HiddenMarkovModel hmm;
boolean isHMMConsensusSequence = false;
-
private DBModList<DBRefEntry> dbrefs; // controlled access
/**
{
this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
}
-
}
@Override
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
+ return getAlignmentAnnotations(calcId, label, null, true);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description)
+ {
+ return getAlignmentAnnotations(calcId, label, description, false);
+ }
+
+ private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description, boolean ignoreDescription)
+ {
List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
{
String id = ann.getCalcId();
- if (id != null && id.equals(calcId)
- && ann.label != null && ann.label.equals(label))
+ if ((id != null && id.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
{
result.add(ann);
}
}
return false;
}
-
/**
* {@inheritDoc}
*/