import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
import java.util.ArrayList;
import java.util.Arrays;
private String vamsasId;
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
private DBModList<DBRefEntry> dbrefs; // controlled access
/**
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+ }
}
@Override
public void setStart(int start)
{
this.start = start;
+ sequenceChanged();
}
/**
@Override
public ContiguousI findPositions(int fromColumn, int toColumn)
{
- if (toColumn < fromColumn || fromColumn < 1)
+ fromColumn = Math.max(fromColumn, 1);
+ if (toColumn < fromColumn)
{
return null;
}
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO JAL-3980 maintain as sorted list
if (datasetSequence != null)
{
datasetSequence.addDBRef(entry);
{
dbrefs = new DBModList<>();
}
+ // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
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)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
- && ann.label != null && ann.label.equals(label))
+ String id = ann.getCalcId();
+ 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);
}
}
}
+ @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;
+ }
}