Program: 12733
Project: 12733
Buggy source:
private static ComponentDefinition parseComponentDefinitions(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  String displayId=null;
  String name=null;
  String description=null;
  URI persistentIdentity=null;
  URI structure=null;
  String version=null;
  URI wasDerivedFrom=null;
  Set<URI> type=new HashSet<>();
  Set<URI> roles=new HashSet<>();
  List<Component> components=new ArrayList<>();
  List<Annotation> annotations=new ArrayList<>();
  List<SequenceAnnotation> sequenceAnnotations=new ArrayList<>();
  List<SequenceConstraint> sequenceConstraints=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     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.ComponentDefinition.type)) {
      type.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Model.roles)) {
      roles.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent)) {
      components.add(parseSubComponent(((NestedDocument<QName>)namedProperty.getValue())));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequence)) {
      structure=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceAnnotations)) {
      sequenceAnnotations.add(parseSequenceAnnotation((NestedDocument<QName>)namedProperty.getValue()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceConstraints)) {
      sequenceConstraints.add(parseSequenceConstraint(((NestedDocument<QName>)namedProperty.getValue())));
    }
 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));
    }
  }
  ComponentDefinition c=SBOLDoc.createComponentDefinition(topLevel.getIdentity(),type);
  if (roles != null)   c.setRoles(roles);
  if (displayId != null)   c.setDisplayId(displayId);
  if (persistentIdentity != null)   c.setPersistentIdentity(persistentIdentity);
  if (structure != null)   c.setSequence(structure);
  if (!components.isEmpty())   c.setComponents(components);
  if (!sequenceAnnotations.isEmpty())   c.setSequenceAnnotations(sequenceAnnotations);
  if (!sequenceConstraints.isEmpty())   c.setSequenceConstraints(sequenceConstraints);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  if (version != null)   c.setVersion(version);
  if (wasDerivedFrom != null)   c.setWasDerivedFrom(wasDerivedFrom);
  return c;
}

Fixed version (ground truth):
private static ComponentDefinition parseComponentDefinitions(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  String displayId=null;
  String name=null;
  String description=null;
  URI persistentIdentity=null;
  URI structure=null;
  String version=null;
  URI wasDerivedFrom=null;
  Set<URI> type=new HashSet<>();
  Set<URI> roles=new HashSet<>();
  List<Component> components=new ArrayList<>();
  List<Annotation> annotations=new ArrayList<>();
  List<SequenceAnnotation> sequenceAnnotations=new ArrayList<>();
  List<SequenceConstraint> sequenceConstraints=new ArrayList<>();
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
      version=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     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.ComponentDefinition.type)) {
      type.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Model.roles)) {
      roles.add(URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent)) {
      components.add(parseSubComponent(((NestedDocument<QName>)namedProperty.getValue())));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequence)) {
      structure=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceAnnotations)) {
      sequenceAnnotations.add(parseSequenceAnnotation((NestedDocument<QName>)namedProperty.getValue()));
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasSequenceConstraints)) {
      sequenceConstraints.add(parseSequenceConstraint(((NestedDocument<QName>)namedProperty.getValue())));
    }
 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));
    }
  }
  ComponentDefinition c=SBOLDoc.createComponentDefinition(topLevel.getIdentity(),type);
  if (roles != null)   c.setRoles(roles);
  if (displayId != null)   c.setDisplayId(displayId);
  if (persistentIdentity != null)   c.setPersistentIdentity(persistentIdentity);
  if (structure != null)   c.setSequence(structure);
  if (!components.isEmpty())   c.setComponents(components);
  if (!sequenceAnnotations.isEmpty())   c.setSequenceAnnotations(sequenceAnnotations);
  if (!sequenceConstraints.isEmpty())   c.setSequenceConstraints(sequenceConstraints);
  if (name != null)   c.setName(name);
  if (description != null)   c.setDescription(description);
  if (!annotations.isEmpty())   c.setAnnotations(annotations);
  if (version != null)   c.setVersion(version);
  if (wasDerivedFrom != null)   c.setWasDerivedFrom(wasDerivedFrom);
  return c;
}