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LinearMafDisplay

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

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.

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,
    conservation: { show: true, height: 40 },
    axis: { labels: true },
  },
}

Config slots

Display 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.

SlotDescription
fetchSizeLimit
number = 5000000		The whole budget the byte gate measures against, since no MAF adapter declares a fetchSizeLimit. 5 Mb, as LinearBasicDisplay uses, because the index estimate is block-granular. SUB_FLOOR_BYTE_BUDGET_FACTOR lets deep data through below the force-load floor. Measurements: MAF_LARGE_BLOCKS.md, "Fetch dominates at 470-way".
advanced
encoding
MafEncoding		The channels the aligned cells paint through: encoding.color, the field that colors them (see MafColor), and encoding.y, the field a row's bar height shows.
{ encoding: { color: 'identity' } }
axis
RowAxis		The guide down the left of the species rows: the species tree and each species' name. No grid: the rows keep a gap instead. The coverage band's value axis is coverage.encoding.y.axis.
rows
SampleRows		The arrangement a reader gives the species rows, each member by row name. sort is the row order: the guide tree rotates to it while some rotation lists the species in that order; otherwise the listed species lead and the rest keep adapter order. labels, tree, treeProvenance and kept are what the arrangement dialog, a clustering run and a focus write. The adapter's guide tree is never written here.
{ rows: { sort: ['mm10'], labels: { mm10: 'Mouse' } } }
rowColor
RowColor		A color per species row, drawn as the bar beside its label, over the color the adapter's samples entry gives it.
{ rowColor: { scale: { domain: ['mm10'], range: ['#f28e2b'] } } }
legend
Legend		The color key for the active row rendering: codon-change categories, source-chromosome ranks, the identity ramp and the CDS frame swatches. In bases mode nothing draws, since there is nothing to key.
coverage
CoverageBand		The coverage band: show, height, encoding.y, interbase and alleles, as the alignments display spells it.
alignments
MafAlignments		The per-species rows, which take the height the bands above them leave: show, rowProportion, and the inversions, frames and reference parts.
conservation
MafConservation		The band of identity to the reference: show (default off), height and unit, base or codon.
height
number = 300		display height in pixels, the bands above the rows included; the rows divide what is left while row height fits, however many there are
rowHeight
number = 0		per-row height in px, scrolling the rows that do not fit; 0 (the default) fits the rows to the display height instead, dividing it between them
Inherited from BaseLinearDisplay1 slot
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
maxFeatureScreenDensityignored
maxDisplayedBpPerPxignored
mouseoverignored
jexlFiltersmoved into a current slot
rowProportionmoved into a current slot
showAllLettersignored
showAsUpperCaseignored
ymoved into a current slot
scalesmoved into a current slot
showTreemoved into a current slot
showBranchLengthmoved into a current slot
showRowLabelsmoved into a current slot
treeAreaWidthmoved into a current slot