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DotplotView

Note: this document is automatically generated from 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

DotplotView - Properties​

property: id​

// type signature
IOptionalIType<ISimpleType<string>, [undefined]>
// code
id: ElementId

property: type​

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

property: height​

// type signature
number
// code
height: 600

property: borderSize​

// type signature
number
// code
borderSize: 20

property: tickSize​

// type signature
number
// code
tickSize: 5

property: vtextRotation​

// type signature
number
// code
vtextRotation: 0

property: htextRotation​

// type signature
number
// code
htextRotation: -90

property: fontSize​

// type signature
number
// code
fontSize: 15

property: trackSelectorType​

// type signature
string
// code
trackSelectorType: 'hierarchical'

property: assemblyNames​

// type signature
IArrayType<ISimpleType<string>>
// code
assemblyNames: types.array(types.string)

property: drawCigar​

// type signature
true
// code
drawCigar: true

property: hview​

// type signature
IOptionalIType<IModelType<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; displayedRegions: IOptionalIType<IType<Region[], Region[], Region[]>, [...]>; bpPerPx: IType<...>; offsetPx: IType<...>; interRegionPaddingWidth: IOptionalIType<...>; minimumBlockWidth: IOptionalIType<...>; }, { ...; } & ... 8 more ......
// code
hview: types.optional(DotplotHView, {})

property: vview​

// type signature
IOptionalIType<IModelType<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; displayedRegions: IOptionalIType<IType<Region[], Region[], Region[]>, [...]>; bpPerPx: IType<...>; offsetPx: IType<...>; interRegionPaddingWidth: IOptionalIType<...>; minimumBlockWidth: IOptionalIType<...>; }, { ...; } & ... 8 more ......
// code
vview: types.optional(DotplotVView, {})

property: tracks​

// type signature
IArrayType<IModelType<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; type: ISimpleType<string>; configuration: AnyConfigurationSchemaType; minimized: IType<...>; displays: IArrayType<...>; }, { ...; } & ... 1 more ... & { ...; }, _NotCustomized, _NotCustomized>>
// code
tracks: types.array(
          pm.pluggableMstType('track', 'stateModel') as BaseTrackStateModel,
        )

property: viewTrackConfigs​

this represents tracks specific to this view specifically used for read vs ref dotplots where this track would not really apply elsewhere

// type signature
IArrayType<IAnyModelType>
// code
viewTrackConfigs: types.array(pm.pluggableConfigSchemaType('track'))

DotplotView - Getters​

getter: width​

// type
number

getter: assemblyErrors​

// type
string

getter: assembliesInitialized​

// type
boolean

getter: initialized​

// type
boolean

getter: hticks​

// type
any[]

getter: vticks​

// type
any[]

getter: loading​

// type
boolean

getter: viewWidth​

// type
number

getter: viewHeight​

// type
number

getter: views​

// type
({ id: string; displayedRegions: Region[] & IStateTreeNode<IOptionalIType<IType<Region[], Region[], Region[]>, [undefined]>>; bpPerPx: number; offsetPx: number; interRegionPaddingWidth: number; minimumBlockWidth: number; } & ... 11 more ... & IStateTreeNode<...>)[]

getter: error​

// type
unknown

DotplotView - Methods​

method: renderProps​

// type signature
renderProps: () => any

method: menuItems​

// type signature
menuItems: () => ({ label: string; onClick: () => void; icon: OverridableComponent<SvgIconTypeMap<{}, "svg">> & { muiName: string; }; } | { label: string; onClick: () => void; icon?: undefined; } | { ...; })[]

DotplotView - Actions​

action: setShowPanButtons​

// type signature
setShowPanButtons: (flag: boolean) => void

action: setWheelMode​

// type signature
setWheelMode: (str: string) => void

action: setCursorMode​

// type signature
setCursorMode: (str: string) => void

action: setDrawCigar​

// type signature
setDrawCigar: (flag: boolean) => void

action: clearView​

returns to the import form

// type signature
clearView: () => void

action: setBorderX​

// type signature
setBorderX: (n: number) => void

action: setBorderY​

// type signature
setBorderY: (n: number) => void

action: setWidth​

// type signature
setWidth: (newWidth: number) => number

action: setHeight​

// type signature
setHeight: (newHeight: number) => number

action: setError​

// type signature
setError: (e: unknown) => void

action: zoomOut​

// type signature
zoomOut: () => void

action: zoomIn​

// type signature
zoomIn: () => void

action: activateTrackSelector​

// type signature
activateTrackSelector: () => Widget

action: showTrack​

// type signature
showTrack: (trackId: string, initialSnapshot?: {}) => void

action: hideTrack​

// type signature
hideTrack: (trackId: string) => number

action: toggleTrack​

// type signature
toggleTrack: (trackId: string) => boolean

action: setAssemblyNames​

// type signature
setAssemblyNames: (target: string, query: string) => void

action: setViews​

// type signature
setViews: (arr: ModelCreationType<ExtractCFromProps<{ id: IOptionalIType<ISimpleType<string>, [undefined]>; displayedRegions: IOptionalIType<IType<Region[], Region[], Region[]>, [...]>; bpPerPx: IType<...>; offsetPx: IType<...>; interRegionPaddingWidth: IOptionalIType<...>; minimumBlockWidth: IOptionalIType<...>; }>>[]) => void

action: getCoords​

// type signature
getCoords: (mousedown: Coord, mouseup: Coord) => { coord: number; index: number; refName: string; oob: boolean; assemblyName: string; offset: number; start: number; end: number; reversed?: boolean; }[]

action: zoomInToMouseCoords​

zooms into clicked and dragged region

// type signature
zoomInToMouseCoords: (mousedown: Coord, mouseup: Coord) => void

action: showAllRegions​

// type signature
showAllRegions: () => void

action: onDotplotView​

creates a linear synteny view from the clicked and dragged region

// type signature
onDotplotView: (mousedown: Coord, mouseup: Coord) => void

action: exportSvg​

creates an svg export and save using FileSaver

// type signature
exportSvg: (opts?: ExportSvgOptions) => Promise<void>

action: squareView​

// type signature
squareView: () => void

action: squareViewProportional​

// type signature
squareViewProportional: () => void