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LinearReferenceSequenceDisplay

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the sequence plugin. View source.

Draws a ReferenceSequenceTrack as rows of bases: the forward strand, the reverse complement and the translation frames.

Example usage

The display goes in the displays array of the assembly's sequence track, which is where a ReferenceSequenceTrack is authored, so the display sets no assembly name. forward, reverse and translation each turn their rows on and off with show:

sequence: {
  type: 'ReferenceSequenceTrack',
  trackId: 'refseq',
  adapter: {
    type: 'IndexedFastaAdapter',
    uri: 'https://example.com/genome.fa',
  },
  displays: [
    {
      type: 'LinearReferenceSequenceDisplay',
      displayId: 'refseq-LinearReferenceSequenceDisplay',
      translation: { show: false },
    },
  ],
}

Config slots

Display slots go on a display entry: "displays": [{ "type": "LinearReferenceSequenceDisplay", ... }], or in the track's displayDefaults when this is its default display. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
height
maybeNumber		explicit display height (e.g. from a drag-resize); unset means auto-fit to the zoom-aware computed height. See the model's height getter.
forward
SequenceForward sub-schema		The forward-strand base row.
forward.show
boolean = true		draw the rows
reverse
SequenceReverse sub-schema		The reverse-complement base row; a protein sequence has none.
reverse.show
boolean = true		draw the rows
translation
SequenceTranslation sub-schema		The three translation frame rows per drawn strand; a protein sequence has none.
translation.show
boolean = true		draw the rows
fetchSizeLimit
number = 1000000		bytes a region may fetch before the display asks first; an adapter that sets its own limit overrides this
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
rendererignored
showForwardmoved into a current slot
showReversemoved into a current slot
showTranslationmoved into a current slot