import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
import java.util.ArrayList;
import java.util.Arrays;
int end;
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
+
Vector<PDBEntry> pdbIds;
String vamsasId;
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+ }
+
}
@Override
{
for (AlignmentAnnotation ann : annotation)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
+ String id = ann.getCalcId();
+ if (id != null && id.equals(calcId)
&& ann.label != null && ann.label.equals(label))
{
result.add(ann);
}
}
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ if (this.annotation == null) {
+ return false;
+ }
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
/**
* {@inheritDoc}
*/
// otherwise, sequence was completely hidden
return 0;
}
+
+ @Override
+ public boolean hasHMMProfile()
+ {
+ return hmm != null;
+ }
}