import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
args.add(ARG_DNA);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(sequencesFile));
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(sequencesFile, true));
return runCommand(args);
}
HMMFile file = new HMMFile(
new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+ ResidueCount counts = new ResidueCount(alignment.getSequences());
+ hmmSeq.getHMM().setBackgroundFrequencies(counts);
if (hmmSeq == null)
{