LinearMafDisplay

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the maf plugin. View source.

Example usage#

Set through the track's displayDefaults, which is what makes a track open in this state rather than requiring every viewer to set it from the menu. A whole-genome alignment with many species is the case worth tuning: a shorter rowHeight fits more rows on screen, and the conservation band is what most readers scan first.

{
  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,
  },
}

See the Config slots section below for all available configuration fields.

the display for a MafTrack: one row per aligned species, with a conservation summary above them. The conservation band, per-row identity, color-by-source-chromosome, and inversion overlays are all derived from the alignment itself and toggled from the track menu, so the slots here are show/hide defaults and band sizes.

Related links#

• Adapter: BgzipMafAdapter
• Adapter: BgzipTaffyAdapter
• Adapter: BigMafAdapter
• Adapter: MafTabixAdapter
• State model: runtime API
• Base config: BaseLinearDisplay
• Guide: Custom track and display types
• Guide: Tracks

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.

'jexl:get(feature,'_mouseOver')||get(feature,'name')||get(feature,'function')||get(feature,'id')'