try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+ ap.alignFrame);
if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
// ////////////////////////////////
// /StructureListener
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return new String[] { pdbentry.getFile() };
}