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
data `types.stripDefault(syntenyDataConfigSchema, {})`	What the fetch reads, a SyntenyData object: `resolution` picks a tiered file's stored tier. One value for the view, so every track draws at the same tier.
legend `types.stripDefault(legendConfigSchema, {})`	Whether the view draws its color key, a Legend object. The key's close button hides it for the current mode only and is never saved.

4 inherited properties from 3 models

From TrackColorsMixin: encoding, trackColors

From ParkedColorMixin: parkedColors

From SyntenyFilterMixin: filter

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.
resolution `LodMode`	`data.resolution`: the stored tier every track fetches.
showLegend `boolean`	The legend-host half of `LegendMixin` a view needs: whether the key draws, which is `legend.show`, the mode having a key, 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.

24 inherited getters from 4 models

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

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

11 inherited methods from 4 models

From SyntenyColorsMixin: syntenyTracks, colorableTrackConfigs, colorableAttributeNames, legendAlpha

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

From ParkedColorMixin: parkedColorOf

From SyntenyFilterMixin: lowerBound

Actions

Member	Description
setResolution `(resolution: 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.
setLegendShow `(show: boolean) => void`	The "Show legend" checkbox: writes `legend.show`, and showing it brings back a key closed in this mode.
dismissLegendSection `() => void`	One section is the whole key here.