimpleType<number>, [undefined]>
// code
treeAreaWidth: types.optional(types.number, 80)

property: lineZoneHeight​

Height reserved for elements above the main display (e.g., connecting lines in matrix view)

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

MultiVariantBaseModel - Getters​

getter: renderingMode​

Returns the effective rendering mode, falling back to config

// type
string

getter: autoHeight​

// type
boolean

getter: minorAlleleFrequencyFilter​

Returns the effective minor allele frequency filter, falling back to config

// type
any

getter: showSidebarLabels​

Returns the effective showSidebarLabels setting, falling back to config

// type
any

getter: showTree​

Returns the effective showTree setting, falling back to config

// type
any

getter: referenceDrawingMode​

Returns the effective reference drawing mode, derived from config showReferenceAlleles

// type
string

getter: activeFilters​

// type
any

getter: sources​

// type
Source[]

getter: root​

// type
any

getter: sourceMap​

// type
{ [k: string]: Source; }

getter: availableHeight​

Available height for rows (total height minus lineZoneHeight)

// type
number

getter: nrow​

// type
number

getter: rowHeight​

// type
number

getter: hierarchy​

// type
any

getter: canDisplayLabels​

// type
any

getter: totalHeight​

// type
number

getter: featuresReady​

// type
boolean

MultiVariantBaseModel - Methods​

method: adapterProps​

// type signature
adapterProps: () => any

method: trackMenuItems​

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

method: getPortableSettings​

// type signature
getPortableSettings: () => { minorAlleleFrequencyFilter: any; showSidebarLabelsSetting: boolean; showTree: any; renderingMode: string; lengthCutoffFilter: number; jexlFilters: IMSTArray<ISimpleType<string>> & IStateTreeNode<...>; ... 4 more ...; height: number; }

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: legendItems​

Returns legend items for rendering colors based on current mode

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

MultiVariantBaseModel - Actions​

action: setJexlFilters​

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

action: setRowHeight​

// type signature
setRowHeight: (arg: number | "auto") => void

action: setHoveredGenotype​

// type signature
setHoveredGenotype: (arg?: { genotype: string; name: string; }) => void

action: setHoveredTreeNode​

// type signature
setHoveredTreeNode: (node?: HoveredTreeNode) => void

action: setTreeCanvasRef​

// type signature
setTreeCanvasRef: (ref: HTMLCanvasElement) => void

action: setMouseoverCanvasRef​

// type signature
setMouseoverCanvasRef: (ref: HTMLCanvasElement) => void

action: setTreeAreaWidth​

// type signature
setTreeAreaWidth: (width: number) => void

action: setFeatures​

// type signature
setFeatures: (f: Feature[]) => void

action: setColorByApplied​

// type signature
setColorByApplied: (value: boolean) => void

action: setLayout​

// type signature
setLayout: (layout: Source[], clearTree?: boolean) => void

action: clearLayout​

// type signature
clearLayout: () => void

action: setClusterTree​

// type signature
setClusterTree: (tree?: string) => void

action: setSourcesLoading​

// type signature
setSourcesLoading: (token: StopToken) => void

action: setSimplifiedFeaturesLoading​

// type signature
setSimplifiedFeaturesLoading: (token: StopToken) => void

action: setSources​

// type signature
setSources: (sources: Source[]) => void

action: setMafFilter​

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

action: setShowSidebarLabels​

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

action: setShowTree​

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

action: setPhasedMode​

// type signature
setPhasedMode: (arg: string) => void

action: setAutoHeight​

Toggle auto height mode. When turning off, uses default of 10px per row.

// type signature
setAutoHeight: (auto: boolean) => void

action: setHasPhased​

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

action: setSampleInfo​

// type signature
setSampleInfo: (arg: Record<string, SampleInfo>) => void

action: setReferenceDrawingMode​

// type signature
setReferenceDrawingMode: (arg: string) => void