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ScoreScaleMixin

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

Value scale, read and written at a YScalePaths map's paths (encoding.y, the coverage band's coverage.encoding.y). yChannelSchema / yFieldChannelSchema. Brings ScoreAxisMixin plus scaleType / scaleZero / fenceQuantile / clipFenceQuantile / symlogConstant / manual* and their setters, i.e. the whole ScoreScaleModel interface the Y axis row and its drawer widget consume

The value scale of every quantitative display: wiggle and the mark display, Manhattan among them, declare encoding.y, and the alignments, LGVSynteny and MAF coverage band coverage.encoding.y, each through yChannelSchema; each composes this with the map to its members. It backs ScoreAxisMixin's three overridable members off that object and adds the setters that write it, so composing this is how a display satisfies ScoreScaleModel in scoreMenuItems.ts — the interface the Y axis row and its drawer widget consume.

Deliberately just the scale and the guides it owns. Colors, resolution and the autoscale computation stay in WiggleScoreConfigMixin / WiggleCommonMixin — the alignments coverage band shares this scale but none of the rest.

Each section ends with the members a composed model contributes, linked to the page that documents them.

Volatiles

MemberDescription
unclippedFenceQuantile
number | undefined

Getters

MemberDescription
scaleType
string
scaleZero
boolean		The y scale's zero: whether an autoscaled linear or symlog axis reaches 0.
fenceQuantile
number		The y scale's fence quantile: what an unpinned end follows, 1 the extremes and below it that quantile of each sign.
clipFenceQuantile
number		The quantile "Clip extreme outliers" fences at: the one an untick this session wrote over, else the scale's own default where that is below 1, else 0.99.
symlogConstant
number		Raw slot; 0 means "derive from the domain". Resolve it with resolveSymlogConstant once the domain is known.
domainMin
number | undefined		The lower bound the config pins, undefined where it pins none.
domainMax
number | undefined		The upper bound the config pins, undefined where it pins none.
autoscaleGroup
string | undefined		The y scale's autoscale group, undefined while it names none.
scaleTitle
string		The y axis title, '' while unset
grid
boolean		The y axis grid
showAxis
boolean		Whether the y axis draws, axis.show
scoreRulesDrawn
boolean		Whether this display draws the y scale's rules, which is whether the Y axis panel offers Include 0 and the reference lines: a scale it places y through rules a band for them to cross, which a density plot's color-mapped rows and a color ramp do not.
scoreRules
ValueScaleRule[]		The y scale's rules, read off the live nodes.
axisGuide
Pick<ValueScale, "caption" | "grid" | "rules" | "showAxis">		What the y channel's axis and rules say of a value scale, which each display spreads onto the scales it declares.
9 inherited getters from one model

From ScoreAxisMixin: defaultScoreDomain, valueScales, autoscaleRange, axisReachesZero, autoscaledDomain, resolvedDomainMin, resolvedDomainMax, pinsDomain, axes

Actions

MemberDescription
setScaleType
(scaleType: string) => void
setScaleZero
(zero: boolean) => void
setFenceQuantile
(quantile: number) => void
setDomainMin
(val?: number | undefined) => void
setDomainMax
(val?: number | undefined) => void
setMinScore
(val?: number | undefined) => void		v4's name for setDomainMin.
setMaxScore
(val?: number | undefined) => void		v4's name for setDomainMax.
setAutoscaleGroup
(group?: string | undefined) => void
setGrid
(grid: boolean) => void
setScoreRules
(rules: (number | ValueScaleRule)[]) => void		Replaces the y scale's rules whole, each entry in a form the config takes: a number, or { value, color, label }.
resetYScale
() => void		Back to what the config.json says, or to what a session-owned track was added with, so an admin's declared axis survives a reset; slots the base leaves unset take their defaults.