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SyntenyColorsMixin

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

The color settings every view drawing synteny tracks shares — the linear synteny view, the dotplot and the circular view: TrackColorsMixin's color object and palette, the opacity object and the shortest alignment drawn, over the tracks the view says it draws. A view supplies syntenyTracks(), its opacity default and, optionally, the field it paints by until told otherwise.

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

Properties

MemberDescription
opacity
opacity: types.stripDefault(syntenyOpacityConfigSchema, {})		The opacity every alignment draws at, a SyntenyOpacity object: a number for all of them, or a field each carries read into opacities, { field: "identity" } or a column the tracks declare. Unset, the view's default: low on the synteny view for dense whole-genome hairballs, opaque on the dotplot.
minAlignmentLength
minAlignmentLength: types.stripDefault(
          types.number,
          DEFAULT_MIN_ALIGNMENT_LENGTH,
        )
Hide alignment blocks shorter than this many bp, which cuts whole-genome hairball noise.
3 inherited properties from one model

From TrackColorsMixin: color, trackColors, hideUnlabelled

Volatiles

1 inherited volatile from one model

From TrackColorsMixin: seenAttributeRanges

Getters

MemberDescription
defaultOpacity
number		The constant opacity a reset returns to.
opacitySetting
SyntenyOpacitySnapshot		The opacity object as its snapshot holds it.
opacityFade
SyntenyOpacitySnapshot | undefined		What the color pass fades each alignment by: the field's mapping with its range as shares of opacityLevel, or undefined while opacity draws its constant, so the slider recolors nothing either way.
opacityLevel
number		The opacity every alignment draws at before a field's fade: the shader's uniform (opacityLevel).
opacityField
string		The field opacity fades by, '' while it draws its constant.
13 inherited getters from one model

From TrackColorsMixin: colorSetting, colorPaint, colorValue, colorDomain, colorRange, colorableAttributes, attributeRanges, colorableTracks, trackColorAssignments, colorField, hasLegendKey, colorLegendChips, colorScales

Methods

MemberDescription
syntenyTracks
() => ComparativeTrackModel[]		Overridable hook: every synteny track in the view, in paint order.
colorableTrackConfigs
() => { trackId: string; name: string; }[]
colorableAttributeNames
() => string[]		The columns the tracks declare in their adapter's attributeColumns (the ortholog-table adapter's slot), one color mode each.
legendAlpha
() => number		The key's chips are composited by the plot's opacity, as the alignments are.
6 inherited methods from one model

From TrackColorsMixin: loadedAttributeRanges, legendCigarOps, colorSurface, offersReferenceColor, shapeShowsStrand, trackColorFor

Actions

MemberDescription
setOpacity
(value: number) => void		The opacity slider: the constant, or under a field its range scaled so its most opaque end lands on value.
setOpacityField
(field: string) => void		Fade by field from the current opacity down to 0.3 of it, or with '' draw every alignment at the opacity the fade reached.
setMinAlignmentLength
(value: number) => void
7 inherited actions from one model

From TrackColorsMixin: observeAttributeRanges, resetAttributeRanges, setHideUnlabelled, setColorField, setColorDomain, setTrackColor, clearTrackColors