Program: 37785
Project: 37785
Buggy source:
public static Cell parseStructure(StructureOrg c,String output){
  GAParameters params=GAParameters.getParams();
  List<Site> sites=c.getCell().getSites();
  List<Vect> newVects=new LinkedList<Vect>();
  List<Site> newSites=new LinkedList<Site>();
  String line=null;
  Pattern goodPattern=Pattern.compile("String_Node_Str");
  Matcher goodMatcher=goodPattern.matcher(output);
  try {
    BufferedReader t=new BufferedReader(new FileReader(output));
    try {
      while ((line=t.readLine()) != null) {
        goodMatcher.reset(line);
        if (goodMatcher.find()) {
          System.out.println("String_Node_Str");
          return c.getCell();
        }
      }
    }
 catch (    IOException x) {
      GAOut.out().stdout("String_Node_Str" + x.getLocalizedMessage(),GAOut.CRITICAL,c.getID());
    }
  }
 catch (  FileNotFoundException e) {
    System.out.println("String_Node_Str");
    return c.getCell();
  }
  line=null;
  Pattern coordsPattern=Pattern.compile("String_Node_Str");
  Matcher coordsMatcher=coordsPattern.matcher(output);
  try {
    BufferedReader r=new BufferedReader(new FileReader(output));
    try {
      while ((line=r.readLine()) != null) {
        coordsMatcher.reset(line);
        if (coordsMatcher.find()) {
          while ((line=r.readLine()) != null) {
            coordsMatcher.reset(line);
            if (coordsMatcher.find()) {
              r.readLine();
              r.readLine();
              line=r.readLine().replace("String_Node_Str","String_Node_Str");
              coordsMatcher.reset(line);
              try {
                for (                Site s : sites) {
                  StringTokenizer t=new StringTokenizer(line);
                  t.nextToken();
                  t.nextToken();
                  Double x=Double.parseDouble(t.nextToken());
                  Double y=Double.parseDouble(t.nextToken());
                  Double z=Double.parseDouble(t.nextToken());
                  Vect v=new Vect(x,y,z);
                  newSites.add(new Site(s.getElement(),v));
                  line=r.readLine().replace("String_Node_Str","String_Node_Str");
                }
                for (int k=0; k < Constants.numDimensions; k++) {
                  StringTokenizer m=new StringTokenizer(line);
                  m.nextToken();
                  m.nextToken();
                  Double x=Double.parseDouble(m.nextToken());
                  Double y=Double.parseDouble(m.nextToken());
                  Double z=Double.parseDouble(m.nextToken());
                  Vect v=new Vect(x,y,z);
                  newVects.add(v);
                  line=r.readLine().replace("String_Node_Str","String_Node_Str");
                }
              }
 catch (              NumberFormatException x) {
                GAOut.out().stdout("String_Node_Str" + x.getMessage(),GAOut.NOTICE,c.getID());
                GAOut.out().stdout("String_Node_Str",GAOut.DEBUG,c.getID());
                GAOut.out().stdout(output,GAOut.DEBUG,c.getID());
              }
              break;
            }
          }
        }
      }
    }
 catch (    IOException x) {
      GAOut.out().stdout("String_Node_Str" + x.getLocalizedMessage(),GAOut.CRITICAL,c.getID());
    }
  }
 catch (  FileNotFoundException e) {
    System.out.println("String_Node_Str");
    return c.getCell();
  }
  Cell p=new Cell(newVects,newSites);
  return p;
}

Fixed version (ground truth):
public static Cell parseStructure(StructureOrg c,String output){
  GAParameters params=GAParameters.getParams();
  List<Site> sites=c.getCell().getSites();
  List<Vect> newVects=new LinkedList<Vect>();
  List<Site> newSites=new LinkedList<Site>();
  String line=null;
  Pattern goodPattern=Pattern.compile("String_Node_Str");
  Matcher goodMatcher=goodPattern.matcher(output);
  try {
    BufferedReader t=new BufferedReader(new FileReader(output));
    try {
      while ((line=t.readLine()) != null) {
        goodMatcher.reset(line);
        if (goodMatcher.find()) {
          System.out.println("String_Node_Str");
          return c.getCell();
        }
      }
    }
 catch (    IOException x) {
      GAOut.out().stdout("String_Node_Str" + x.getLocalizedMessage(),GAOut.CRITICAL,c.getID());
    }
  }
 catch (  FileNotFoundException e) {
    System.out.println("String_Node_Str");
    return c.getCell();
  }
  line=null;
  boolean finalGeometryFound=false;
  Pattern coordsPattern=Pattern.compile("String_Node_Str");
  Matcher coordsMatcher=coordsPattern.matcher(output);
  try {
    BufferedReader r=new BufferedReader(new FileReader(output));
    try {
      while ((line=r.readLine()) != null) {
        coordsMatcher.reset(line);
        if (coordsMatcher.find()) {
          while ((line=r.readLine()) != null) {
            coordsMatcher.reset(line);
            if (coordsMatcher.find()) {
              finalGeometryFound=true;
              r.readLine();
              r.readLine();
              line=r.readLine().replace("String_Node_Str","String_Node_Str");
              coordsMatcher.reset(line);
              try {
                for (                Site s : sites) {
                  StringTokenizer t=new StringTokenizer(line);
                  t.nextToken();
                  t.nextToken();
                  Double x=Double.parseDouble(t.nextToken());
                  Double y=Double.parseDouble(t.nextToken());
                  Double z=Double.parseDouble(t.nextToken());
                  Vect v=new Vect(x,y,z);
                  newSites.add(new Site(s.getElement(),v));
                  line=r.readLine().replace("String_Node_Str","String_Node_Str");
                }
                for (int k=0; k < Constants.numDimensions; k++) {
                  StringTokenizer m=new StringTokenizer(line);
                  m.nextToken();
                  m.nextToken();
                  Double x=Double.parseDouble(m.nextToken());
                  Double y=Double.parseDouble(m.nextToken());
                  Double z=Double.parseDouble(m.nextToken());
                  Vect v=new Vect(x,y,z);
                  newVects.add(v);
                  line=r.readLine().replace("String_Node_Str","String_Node_Str");
                }
              }
 catch (              NumberFormatException x) {
                GAOut.out().stdout("String_Node_Str" + x.getMessage(),GAOut.NOTICE,c.getID());
                GAOut.out().stdout("String_Node_Str",GAOut.DEBUG,c.getID());
                GAOut.out().stdout(output,GAOut.DEBUG,c.getID());
              }
              break;
            }
          }
        }
      }
    }
 catch (    IOException x) {
      GAOut.out().stdout("String_Node_Str" + x.getLocalizedMessage(),GAOut.CRITICAL,c.getID());
    }
  }
 catch (  FileNotFoundException e) {
    System.out.println("String_Node_Str");
    return c.getCell();
  }
  if (finalGeometryFound)   return new Cell(newVects,newSites);
 else   return null;
}