Program: 37783
Project: 37783
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()) {
          r.readLine();
          r.readLine();
          for (int e=0; e < (3 * sites.size() + 16); e++) {
            r.readLine();
          }
          line=r.readLine();
          coordsMatcher.reset(line);
          try {
            for (            Site s : sites) {
              StringTokenizer t=new StringTokenizer(line);
              t.nextToken();
              t.nextToken();
              Double x=Double.parseDouble(t.nextToken());
              t.nextToken();
              Double y=Double.parseDouble(t.nextToken());
              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();
            }
            for (int k=0; k < Constants.numDimensions; k++) {
              StringTokenizer m=new StringTokenizer(line);
              m.nextToken();
              m.nextToken();
              Double x=Double.parseDouble(m.nextToken());
              m.nextToken();
              Double y=Double.parseDouble(m.nextToken());
              m.nextToken();
              Double z=Double.parseDouble(m.nextToken());
              Vect v=new Vect(x,y,z);
              newVects.add(v);
              line=r.readLine();
            }
          }
 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;
  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()) {
          r.readLine();
          r.readLine();
          for (int e=0; e < (3 * sites.size() + 16); e++) {
            r.readLine();
          }
          line=r.readLine();
          coordsMatcher.reset(line);
          try {
            for (            Site s : sites) {
              StringTokenizer t=new StringTokenizer(line);
              t.nextToken();
              t.nextToken();
              Double x=Double.parseDouble(t.nextToken());
              t.nextToken();
              Double y=Double.parseDouble(t.nextToken());
              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();
            }
            for (int k=0; k < Constants.numDimensions; k++) {
              StringTokenizer m=new StringTokenizer(line);
              m.nextToken();
              m.nextToken();
              Double x=Double.parseDouble(m.nextToken());
              m.nextToken();
              Double y=Double.parseDouble(m.nextToken());
              m.nextToken();
              Double z=Double.parseDouble(m.nextToken());
              Vect v=new Vect(x,y,z);
              newVects.add(v);
              line=r.readLine();
            }
          }
 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;
  try {
    p=new Cell(newVects,newSites);
  }
 catch (  Exception x) {
    GAOut.out().stdout("String_Node_Str",GAOut.WARNING,0);
    GAOut.out().stdout("String_Node_Str" + output,GAOut.WARNING,0);
    x.printStackTrace();
    p=null;
  }
  return p;
}