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Base1DView

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Built into JBrowse core. View source.

Holds a one-dimensional axis of displayed regions, with its zoom and scroll offset, for views other than the linear genome view, such as the two axes of the dotplot.

Its page sits under General because it is not a pluggable view type.

Properties

MemberDescription
id
id: ElementId
displayedRegions
displayedRegions: types.optional(types.frozen<IRegion[]>(), [])
bpPerPx
bpPerPx: 0
offsetPx
offsetPx: 0
minimumBlockWidth
minimumBlockWidth: types.stripDefault(types.number, 0)

Volatiles

MemberDescription
volatileWidth
number

Getters

MemberDescription
width
number
minBpPerPx
number		zoom-in floor; overridden by extensions (e.g. the dotplot axes)
maxBpPerPx
number		zoom-out ceiling; overridden by extensions (e.g. the dotplot axes)
assemblyNames
string[]
displayedRegionsTotalPx
number
maxOffset
number
minOffset
number
totalBp
number
dynamicBlocks
BlockSet
staticBlocks
BlockSet
currBp
number

Methods

MemberDescription
pxToBp
(px: number) => PxToBpResult
bpToPx
(args: { refName: string; coord: number; displayedRegionIndex?: number | undefined; }) => number | undefined

Actions

MemberDescription
setDisplayedRegions
(regions: Region[]) => void
setBpPerPx
(val: number) => void
setVolatileWidth
(width: number) => void
showAllRegions
() => void		this makes a zoomed out view that shows all displayedRegions that makes the overview bar square with the scale bar
zoomOut
() => void
zoomIn
() => void
zoomTo
(bpPerPx: number, offset?: any) => number
scrollTo
(offsetPx: number) => number
centerAt
(coord: number, refName: string | undefined, displayedRegionIndex: number) => void
scroll
(distance: number) => number		note: the scroll is clamped to keep the view on the main screen
moveTo
(start?: BpOffset | undefined, end?: BpOffset | undefined, minBpPerPx?: number | undefined) => void
offset is the base-pair-offset in the displayed region, index is the index of the displayed region in the linear genome view