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.search.mb;
  
  import edu.cmu.tetrad.data.DataSet;
  import edu.cmu.tetrad.data.IKnowledge;
  import edu.cmu.tetrad.data.Knowledge2;
  import edu.cmu.tetrad.graph.EdgeListGraph;
  import edu.cmu.tetrad.graph.Graph;
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.search.FgesOrienter;
  import edu.cmu.tetrad.search.GraphSearch;
  import edu.cmu.tetrad.search.IndependenceTest;
  
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  /**
   * Implements the MMHC algorithm.
   *
   * @author Joseph Ramsey (this version).
   */
  public class Mmhc implements GraphSearch {
  
      /**
       * The independence test used for the PC search.
       */
      private IndependenceTest independenceTest;
  
      /**
       * The maximum number of nodes conditioned on in the search.
       */
      private int depth = Integer.MAX_VALUE;
      private DataSet data;
      private IKnowledge knowledge = new Knowledge2();
  
      //=============================CONSTRUCTORS==========================//
  
      public Mmhc(IndependenceTest test, DataSet dataSet) {
          this.depth = -1;
          this.independenceTest = test;
          this.data = dataSet;
      }
  
      //==============================PUBLIC METHODS========================//
  
  
      public IndependenceTest getIndependenceTest() {
          return independenceTest;
      }
  
      public int getDepth() {
          return depth;
      }
  
      public long getElapsedTime() {
          return 0;
      }
  
  
      /**
       * Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.
       */
      public Graph search() {
          List<Node> variables = independenceTest.getVariables();
          Mmmb mmmb = new Mmmb(independenceTest, getDepth(), true);
          Map<Node, List<Node>> pc = new HashMap<>();
  
          for (Node x : variables) {
              pc.put(x, mmmb.getPc(x));
          }
  
          Graph graph = new EdgeListGraph();
  
          for (Node x : variables) {
              graph.addNode(x);
          }
  
          for (Node x : variables) {
              for (Node y : pc.get(x)) {
                  if (!graph.isAdjacentTo(x, y)) {
                      graph.addUndirectedEdge(x, y);
                  }
              }
          }
  
          FgesOrienter orienter = new FgesOrienter(data);
          orienter.orient(graph);
          return graph;
      }
  
      public IKnowledge getKnowledge() {
          return knowledge;
      }
  
      public void setKnowledge(IKnowledge knowledge) {
          if (knowledge == null) {
              throw new NullPointerException();
          }
  
          this.knowledge = knowledge;
      }
  
      public void setDepth(int depth) {
          this.depth = depth;
      }
  }
  
  
  
  