Program: 37793
Project: 37793
Buggy source:
public boolean matchesCell(Cell other,double atomicMisfit,double lengthMisfit,double angleMisfit){
  Cell n1=this.getNigliReducedCell().getWyckoffCell();
  Cell n2=null;
  if (other.getBasisSize() <= 0)   n2=other.getNigliReducedCell().getWyckoffCell();
 else   n2=other.getNigliReducedCell().getWyckoffCell().getCellWithSiteIShiftedToOrigin(0);
  if (n1 == null || n2 == null)   return false;
  if (n1.getBasisSize() != n2.getBasisSize())   return false;
  int numWSites=n1.getBasisSize();
  for (  Element e : n1.getComposition().getElements())   if (n2.getNumSitesWithElement(e) != n1.getNumSitesWithElement(e))   return false;
  for (  Cell n1rotated : n1.getCellWithAlternateAxesLabeling()) {
    List<Double> parms1=n1rotated.getLatticeParameters();
    List<Double> parms2=n2.getLatticeParameters();
    if (Math.abs(parms1.get(0) - parms2.get(0)) > lengthMisfit || Math.abs(parms1.get(1) - parms2.get(1)) > lengthMisfit || Math.abs(parms1.get(2) - parms2.get(2)) > lengthMisfit || Math.abs(parms1.get(3) - parms2.get(3)) > angleMisfit * Math.PI / 180 || Math.abs(parms1.get(4) - parms2.get(4)) > angleMisfit * Math.PI / 180 || Math.abs(parms1.get(5) - parms2.get(5)) > angleMisfit * Math.PI / 180)     continue;
    for (int i=0; i < numWSites; i++) {
      Cell n1shifted=n1rotated.getCellWithSiteIShiftedToOrigin(i);
      boolean allSitesLineUp=true;
      for (int j=0; j < numWSites; j++) {
        if (!sitesArrayContainsElement(n1shifted.getAtomsInSphereSorted(n2.getSite(j).getCoords(),atomicMisfit),n2.getSite(j).getElement())) {
          allSitesLineUp=false;
          break;
        }
      }
      if (allSitesLineUp)       return true;
    }
  }
  return false;
}

Fixed version (ground truth):
public boolean matchesCell(Cell other,double atomicMisfit,double lengthMisfit,double angleMisfit){
  Cell n1=this.getWyckoffCell();
  Cell n2=null;
  if (other.getBasisSize() <= 0)   n2=other.getWyckoffCell();
 else   n2=other.getWyckoffCell().getCellWithSiteIShiftedToOrigin(0);
  if (n1 == null || n2 == null)   return false;
  if (n1.getBasisSize() != n2.getBasisSize())   return false;
  int numWSites=n1.getBasisSize();
  for (  Element e : n1.getComposition().getElements())   if (n2.getNumSitesWithElement(e) != n1.getNumSitesWithElement(e))   return false;
  for (  Cell n1rotated : n1.getCellWithAlternateAxesLabeling()) {
    List<Double> parms1=n1rotated.getLatticeParameters();
    List<Double> parms2=n2.getLatticeParameters();
    if (Math.abs(parms1.get(0) - parms2.get(0)) > lengthMisfit || Math.abs(parms1.get(1) - parms2.get(1)) > lengthMisfit || Math.abs(parms1.get(2) - parms2.get(2)) > lengthMisfit || Math.abs(parms1.get(3) - parms2.get(3)) > angleMisfit * Math.PI / 180 || Math.abs(parms1.get(4) - parms2.get(4)) > angleMisfit * Math.PI / 180 || Math.abs(parms1.get(5) - parms2.get(5)) > angleMisfit * Math.PI / 180)     continue;
    for (int i=0; i < numWSites; i++) {
      Cell n1shifted=n1rotated.getCellWithSiteIShiftedToOrigin(i);
      boolean allSitesLineUp=true;
      for (int j=0; j < numWSites; j++) {
        if (!sitesArrayContainsElement(n1shifted.getAtomsInSphereSorted(n2.getSite(j).getCoords(),atomicMisfit),n2.getSite(j).getElement())) {
          allSitesLineUp=false;
          break;
        }
      }
      if (allSitesLineUp)       return true;
    }
  }
  return false;
}