@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) {
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;
}
/**
* Add subpart to a SequenceAnnotation
*
* @param sub Subpart to create SequenceAnnotation
* @param place
* @return
*/
private SequenceAnnotation createAnnotation(Subpart sub, int place) {
SequenceAnnotation annotation2 = SBOLFactory.createSequenceAnnotation();
annotation2.setURI(
URI.create("http://sbols.org/anot/an_" + this.partId + "_" + sub.id + "_" + place));
DnaComponent dnaComponent2 = SBOLFactory.createDnaComponent();
dnaComponent2.setURI(URI.create("http://partsregistry.org/Part/" + sub.getPart_name()));
dnaComponent2.setDescription(sub.description);
dnaComponent2.setDisplayId(sub.getPart_name());
dnaComponent2.setName(sub.nickName);
dnaComponent2.addType(SequenceOntology.type(sub.getType().toString()));
annotation2.setSubComponent(dnaComponent2);
return annotation2;
}
private SequenceAnnotation createAnnotation(feature sub, int place) {
SequenceAnnotation annotation2 = SBOLFactory.createSequenceAnnotation();
annotation2.setBioStart(sub.startpos);
annotation2.setBioEnd(sub.endpos);
if (sub.direction.equals("forward")) annotation2.setStrand(StrandType.POSITIVE);
else annotation2.setStrand(StrandType.NEGATIVE);
annotation2.setURI(URI.create("http://sbols.org/anot/f_" + sub.id));
DnaComponent dnaComponent2 = SBOLFactory.createDnaComponent();
dnaComponent2.setURI(URI.create("http://partsregistry.org/feat/f_" + sub.id));
dnaComponent2.setDisplayId("f_" + sub.id);
dnaComponent2.setName(sub.type);
dnaComponent2.addType(SequenceOntology.type(sub.type));
annotation2.setSubComponent(dnaComponent2);
return annotation2;
}