boolean ran = runCommand(alignmentFile, hmmFile, ac);
if (!ran)
{
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmbuild"));
return;
}
importData(hmmFile, ac);
*/
void deleteHmmSequences(AnnotatedCollectionI ac)
{
- SequenceI hmmSeq = ac.getHmmConsensus();
- if (hmmSeq != null)
+ List<SequenceI> hmmSeqs = ac.getHmmSequences();
+ for (SequenceI hmmSeq : hmmSeqs)
{
if (ac instanceof SequenceGroup)
{
args.add(ARG_DNA);
}
- args.add(hmmFile.getAbsolutePath());
- args.add(sequencesFile.getAbsolutePath());
+ args.add(getFilePath(hmmFile));
+ args.add(getFilePath(sequencesFile));
return runCommand(args);
}
alignment.insertSequenceAt(topIndex, hmmSeq);
ac.setSeqrep(hmmSeq);
grp.addSequence(hmmSeq, false);
- grp.setHmmConsensus(hmmSeq);
}
else
{
alignment.insertSequenceAt(0, hmmSeq);
- alignment.setHmmConsensus(hmmSeq);
- }
-
- if (af.getSelectedHMM() == null)
- {
- af.setSelectedHMMSequence(hmmSeq);
}
}
}