@Override
public void run()
{
- HiddenMarkovModel hmm = af.getSelectedHMM();
- if (hmm == null)
- {
- System.err.println("Can't run hmmalign as no HMM profile selected");
- return;
- }
+ HiddenMarkovModel hmm = getHmmProfile();
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
boolean ran = runCommand(modelFile, alignmentFile, resultFile);
if (!ran)
{
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmalign_failed"));
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmalign"));
return;
}
al.setDataset(dataset);
}
- /*
- * hack to ensure hmm set on alignment
- */
- if (al.getSequenceAt(0).hasHMMProfile())
- {
- al.setHmmConsensus(al.getSequenceAt(0));
- }
-
displayInNewFrame(al, allOrders, hidden, title);
}