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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 encoding and palette, the encoding.opacity it fades by and the filter, over the tracks the view 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

4 inherited properties from 3 models

From TrackColorsMixin: encoding, trackColors

From ParkedColorMixin: parkedColors

From SyntenyFilterMixin: filter

Volatiles

1 inherited volatile from one model

From TrackColorsMixin: seenAttributeRanges

Getters

MemberDescription
defaultOpacity
number		The constant opacity a reset returns to: low on the synteny view for dense whole-genome hairballs, opaque on the dotplot.
opacitySetting
SyntenyOpacitySnapshot		encoding.opacity 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 encoding.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 | undefined		The field encoding.opacity fades by, undefined while it draws its constant.
19 inherited getters from 3 models

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

From ParkedColorMixin: parkedColor, parkedIdentity

From SyntenyFilterMixin: predicates, minLength

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 plot's opacity composites the key's chips, as it does the alignments.
7 inherited methods from 3 models

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

From ParkedColorMixin: parkedColorOf

From SyntenyFilterMixin: lowerBound

Actions

MemberDescription
setOpacity
(value: number) => void		The opacity slider: the constant, or under a field its range scaled so its most opaque end equals value.
setOpacityField
(field: string | undefined) => void		Fade by field from the current opacity down to 0.3 of it, or with undefined draw every alignment at the opacity the fade reached.
12 inherited actions from 3 models

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

From ParkedColorMixin: parkColor

From SyntenyFilterMixin: setFilter, setLowerBound