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SyntenyFadeMixin

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Built into JBrowse core. View source.

The two fades a view drawing synteny ribbons offers, whatever the colour mode: an alignment by its sequence identity, and a sub-pixel alignment by its on-screen width, so a dense whole-genome picture keeps its density instead of saturating. The linear synteny view and the circular view both compose it; a view supplies autoFadeWidthPx.

Properties

MemberDescription
opacityByIdentity
opacityByIdentity: types.stripDefault(types.boolean, false)		Fade alignment blocks by per-feature identity (lower identity = more transparent), whatever the color mode.
fadeThinAlignmentsMode
fadeThinAlignmentsMode: types.stripDefault(
        types.enumeration('FadeThinMode', ['auto', 'on', 'off']),
        'auto',
      )
Fade a sub-pixel-thin ribbon's opacity by its on-screen width, so an unfiltered whole-genome view doesn't read as a full-opacity hairball. 'auto' fades once a display is dominated by sub-pixel ribbons and leaves a sparse comparison at full alpha; 'on'/'off' pin it. Resolved view-wide by fadeThinAlignments.

Volatiles

MemberDescription
fadeThinLatch
fadeThinLatch: false		Whether the 'auto' thin-fade is latched on (see fadeThinAlignments).

Getters

MemberDescription
autoFadeWidthPx
number		Overridable hook: the width 'auto' compares against its thresholds, the narrowest capped mean block width of any display with enough blocks to judge, or Infinity with none.
fadeThinAlignments
boolean		The resolved fade-thin flag every display renders by. 'auto' fades once any loaded display is dominated by sub-pixel ribbons, latched with a deadband (fadesThinAt, ADR-083) so a view near the threshold does not flip while panning. View-wide, so every display fades together.

Actions

MemberDescription
setOpacityByIdentity
(arg: boolean) => void
setFadeThinAlignmentsMode
(arg: FadeThinMode) => void
setFadeThinLatch
(arg: boolean) => void		Move the latched 'auto' thin-fade decision — installAutoFadeLatch is the only caller.