// the start and end points.
// Align the sequence to the pdb
// 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);
+ AlignSeq as = new AlignSeq(sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
// /StructureListener
public String[] getPdbFile()
{
- return new String[] { pdbentry.getFile() };
+ return new String[]
+ { pdbentry.getFile() };
}
String lastMessage;