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 origin, 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 gccontent's two GC displays.
Members a composed model contributes are listed here too, so these tables are the whole surface.
Getters
| Member | Description | Defined by |
|---|---|---|
resolutionnumber | Points per pixel the fetch asks for, clamped to what the Resolution menu offers: the slot is reachable from a track config, which runs no setter, and 0 there divides by zero inside the adapter. | WiggleCommonMixin |
rpcDataMapReadonlyMap<number, WiggleDataResult> | The fetched scores, keyed by displayedRegionIndex — the foundation's per-region store, narrowed. | WiggleCommonMixin |
originnumber | The value bars grow from, which a colour scale also reads where its own domain says nothing. | 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. The wiggle display 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 display that draws scales.y.rules. | 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 |
scaleTypestring | ScoreScaleMixin | |
scaleTypeChoicesstring[] | The scale types this display's own enum admits, which is what the scale-type radio offers; a display with one draws no radio. | ScoreScaleMixin |
autoscaleTypestring | undefined | undefined on a display whose domain consults no autoscale mode. | ScoreScaleMixin |
numStdDevnumber | ScoreScaleMixin | |
numQuantilenumber | ScoreScaleMixin | |
symlogConstantnumber | Raw slot; 0 means "derive from the domain". Resolve it with resolveSymlogConstant once the domain is known. | ScoreScaleMixin |
manualMinScorenumber | undefined | The lower bound the config pins, undefined where it pins none. | ScoreScaleMixin |
manualMaxScorenumber | undefined | The upper bound the config pins, undefined where it pins none. | ScoreScaleMixin |
scaleTitlestring | undefined | scales.y.title as written: undefined while unset, which leaves the caption to the display, and the empty string for an axis the author wants bare. Also undefined on a display whose scale declares no title. | ScoreScaleMixin |
scoreRulesDrawnboolean | Whether this display draws scales.y.rules, which is whether the score menu offers the reference lines: its scale declares them, and a scale it places y through rules a band for them to cross, which a density plot's colour-mapped rows and a colour ramp do not. | ScoreScaleMixin |
scoreRulesValueScaleRule[] | scales.y.rules, read off the live nodes: a snapshot strips a slot at its default, and a rule at 0 is one. Empty on a display whose scale declares no rules. | 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, which is the one thing that must not be duplicated: config bounds still win, precisely because they are checked before this is consulted. | ScoreAxisMixin |
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. | ScoreAxisMixin |
minScoreBoundnumber | undefined | Resolved lower bound; undefined means autoscale this end. | ScoreAxisMixin |
maxScoreBoundnumber | undefined | Resolved upper bound; undefined means autoscale this end. | ScoreAxisMixin |
hasManualScoreBoundsboolean | Whether the user has pinned either end, which is a different question from whether either end resolved to a number: defaultScoreDomain fills the unset ends 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 nothing already there is a row that does nothing and never goes away. | ScoreAxisMixin |
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, and where each of the scale's rules inside the domain lands in that same box, through the scale type the renderer places its values by. | ScoreAxisMixin |
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 | |
setOrigin(val?: number | 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 | |
setScoreRules(rules: (number | ValueScaleRule)[]) => void | Replaces scales.y.rules whole, each entry in a form the config takes: a number, or { value, color, label }. | ScoreScaleMixin |