}
for (int apos : sq.gapMap())
{
+ char sqc = sq.getCharAt(apos);
if (!filterNonStandardResidues
- || ResidueProperties.aaIndex[sq.getCharAt(apos)] < 20)
+ || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
+ : ResidueProperties.nucleotideIndex[sqc] < 5))
{
gapMap[apos] = true; // aligned and real amino acid residue
}