SyntenyViewMixin

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

What the linear synteny and dotplot views share beyond SyntenyColorsMixin: the level-of-detail tier every track draws at, and a color key the reader closes per mode.

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

Properties

Member	Description
lodMode `lodMode: types.stripDefault( types.enumeration<LodMode>('LodMode', ['auto', 'fine', 'coarse']), 'auto', )`	Level-of-detail tier selection for PIF adapters. 'auto' uses the adapter's bpPerPx threshold; 'fine' forces the per-row CIGAR tier (t/q); 'coarse' forces the tier whose CIGAR is folded to its large indels (T/Q) when present. One value for the view, so every track draws at the same tier.

5 inherited properties from 2 models

From SyntenyColorsMixin: opacity, minAlignmentLength

From TrackColorsMixin: color, trackColors, hideUnlabelled

Volatiles

Member	Description
colorLegendDismissedFor `string \| undefined`	The field whose legend the reader closed. The legend comes back with the next field that has one, so a dismissal is scoped to the field it was made in rather than being a setting to find again.

1 inherited volatile from one model

From TrackColorsMixin: seenAttributeRanges

Getters

Member	Description
hasLodCapableAdapter `boolean`	Whether any track's adapter has tiers to switch between, which gates the "Level of detail" setting.
showLegend `boolean`	The legend-host half of `LegendMixin` a view needs: whether the key draws, which is the mode having one and the reader not having closed it in this mode. `ChromeLegend` and `SvgLegend` read it.
legendSpec `LegendSpec`	The key `ChromeLegend` draws on screen and `SvgLegend` in the export.

18 inherited getters from 2 models

From SyntenyColorsMixin: defaultOpacity, opacitySetting, opacityFade, opacityLevel, opacityField

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

Methods

10 inherited methods from 2 models

From SyntenyColorsMixin: syntenyTracks, colorableTrackConfigs, colorableAttributeNames, legendAlpha

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

Actions

Member	Description
setLodMode `(value: LodMode) => void`
setShowLegend `(show: boolean) => void`	The legend host's setter: closing the key hides it for this mode only, so picking another mode brings its key up.
dismissLegendSection `() => void`	One section is the whole key here.