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.biolingua;
  
  /**
   * Implements a digraph to be used by the Biolingua algorithm.<p>
   *
   * @author
   * <a href="http://www.eecs.tulane.edu/Saavedra" target="_TOP">Raul Saavedra</a>
   * (<a href="mailto:rsaavedr@ai.uwf.edu">rsaavedr@ai.uwf.edu</A>)
   */
  
  import edu.cmu.tetrad.gene.tetrad.gene.algorithm.util.OutputGraph;
  
  import java.io.FileNotFoundException;
  import java.io.IOException;
  
  public class BiolinguaDigraph extends Digraph implements OutputGraph {
  
      /**
       * Creates a BiolinguaDigraph with name <code>gName</code> and
       * <code>n</code> nodes
       */
      public BiolinguaDigraph(String gName, int n) {
          super(gName, n);
      }
  
      /**
       * Creates a BiolinguaDigraph reading it from file <code>fname</code>.
       */
      public BiolinguaDigraph(String fname)
              throws FileNotFoundException, IOException {
          super(fname);
      }
  
      /**
       * Copy constructor.
       */
      public BiolinguaDigraph(BiolinguaDigraph digraph) {
          this("Clone_of_[" + digraph + "]", digraph.nNodes);
          for (int i = 0; i < digraph.nNodes; i++) {
              this.nodeNames[i] = digraph.nodeNames[i];
              for (int j = 0; j < i; j++) {
                  this.setEdge(i, j, digraph.getEdge(i, j));
              }
          }
      }
  
      /**
       * Returns a clone of this graph
       */
      public Object clone() {
          BiolinguaDigraph g2 = new BiolinguaDigraph(
                  "Clone_of_[" + this.graphName + "]", this.nNodes);
          for (int i = 0; i < this.nNodes; i++) {
              g2.nodeNames[i] = this.nodeNames[i];
              for (int j = 0; j < i; j++) {
                  g2.setEdge(i, j, this.getEdge(i, j));
              }
          }
          return g2;
      }
  
      /**
       * Returns true if node p is parent of node c.<p>
       */
      public boolean isParent(int p, int c) {
          return (this.getEdges().getDoubleValue(p, c) != 0.0);
      }
  
      /**
       * Returns a string with the indexes of all parents of node i separated by
       * spaces (useful for printouts)
       */
      public String strOfParents(int i) {
          int[] ap = this.getParents(i);
          String s = "";
  
          for (int anAp : ap) {
              s = s + " " + anAp;
          }
  
          return s;
      }
  
      /**
       * Returns null (no lag information is stored in a BiolinguaDigraph).
       */
      public int[] getLags(int i) {
          return null;
      }
  
      /**
       * Returns a specially formatted string with all the contents of this Graph.
       * Actually this string is compliant with the same format expected when
       * reading the graph from a file.
       */
      public String toString() {
          String s = this.getClass().getName() + " " + this.graphName + "\n" +
                  this.nNodes + "\t// <-- Total # nodes\n" + "// " +
                  this.getNumEdges() + "\t// <-- Total # edges\n";
  
          s = s + "\n// Node names:\n";
          for (int i = 0; i < this.nNodes; i++) {
              s = s + this.getNodeName(i);
              s = s + "\t// #" + i + " \tParents = {" + this.strOfParents(i) +
                      " }\n";
          }
  
          s = s + "\n// edges:\n";
          s = s + this.EdgesToString();
          return s;
      }
  }
  
  
  
  
  
  