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MafBases

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

The MAF display's alignments.bases layer, a cell per position over the rows, as alignments' pileup.bases: show turns it on and encoding.color names what it paints. base paints every base in its color with its letter. codon paints each codon by its amino-acid change against the reference, with the amino acid's letter, from the reading frames of the MAF adapter's framesAdapter, at base level. The mismatches do not draw while the layer does.

Example usage

{ type: 'LinearMafDisplay', alignments: { bases: { show: true } } }
{
  type: 'LinearMafDisplay',
  alignments: { bases: { show: true, encoding: { color: 'codon' } } },
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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
show
boolean = false		draw the per-position layer over the rows
encoding
MafBasesEncoding sub-schema		The layer's channels: encoding.color, the per-position variable.
encoding.color
MafBasesColor sub-schema		The per-position variable the layer paints: base or codon.
encoding.color.field
stringEnum (base, codon) = 'base'		the per-position variable: base, every base in its color, or codon, each codon by its amino-acid change