Program: 12615
Project: 12615
Buggy source:
private static Sequence parseSequences(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  String displayId=null;
  String name=null;
  String description=null;
  URI persistentIdentity=null;
  String version=null;
  String elements=null;
  URI encoding=null;
  URI wasDerivedFrom=null;
  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.Identified.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Sequence.elements)) {
      elements=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Sequence.encoding)) {
      encoding=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.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));
    }
  }
  Sequence sequence=new Sequence(topLevel.getIdentity(),elements,encoding);
  if (persistentIdentity != null)   sequence.setPersistentIdentity(persistentIdentity);
  if (version != null)   sequence.setVersion(version);
  if (displayId != null)   sequence.setDisplayId(displayId);
  if (name != null)   sequence.setName(name);
  if (description != null)   sequence.setDescription(description);
  if (wasDerivedFrom != null)   sequence.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   sequence.setAnnotations(annotations);
  Sequence oldS=SBOLDoc.getSequence(topLevel.getIdentity());
  if (oldS == null) {
    SBOLDoc.addSequence(sequence);
  }
 else {
    if (!sequence.equals(oldS)) {
      throw new SBOLValidationException("String_Node_Str" + topLevel.getIdentity());
    }
  }
  return sequence;
}

Fixed version (ground truth):
private static Sequence parseSequences(SBOLDocument SBOLDoc,TopLevelDocument<QName> topLevel){
  String displayId=null;
  String name=null;
  String description=null;
  URI persistentIdentity=null;
  String version=null;
  String elements=null;
  URI encoding=null;
  URI wasDerivedFrom=null;
  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.Identified.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Sequence.elements)) {
      elements=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Sequence.encoding)) {
      encoding=URI.create(((Literal<QName>)namedProperty.getValue()).getValue().toString());
      if (encoding.toString().equals("String_Node_Str")) {
        encoding=Sequence.IUPAC_DNA;
      }
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
      name=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Identified.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));
    }
  }
  Sequence sequence=new Sequence(topLevel.getIdentity(),elements,encoding);
  if (persistentIdentity != null)   sequence.setPersistentIdentity(persistentIdentity);
  if (version != null)   sequence.setVersion(version);
  if (displayId != null)   sequence.setDisplayId(displayId);
  if (name != null)   sequence.setName(name);
  if (description != null)   sequence.setDescription(description);
  if (wasDerivedFrom != null)   sequence.setWasDerivedFrom(wasDerivedFrom);
  if (!annotations.isEmpty())   sequence.setAnnotations(annotations);
  Sequence oldS=SBOLDoc.getSequence(topLevel.getIdentity());
  if (oldS == null) {
    SBOLDoc.addSequence(sequence);
  }
 else {
    if (!sequence.equals(oldS)) {
      throw new SBOLValidationException("String_Node_Str" + topLevel.getIdentity());
    }
  }
  return sequence;
}