- AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
- .elementAt(i)).sequence, "pep");
+ // TODO: DNa/Pep switch
+ AlignSeq as = new AlignSeq(sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);