code: ///////////////////////////////////////////////////////////////////////////////
  // For information as to what this class does, see the Javadoc, below.       //
  // Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006,       //
  // 2007, 2008, 2009, 2010, 2014, 2015 by Peter Spirtes, Richard Scheines, Joseph   //
  // Ramsey, and Clark Glymour.                                                //
  //                                                                           //
  // This program is free software; you can redistribute it and/or modify      //
  // it under the terms of the GNU General Public License as published by      //
  // the Free Software Foundation; either version 2 of the License, or         //
  // (at your option) any later version.                                       //
  //                                                                           //
  // This program is distributed in the hope that it will be useful,           //
  // but WITHOUT ANY WARRANTY; without even the implied warranty of            //
  // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the             //
  // GNU General Public License for more details.                              //
  //                                                                           //
  // You should have received a copy of the GNU General Public License         //
  // along with this program; if not, write to the Free Software               //
  // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA //
  ///////////////////////////////////////////////////////////////////////////////
  
  package edu.cmu.tetrad.gene.tetrad.gene.algorithm.urchin;
  
  import java.io.*;
  import java.util.StringTokenizer;
  
  /**
   * This is merely a main program used to read a binarized measurement data set
   * and to instantiate a BoolSearch and run one or more search methods of that
   * instance.
   *
   * @author Frank Wimberly
   */
  public class LTestBoolSearch {
      static int ngenes = 6;
      static int ntimes = 80;
  
      static int[][] cases = new int[ntimes][ngenes];
  
      public static void main(String[] argv) {
  
          String fileName = argv[0];
  
          InputStream s;
          StringTokenizer st;
  
          try {
              s = new FileInputStream(fileName);
          }
          catch (IOException e) {
              System.out.println("Cannot open file " + fileName);
              return;
          }
  
          BufferedReader in = new BufferedReader(new InputStreamReader(s));
          for (int k = 0; k < ntimes; k++) {
              try {
                  st = new StringTokenizer(in.readLine());
                  for (int j = 0; j < ngenes; j++) {
                      cases[k][j] = Integer.parseInt(st.nextToken("\t"));
                  }
              }
              catch (IOException e) {
                  System.out.println("Read error in " + fileName);
                  return;
              }
          }
  
          for (int k = 0; k < ntimes; k++) {
              for (int j = 0; j < ngenes; j++) {
                  if (cases[k][j] == -1) {
                      cases[k][j] = 0;
                  }
              }
          }
  
          String[] names = {"Wnt8", "Krl", "SoxB1", "Krox", "Otx", "Eve"};
  
          BoolSearch bs = new BoolSearch(cases, names);
  
          bs.bool2(3);
      }
  
  }
  
  
  
  
  