@Override
public void visit(SequenceAnnotation annotation) {
super.visit(annotation);
add(annotation);
if (duplicates.contains(annotation.getSubComponent())) {
annotation.setSubComponent(map(annotation.getSubComponent()));
}
}
@Override
public void visit(DnaComponent component) {
super.visit(component);
add(component);
if (duplicates.contains(component)) {
component.setDnaSequence(map(component.getDnaSequence()));
}
removeDuplicates(component.getAnnotations());
}
@Override
public void visit(DnaComponent component) {
Map<URI, SequenceAnnotation> previous = current;
current = new HashMap<URI, SequenceAnnotation>();
for (SequenceAnnotation annotation : component.getAnnotations()) {
current.put(annotation.getURI(), annotation);
}
super.visit(component);
current = previous;
}
@Override
public void visit(SequenceAnnotation annotation) {
for (PrecedeReference reference :
((SequenceAnnotationImpl) annotation).getPrecedeReferences()) {
SequenceAnnotation sa = current.get(reference.resource);
if (sa != null) {
reference.setValue(sa);
} else if (validate) {
throw new SBOLValidationException(
"Cannot resolve precede reference to sequence annotation: " + reference.resource);
}
}
super.visit(annotation);
}
@Override
public void visit(DnaSequence sequence) {
super.visit(sequence);
add(sequence);
}
@Override
public void visit(Collection coll) {
super.visit(coll);
add(coll);
removeDuplicates(coll.getComponents());
}
@Override
public void visit(SBOLDocument doc) {
super.visit(doc);
removeDuplicates(doc.getContents());
}