Program: 12738
Project: 12738
Buggy source:
private static Collection parseCollections(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  URI persistentIdentity=null;
  String version=null;
  String displayId=null;
  String name=null;
  String description=null;
  URI wasDerivedFrom=null;
  Set<URI> members=new HashSet<>();
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
      persistentIdentity=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Collection.hasMembers)) {
      members.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.title)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.description)) {
      description=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(ProvTerms.Prov.wasDerivedFrom)) {
      wasDerivedFrom=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Collection c=SBOLDoc.createCollection(topLevel.getIdentity());
  if (displayId != null)   c.setDisplayId(displayId);
  if (version != null)   c.setVersion(version);
  if (persistentIdentity != null)   c.setPersistentIdentity(persistentIdentity);
  if (!members.isEmpty())   c.setMembers(members);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (wasDerivedFrom != null)   c.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  return c;
}

Fixed version (ground truth):
private static Collection parseCollections(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  URI persistentIdentity=null;
  String version=null;
  String displayId=null;
  String name=null;
  String description=null;
  URI wasDerivedFrom=null;
  Set<URI> members=new HashSet<>();
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
      persistentIdentity=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Collection.hasMembers)) {
      members.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.title)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.description)) {
      description=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
      wasDerivedFrom=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Collection c=SBOLDoc.createCollection(topLevel.getIdentity());
  if (displayId != null)   c.setDisplayId(displayId);
  if (version != null)   c.setVersion(version);
  if (persistentIdentity != null)   c.setPersistentIdentity(persistentIdentity);
  if (!members.isEmpty())   c.setMembers(members);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (wasDerivedFrom != null)   c.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  return c;
}