Program: 17091
Project: 17091
Buggy source:
/** 
 * returns the full sequence of the Atom records of a parent with X instead of HETATMSs. The advantage of this is that it allows us to also align HETATM groups back to the SEQRES.
 * @param groups the list of groups in a parent
 * @return string representations
 */
public String getFullAtomSequence(List<Group> groups){
  StringBuffer sequence=new StringBuffer();
  for (int i=0; i < groups.size(); i++) {
    Group g=(Group)groups.get(i);
    if (g instanceof AminoAcid) {
      AminoAcid a=(AminoAcid)g;
      char oneLetter=a.getAminoType();
      if (oneLetter == '?')       oneLetter='X';
      sequence.append(oneLetter);
    }
 else {
      if (excludeTypes.contains(g.getPDBName()))       continue;
      if (g.size() == 1) {
        try {
          Atom a=g.getAtom(0);
          if (a.getElement().isMetal())           continue;
          continue;
        }
 catch (        StructureException e) {
          e.printStackTrace();
          continue;
        }
      }
      ChemComp cc=g.getChemComp();
      if (ResidueType.lPeptideLinking.equals(cc.getResidueType()) || PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) || PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())) {
        String c=cc.getOne_letter_code();
        if (c.equals("String_Node_Str"))         c="String_Node_Str";
        sequence.append(c);
      }
 else {
        continue;
      }
    }
  }
  return sequence.toString();
}

Fixed version (ground truth):
/** 
 * returns the full sequence of the Atom records of a parent with X instead of HETATMSs. The advantage of this is that it allows us to also align HETATM groups back to the SEQRES.
 * @param groups the list of groups in a parent
 * @param positionIndex a Map to keep track of which group is at which sequence position
 * @return string representations
 */
public String getFullAtomSequence(List<Group> groups,Map<Integer,Integer> positionIndex){
  StringBuffer sequence=new StringBuffer();
  int seqIndex=0;
  for (int i=0; i < groups.size(); i++) {
    Group g=(Group)groups.get(i);
    if (g instanceof AminoAcid) {
      AminoAcid a=(AminoAcid)g;
      char oneLetter=a.getAminoType();
      if (oneLetter == '?')       oneLetter='X';
      positionIndex.put(seqIndex,i);
      sequence.append(oneLetter);
      seqIndex++;
    }
 else {
      if (excludeTypes.contains(g.getPDBName()))       continue;
      if (g.size() == 1) {
        try {
          Atom a=g.getAtom(0);
          if (a.getElement().isMetal())           continue;
          continue;
        }
 catch (        StructureException e) {
          e.printStackTrace();
          continue;
        }
      }
      ChemComp cc=g.getChemComp();
      if (ResidueType.lPeptideLinking.equals(cc.getResidueType()) || PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) || PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())) {
        String c=cc.getOne_letter_code();
        if (c.equals("String_Node_Str"))         c="String_Node_Str";
        positionIndex.put(seqIndex,i);
        sequence.append(c);
        seqIndex++;
      }
 else {
        continue;
      }
    }
  }
  return sequence.toString();
}