/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
- 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);
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
// ////////////////////////////////
// /StructureListener
- public String getPdbFile()
+ public String[] getPdbFile()
{
- return pdbentry.getFile();
+ return new String[]
+ { pdbentry.getFile() };
}
String lastMessage;