+
+ if (!al.isNucleotide() && !thisAlignment.isNucleotide())
+ {
+ // link AA to 3di or other kind of 'alternative' 1:1 mapping alignment
+ AlignmentUtils.map3diPeptideToProteinAligment(thisAlignment,al);
+
+ }
+ else
+ {
+ // link CODON triplets to Protein
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;