import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import java.util.List;
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.CDS))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
{
return false;
}
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.CDS))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.CDS))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))