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.bayes;
  
  import edu.cmu.tetrad.graph.Graph;
  import edu.cmu.tetrad.graph.Node;
  
  import java.util.Iterator;
  
  /**
   * <p>Provides a static method for finding the Euclidean distance between a pair
   * of BayesIm's.  That is, it computes the square root of the sum of the squares
   * of the differences between corresponding parameters of the two Bayes
   * nets.</p> <p>The BayesPm's should be equal in the sense of the "equals"
   * method of that class.</p>
   *
   * @author Frank Wimberly
   */
  final class BayesImDistanceFunction {
  
      /**
       * The static distance method's arguments are the two BayesIM's whose
       * BayesPm's are "equal".
       */
      public static double distance(BayesIm firstBn, BayesIm secondBn) {
          if (!firstBn.getBayesPm().equals(secondBn.getBayesPm())) {
              throw new IllegalArgumentException("BayesPms must be equal.");
          }
  
          Graph graph = firstBn.getBayesPm().getDag();
          Node[] nodes = new Node[graph.getNumNodes()];
          Iterator<Node> it = graph.getNodes().iterator();
  
          for (int i = 0; i < nodes.length; i++) {
              nodes[i] = it.next();
              //System.out.println("node " + i + " " + nodes[i]);
          }
  
          double sum = 0.0;
  
          for (int i = 0; i < nodes.length; i++) {
              //int numRows = bayesImMixed.getNumRows(i);
              int numRows = firstBn.getNumRows(i);
  
              //for(int j = 0; j < bayesImMixed.getNumRows(i); j++) {
              for (int j = 0; j < numRows; j++) {
                  int numCols = firstBn.getNumColumns(i);
  
                  for (int k = 0; k < numCols; k++) {
                      double diff = firstBn.getProbability(i, j, k) -
                              secondBn.getProbability(i, j, k);
  //                    if (!Double.isNaN(diff)) {
                      sum += diff * diff;
  //                    }
                  }
              }
          }
  
          return Math.sqrt(sum);
      }
  }
  
  
  
  
  
  