LinearMafDisplay

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

Example usage#

Set through the track's displayDefaults, so the track opens in this state for every viewer.

{
  type: 'MafTrack',
  trackId: 'multiz_example',
  name: 'Multiz alignment',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BigMafAdapter',
    bigBedLocation: { uri: 'https://example.com/multiz.bb' },
    samples: ['hg38', 'panTro6', 'rheMac10', 'mm39'],
  },
  displayDefaults: {
    rowHeight: 12,
    showConservation: true,
    conservationHeight: 40,
    showRowLabels: true,
  },
}

The display for a MafTrack: one row per aligned species, with a conservation summary above them. The slots are show/hide defaults and band sizes; the bands and overlays derive from the alignment and toggle from the track menu.

Related links#

• Adapter: BgzipMafAdapter
• Adapter: BgzipTaffyAdapter
• Adapter: BigMafAdapter
• Adapter: MafTabixAdapter
• State model: runtime API
• Base config: BaseLinearDisplay
• User guide: MAF track
• Config guide: MAF track
• Config guide: Tracks
• Developer guide: Custom track and display types

Config slots#

These slots go on a display entry: "displays": [{ "type": "LinearMafDisplay", ... }], 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.

{ color: 'identity' }

{ rows: { domain: ['mm10'], labels: { mm10: 'Mouse' } } }

{ rowColor: { domain: ['mm10'], range: ['#f28e2b'] } }

Retired keys#

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