Program: 16514
Project: 16514
Buggy source:
/** 
 * The EntityPolySeq object provide the amino acid sequence objects for the Entities. Later on the entities are mapped to the BioJava Chain and Compound objects.
 * @param epolseq the EntityPolySeq record for one amino acid
 */
@Override public void newEntityPolySeq(EntityPolySeq epolseq){
  logger.debug("String_Node_Str" + epolseq);
  int eId=-1;
  try {
    eId=Integer.parseInt(epolseq.getEntity_id());
  }
 catch (  NumberFormatException e) {
    logger.warn("String_Node_Str" + e.getMessage());
  }
  Entity e=getEntity(eId);
  if (e == null) {
    logger.info("String_Node_Str" + epolseq.getEntity_id() + "String_Node_Str");
    return;
  }
  Chain entityChain=getEntityChain(epolseq.getEntity_id());
  if (epolseq.getMon_id().length() == 3 && StructureTools.get1LetterCodeAmino(epolseq.getMon_id()) != null) {
    AminoAcid g=new AminoAcidImpl();
    g.setRecordType(AminoAcid.SEQRESRECORD);
    g.setPDBName(epolseq.getMon_id());
    Character code1=StructureTools.get1LetterCodeAmino(epolseq.getMon_id());
    g.setAminoType(code1);
    g.setResidueNumber(ResidueNumber.fromString(epolseq.getNum()));
    entityChain.addGroup(g);
  }
 else   if (StructureTools.isNucleotide(epolseq.getMon_id())) {
    NucleotideImpl n=new NucleotideImpl();
    n.setResidueNumber(ResidueNumber.fromString(epolseq.getNum()));
    n.setPDBName(epolseq.getMon_id());
    entityChain.addGroup(n);
  }
 else {
    logger.debug("String_Node_Str",epolseq.getNum(),epolseq.getMon_id());
    HetatomImpl h=new HetatomImpl();
    h.setPDBName(epolseq.getMon_id());
    h.setResidueNumber(ResidueNumber.fromString(epolseq.getNum()));
    entityChain.addGroup(h);
  }
}

Fixed version (ground truth):
/** 
 * The EntityPolySeq object provide the amino acid sequence objects for the Entities. Later on the entities are mapped to the BioJava Chain and Compound objects.
 * @param epolseq the EntityPolySeq record for one amino acid
 */
@Override public void newEntityPolySeq(EntityPolySeq epolseq){
  logger.debug("String_Node_Str" + epolseq);
  int eId=-1;
  try {
    eId=Integer.parseInt(epolseq.getEntity_id());
  }
 catch (  NumberFormatException e) {
    logger.warn("String_Node_Str" + e.getMessage());
  }
  Entity e=getEntity(eId);
  if (e == null) {
    logger.info("String_Node_Str" + epolseq.getEntity_id() + "String_Node_Str");
    return;
  }
  Chain entityChain=getEntityChain(epolseq.getEntity_id());
  Group g=ChemCompGroupFactory.getGroupFromChemCompDictionary(epolseq.getMon_id());
  if (g != null && !g.getChemComp().isEmpty()) {
    if (g instanceof AminoAcidImpl) {
      AminoAcidImpl aa=(AminoAcidImpl)g;
      aa.setRecordType(AminoAcid.SEQRESRECORD);
    }
  }
 else {
    if (epolseq.getMon_id().length() == 3 && StructureTools.get1LetterCodeAmino(epolseq.getMon_id()) != null) {
      AminoAcidImpl a=new AminoAcidImpl();
      a.setRecordType(AminoAcid.SEQRESRECORD);
      Character code1=StructureTools.get1LetterCodeAmino(epolseq.getMon_id());
      a.setAminoType(code1);
      g=a;
    }
 else     if (StructureTools.isNucleotide(epolseq.getMon_id())) {
      NucleotideImpl n=new NucleotideImpl();
      g=n;
    }
 else {
      logger.debug("String_Node_Str",epolseq.getNum(),epolseq.getMon_id());
      HetatomImpl h=new HetatomImpl();
      g=h;
    }
  }
  g.setResidueNumber(ResidueNumber.fromString(epolseq.getNum()));
  g.setPDBName(epolseq.getMon_id());
  entityChain.addGroup(g);
}