public void setStart(int start)
{
this.start = start;
+ sequenceChanged();
}
/**
@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))
+ if ((ann.calcId != null && ann.calcId.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
+
{
result.add(ann);
}