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;
  
  import edu.cmu.tetrad.graph.Graph;
  import edu.cmu.tetrad.graph.GraphUtils;
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.util.ChoiceGenerator;
  
  import java.util.List;
  
  /**
   * Selects the maximum p value sepset
   * <p>
   * Created by josephramsey on 3/24/15.
   */
  public class SepsetsMaxScore implements SepsetProducer {
      private final Graph graph;
      private final IndependenceTest independenceTest;
      private final SepsetMap extraSepsets;
      private int depth = 3;
      private double p = Double.NaN;
      //    private IndependenceTest dsep = null;
      private boolean verbose = false;
  
      public SepsetsMaxScore(Graph graph, IndependenceTest independenceTest, SepsetMap extraSepsets, int depth) {
          this.graph = graph;
          this.independenceTest = independenceTest;
          this.extraSepsets = extraSepsets;
          this.depth = depth;
      }
  
      /**
       * Pick out the sepset from among adj(i) or adj(k) with the highest p value.
       */
      public List<Node> getSepset(Node i, Node k) {
          return getMaxScoreSet(i, k);
      }
  
      public boolean isCollider(Node i, Node j, Node k) {
          List<Node> set = getMaxScoreSet(i, k);
          return set != null && !set.contains(j);
      }
  
      public boolean isNoncollider(Node i, Node j, Node k) {
          List<Node> set = getMaxScoreSet(i, k);
          return set != null && set.contains(j);
      }
  
      private List<Node> getMaxScoreSet(Node i, Node k) {
          double _p = 0.0;
          List<Node> _v = null;
  
          if (extraSepsets != null) {
              final List<Node> v = extraSepsets.get(i, k);
              if (v != null) {
                  independenceTest.isIndependent(i, k, v);
                  double p = independenceTest.getScore();
  
                  if (p > _p) {
                      _p = p;
                      _v = v;
                  }
              }
          }
  
          List<Node> adji = graph.getAdjacentNodes(i);
          List<Node> adjk = graph.getAdjacentNodes(k);
          adji.remove(k);
          adjk.remove(i);
  
          for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), adji.size()); d++) {
              ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
              int[] choice;
  
              while ((choice = gen.next()) != null) {
                  List<Node> v = GraphUtils.asList(choice, adji);
  
                  getIndependenceTest().isIndependent(i, k, v);
                  double p = getIndependenceTest().getScore();
  
                  if (p > _p) {
                      _p = p;
                      _v = v;
                  }
              }
          }
  
          for (int d = 0; d <= Math.min((depth == -1 ? 1000 : depth), adjk.size()); d++) {
              ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
              int[] choice;
  
              while ((choice = gen.next()) != null) {
                  List<Node> v = GraphUtils.asList(choice, adjk);
  
                  getIndependenceTest().isIndependent(i, k, v);
                  double p = getIndependenceTest().getScore();
  
                  if (p > _p) {
                      _p = p;
                      _v = v;
                  }
              }
          }
  
          this.p = _p;
          return _v;
      }
  
      @Override
      public boolean isIndependent(Node a, Node b, List<Node> c) {
          return independenceTest.isIndependent(a, b, c);
      }
  
      @Override
      public double getPValue() {
          return p;
      }
  
      @Override
      public double getScore() {
          return -(p - independenceTest.getAlpha());
      }
  
      @Override
      public List<Node> getVariables() {
          return independenceTest.getVariables();
      }
  
      private IndependenceTest getIndependenceTest() {
          return independenceTest;
      }
  
      public boolean isVerbose() {
          return verbose;
      }
  
      @Override
      public void setVerbose(boolean verbose) {
          this.verbose = verbose;
      }
  
  }
  
  