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Dotplot1DView

Auto-generated from the @jbrowse/mobx-state-tree model in the source — see the developer guide for concepts. Provided by the dotplot-view plugin. View source.

Holds one axis of a dotplot: its displayed regions, zoom and scroll offset, and the ticks and labels drawn along it.

Its page sits under General because it is not a pluggable view type. ref https://mobx-state-tree.js.org/concepts/volatiles on volatile state used here

Getters

MemberDescription
dynamicBlocks
BlockSet		this uses padding=false and elision=false
visibleRegions
{ refName: string; start: number; end: number; assemblyName: string; reversed: boolean | undefined; displayedRegionIndex: number; }[]
The on-screen content blocks under the field names LinearGenomeView.visibleRegions uses, so this axis and a synteny row hand the shared comparative fetch window (syntenyFetchRegions) the same thing and the two displays' fetchRegions are one call each. Carries only what that window reads; the screen-px pair an LGV also exposes has no reader here, and deriving it would make this recompute with offsetPx.
fitBpPerPx
number		The zoom that fits this axis' whole genome, with a tenth of the axis to spare. Its own getter, separate from maxBpPerPx, because on a locked plot the two differ — see DotplotHView.
maxBpPerPx
number
minBpPerPx
number
refNameLabels
Map<string, string>		refName -> the string the axis prints for it. Off displayedRegions rather than the visible blocks, so panning and zooming can't change a label, and handed to labelMarginPx so the margin is sized against the very strings drawn.
ticks
Tick[]
visibleTickPositions
VisibleTick[]		The ticks that land on the drawn axis, thinned to what can be read and flagged for labelling. Clipped before thinning: spacing is a question about what is on screen, and offscreen ticks (staticBlocks run a screen past each edge) would otherwise claim slots from visible ones.
blockLabelKeysToHide
Set<string>		Block-label keys whose labels would overlap, and are hidden
regionSignature
string		Signature of the displayed-region order and orientation, which a diagonalize reorder/flip changes and a zoom or pan does not. Its own primitive-valued computed so every display's fetch key reads it without rebuilding a string per region on each wheel step.

Actions

MemberDescription
center
() => void