Program: 12749
Project: 12749
Buggy source:
private static Sequence parseDnaSequenceV1(SBOLDocument SBOLDoc,IdentifiableDocument<QName> topLevel){
  String elements=null;
  String displayId=null;
  String name=null;
  String description=null;
  URI identity=topLevel.getIdentity();
  URI encoding=Sbol2Terms.SequenceURI.DnaSequenceV1;
  List<Annotation> annotations=new ArrayList<Annotation>();
  if (setURIPrefix != null) {
    if (topLevel.getIdentity().toString().lastIndexOf('/') != -1) {
      displayId=topLevel.getIdentity().toString().substring(topLevel.getIdentity().toString().lastIndexOf('/') + 1);
      identity=URI.create(setURIPrefix + "String_Node_Str" + displayId+ "String_Node_Str");
    }
  }
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol1Terms.DNASequence.nucleotides)) {
      elements=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
      if (setURIPrefix != null) {
        identity=URI.create(setURIPrefix + "String_Node_Str" + displayId+ "String_Node_Str");
      }
    }
 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 {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Sequence sequence=SBOLDoc.createSequence(identity,elements,encoding);
  if (identity != topLevel.getIdentity())   sequence.setWasDerivedFrom(topLevel.getIdentity());
  if (displayId != null)   sequence.setDisplayId(displayId);
  if (name != null)   sequence.setName(name);
  if (description != null)   sequence.setDescription(description);
  if (!annotations.isEmpty())   sequence.setAnnotations(annotations);
  return sequence;
}

Fixed version (ground truth):
private static Sequence parseDnaSequenceV1(SBOLDocument SBOLDoc,IdentifiableDocument<QName> topLevel){
  String elements=null;
  String displayId=null;
  String name=null;
  String description=null;
  URI identity=topLevel.getIdentity();
  URI encoding=Sbol2Terms.SequenceURI.DnaSequenceV1;
  List<Annotation> annotations=new ArrayList<Annotation>();
  if (setURIPrefix != null) {
    if (topLevel.getIdentity().toString().lastIndexOf('/') != -1) {
      displayId=topLevel.getIdentity().toString().substring(topLevel.getIdentity().toString().lastIndexOf('/') + 1);
      identity=URI.create(setURIPrefix + "String_Node_Str" + SBOLDocument.TopLevelTypes.sequence+ "String_Node_Str"+ displayId+ "String_Node_Str");
    }
  }
  for (  NamedProperty<QName> namedProperty : topLevel.getProperties()) {
    if (namedProperty.getName().equals(Sbol1Terms.DNASequence.nucleotides)) {
      elements=((Literal<QName>)namedProperty.getValue()).getValue().toString();
    }
 else     if (namedProperty.getName().equals(Sbol2Terms.Documented.displayId)) {
      displayId=((Literal<QName>)namedProperty.getValue()).getValue().toString();
      if (setURIPrefix != null) {
        identity=URI.create(setURIPrefix + "String_Node_Str" + displayId+ "String_Node_Str");
      }
    }
 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 {
      annotations.add(new Annotation(namedProperty));
    }
  }
  Sequence sequence=SBOLDoc.createSequence(identity,elements,encoding);
  if (identity != topLevel.getIdentity())   sequence.setWasDerivedFrom(topLevel.getIdentity());
  if (displayId != null)   sequence.setDisplayId(displayId);
  if (name != null)   sequence.setName(name);
  if (description != null)   sequence.setDescription(description);
  if (!annotations.isEmpty())   sequence.setAnnotations(annotations);
  return sequence;
}