/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
this.pdbentry = pdbentry;
this.sequence = seq;
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = ap.av.getStructureSelectionManager();
try
{
// 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");
+ AlignSeq as = new AlignSeq(sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).sequence, "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;
repaint();
}
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}