Program: 12730
Project: 12730
Buggy source:
private static SequenceAnnotation parseSequenceAnnotation(NestedDocument<QName> sequenceAnnotation){
  URI persistentIdentity=null;
  String displayId=null;
  Location location=null;
  URI componentURI=null;
  String name=null;
  String description=null;
  String version=null;
  URI wasDerivedFrom=null;
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
      persistentIdentity=URI.create(((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.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Location.Location)) {
      location=parseLocation((NestedDocument<QName>)namedProperty.getValue());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.hasComponent)) {
      componentURI=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));
    }
  }
  SequenceAnnotation s=new SequenceAnnotation(sequenceAnnotation.getIdentity(),location);
  if (persistentIdentity != null)   s.setPersistentIdentity(persistentIdentity);
  if (version != null)   s.setVersion(version);
  if (displayId != null)   s.setDisplayId(displayId);
  if (componentURI != null)   s.setComponent(componentURI);
  if (name != null)   s.setName(name);
  if (description != null)   s.setDescription(description);
  if (wasDerivedFrom != null)   s.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   s.setAnnotations(annotations);
  return s;
}

Fixed version (ground truth):
private static SequenceAnnotation parseSequenceAnnotation(NestedDocument<QName> sequenceAnnotation){
  URI persistentIdentity=null;
  String displayId=null;
  Location location=null;
  URI componentURI=null;
  String name=null;
  String description=null;
  String version=null;
  URI wasDerivedFrom=null;
  List<Annotation> annotations=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
      persistentIdentity=URI.create(((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.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Location.Location)) {
      location=parseLocation((NestedDocument<QName>)namedProperty.getValue());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.SequenceAnnotation.hasComponent)) {
      componentURI=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));
    }
  }
  SequenceAnnotation s=new SequenceAnnotation(sequenceAnnotation.getIdentity(),location);
  if (persistentIdentity != null)   s.setPersistentIdentity(persistentIdentity);
  if (version != null)   s.setVersion(version);
  if (displayId != null)   s.setDisplayId(displayId);
  if (componentURI != null)   s.setComponent(componentURI);
  if (name != null)   s.setName(name);
  if (description != null)   s.setDescription(description);
  if (wasDerivedFrom != null)   s.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   s.setAnnotations(annotations);
  return s;
}