WiggleCommonMixin
Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Provided by the wiggle plugin. View source.
Extends ScoreFieldConfigMixin with the narrowed rpcDataMap, the autoscale
domain and the wiggle-specific config: the pos/neg palette, rendering type,
summary mode, resolution and the line/gap settings. Extended on this chain
with .props()/.views() rather than a mixin composed in, so no
types.compose layer is added (ADR-041).
Used by LinearWiggleDisplay and MultiLinearWiggleDisplay.
Members a composed model contributes are listed here too, so these tables are the whole surface.
Properties
| Member | Description |
|---|---|
resolutionresolution: types.stripDefault(types.number, 1) |
Getters
| Member | Description | Defined by |
|---|---|---|
rpcDataMapReadonlyMap<number, WiggleDataResult> | The fetched scores, keyed by displayedRegionIndex — the foundation's per-region store, narrowed. | WiggleCommonMixin |
zoomFetchKeystring | Strict zoom equality (adr-008): the worker bins scores to the requested bpPerPx, so data fetched at another zoom is the wrong summary, however well the viewport still sits inside it. Here rather than on ScoreFieldConfigMixin: the rule is about what a fetch returns, and LinearManhattanDisplay composes that mixin while fetching untransformed SNPs. | WiggleCommonMixin |
symlogConstantnumber | Raw symlogConstant slot; 0 means "derive from the domain". Resolve it with resolveSymlogConstant once the domain is known.Here rather than on the score config because only the wiggle schemas declare the slot, and getConf returns undefined for a composer that does not. | WiggleCommonMixin |
posColorstring | WiggleCommonMixin | |
negColorstring | WiggleCommonMixin | |
bicolorPivotnumber | WiggleCommonMixin | |
densityColorRampstring | Density's colour ramp: 'default' for the white→track-colour fade, or a named 256-entry LUT (see densityColorRamp.ts). Rides the render state, so a change is a uniform flag plus one LUT texture upload — never a refetch or a buffer re-encode. | WiggleCommonMixin |
numQuantilenumber | WiggleCommonMixin | |
lineWidthnumber | WiggleCommonMixin | |
maxGapMultiplenumber | Interpolated-line gap threshold, as a multiple of the track's own mean point spacing (see gapBreakLimit). 0 keeps one connected line. | WiggleCommonMixin |
summaryScoreModestring | WiggleCommonMixin | |
renderingTypestring | WiggleCommonMixin | |
minimalTicksboolean | WiggleCommonMixin | |
hasResolutionboolean | Asked of the display's OWN adapter, which for the GC display is the synthesized GCContentAdapter rather than the track's raw sequence adapter — the two diverged when the adapter config moved onto the shared model. It answers the same today, since only BigWigAdapter and MultiWiggleAdapter declare the capability, and the display's adapter is the honest subject: the resolution slot it gates is passed to whatever this display fetches from. | WiggleCommonMixin |
effectiveSummaryScoreModestring | The summary mode actually drawn. Density has no whiskers presentation — sourceLayers falls back to the average scores — so the autoscale domain reads this rather than the raw slot; otherwise the color ramp spans the whisker extremes while the plot paints averages, and the score legend reports a range nothing on screen reaches. Single-wiggle defaults to whiskers, so plain "plot type → Density" hit this. | WiggleCommonMixin |
autoscaleSourceNamesSet<string> | undefined | Source names to include when computing the autoscale domain; undefined means every fetched source. Multi-wiggle always fetches all sources and filters client-side, so it overrides this to the visible subset — otherwise a subtree filter that hides sources would leave the Y-axis scaled to the hidden ones. | WiggleCommonMixin |
scoreRuleValuesnumber[] | Scores the axis must reach whatever the data does, so a rule drawn at one stays on it. [] here and overridden by the displays that draw score rules — MultiLinearWiggleDisplay stacks a plot box per row and draws none, so it keeps the base. | WiggleCommonMixin |
domain[number, number] | undefined | The autoscaled domain over the sources visible in the settled blocks. undefined until the view and the data are ready, which is not the [0, 1] a caller falls back to — see visibleStatsDomain. | WiggleCommonMixin |
scoreFieldstring | The feature field the worker plots on the score axis, score by default. A fetch input: every composing display carries it in its rpcProps(), since the field is read where the features are. | ScoreFieldConfigMixin |
scatterPointSizenumber | WiggleScoreConfigMixin | |
displayCrossHatchesboolean | The configured cross-hatch setting the menu toggles; showCrossHatches is what draws. | WiggleScoreConfigMixin |
isDensityModeboolean | Whether score maps to color instead of height; a display overrides it. | WiggleScoreConfigMixin |
showCrossHatchesboolean | Whether the score-axis cross hatches draw: never in density mode, which has no height axis to rule and no toggle in its menu. | WiggleScoreConfigMixin |
| declaredValueScale | Overridable hook: a value scale the display declares somewhere other than these slots — the mark display's encoding.y. Where it answers, it is the owner and the slots below stand in only for the ends it leaves open, so a scale is read from one place whichever place that is. Default none, which is every display whose axis IS these slots. | ScoreScaleMixin |
scaleTypestring | ScoreScaleMixin | |
autoscaleTypestring | ScoreScaleMixin | |
numStdDevnumber | ScoreScaleMixin | |
minScorenumber | Raw slot value, sentinel intact — see the class comment. | ScoreScaleMixin |
maxScorenumber | Raw slot value, sentinel intact — see the class comment. | ScoreScaleMixin |
defaultScoreDomain[number | undefined, number | undefined] | Overridable hook: what each end of the domain falls back to where the config leaves its bound unset. [undefined, undefined] — the default — means autoscale both ends, which is right for a track whose scores have no absolute meaning (a bigwig's units are its own).A display whose scores are bounded by construction overrides it, so the axis stops being a function of what happens to be on screen: GC content is a fraction, so 0 and 1 are its real limits and mean the same thing at every locus. Autoscaled, the same GC value drew at different heights depending on where the user had panned, and the track could not be read across loci. A hook rather than a config default because the answer can depend on display state — GC's does, on gcMode — and rather than each display re-resolving the sentinels below, which is the one thing that must not be duplicated: config bounds still win, precisely because they are checked before this is consulted. | ScoreScaleMixin |
manualMinScorenumber | undefined | The lower bound the config really sets, undefined at the sentinel. | ScoreScaleMixin |
manualMaxScorenumber | undefined | The upper bound the config really sets, undefined at the sentinel. | ScoreScaleMixin |
minScoreBoundnumber | undefined | Resolved lower bound; undefined means autoscale this end. | ScoreScaleMixin |
maxScoreBoundnumber | undefined | Resolved upper bound; undefined means autoscale this end. | ScoreScaleMixin |
hasManualScoreBoundsboolean | Whether the user has pinned either end, which is a different question from whether either end resolved to a number: defaultScoreDomain fills the sentinels in, so a GC content track answers yes to the second with nothing configured. The score menu asks this one — it gates the "Clear manual min/max" row, and a Clear that writes the sentinels already there is a row that does nothing and never goes away. | ScoreScaleMixin |
valueScalesValueScale[] | Overridable hook (default none): the scales this display draws its y through. A display that answers it gets an axis per band of each, with its cross-hatches, placed by DisplayChrome and renderDisplaySvg, and the ticks derived below. | ScoreScaleMixin |
axesYAxis[] | The axes, one per declared scale whose domain resolved: where each tick lands in the band's own pixel space, through computeYTicks unless the scale brought its own ladder. | ScoreScaleMixin |
Actions
| Member | Description | Defined by |
|---|---|---|
| setRpcData | Stage a region as fetched, with this mixin's payload shape — so a test stands up a loaded display in one call. Production goes through ctx.commitRegion. | WiggleCommonMixin |
selectFeature(feat: WiggleHoveredFeature) => void | WiggleCommonMixin | |
setResolution(res: number) => void | WiggleCommonMixin | |
setBicolorPivot(val?: number | undefined) => void | WiggleCommonMixin | |
setPosColor(color?: string | undefined) => void | Lives here beside the posColor/negColor getters and setBicolorPivot so both the single- and multi-wiggle color editors write the score-sign palette the same way. | WiggleCommonMixin |
setNegColor(color?: string | undefined) => void | WiggleCommonMixin | |
setRenderingType(type: string) => void | WiggleCommonMixin | |
setSummaryScoreMode(val: string) => void | WiggleCommonMixin | |
setLineWidth(val?: number | undefined) => void | WiggleCommonMixin | |
toggleCrossHatches() => void | WiggleScoreConfigMixin | |
setScatterPointSize(val?: number | undefined) => void | WiggleScoreConfigMixin | |
setScaleType(scaleType: string) => void | ScoreScaleMixin | |
setAutoscale(val?: string | undefined) => void | ScoreScaleMixin | |
setMinScore(val?: number | undefined) => void | ScoreScaleMixin | |
setMaxScore(val?: number | undefined) => void | ScoreScaleMixin |