[Biojava-l] read three letter amino acid sequence

[Hongyu Zhang]

Thanks for the hint, Mark. I found that the NameTokenization class could be used for this purpose, although it can't deal with the ambiguous amino acid "Xaa". The following code will work for regular amino acid such as "Cys" 

            Alphabet ap = AlphabetManager.alphabetForName("PROTEIN");
            NameTokenization nt = new NameTokenization((FiniteAlphabet)ap);
            Symbol s = nt.parseToken("Cys");