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;
  import java.util.Set;
  
  /**
   * One is often faced with the following problem. We start by estimating the adjacencies using
   * FGES followed by FAS. But if X is not adjacent to Z in the resulting graph, and you ask for
   * a sepset, one must be given. So we return a conditioning set that minimizes a score (is as
   * close to independence as possible, or independent).
   *
   * @author jdramsey
   */
  public class SepsetsMinScore implements SepsetProducer {
      private final Graph graph;
      private final IndependenceTest independenceTest;
      private int depth = 3;
      private double p = Double.NaN;
      private boolean verbose = false;
      private boolean returnNullWhenIndep;
  
      public SepsetsMinScore(Graph graph, IndependenceTest independenceTest, int depth) {
          this.graph = graph;
          this.independenceTest = independenceTest;
          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 getMinSepset(i, k);
      }
  
      /**
       * Assumes i--j--k is an unshielded triple.
       */
      public boolean isCollider(Node i, Node j, Node k) {
          return !getMinSepset(i, k).contains(j);
      }
  
      /**
       * Assumes i--j--k is an unshielded triple.
       */
      public boolean isNoncollider(Node i, Node j, Node k) {
          return getMinSepset(i, k).contains(j);
      }
  
      private List<Node> getMinSepset(Node i, Node k) {
          double _p = Double.POSITIVE_INFINITY;
          List<Node> _v = null;
  
          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), Math.max(adji.size(), adjk.size())); d++) {
              if (d <= adji.size()) {
                  ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
                  int[] choice;
  
                  while ((choice = gen.next()) != null) {
                      List<Node> v2 = GraphUtils.asList(choice, adji);
  
                      getIndependenceTest().isIndependent(i, k, v2);
                      double p2 = getIndependenceTest().getScore();
  
                      if (returnNullWhenIndep) {
                          if (p2 < _p && p2 < 0) {
                              _p = p2;
                              _v = v2;
                          }
                      } else {
                          if (p2 < _p) {
                              _p = p2;
                              _v = v2;
                          }
                      }
                  }
              }
  
              if (d <= adjk.size()) {
                  ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
                  int[] choice;
  
                  while ((choice = gen.next()) != null) {
                      List<Node> v2 = GraphUtils.asList(choice, adjk);
  
                      getIndependenceTest().isIndependent(i, k, v2);
                      double p2 = getIndependenceTest().getScore();
  
                      if (returnNullWhenIndep) {
                          if (p2 < _p && p2 < 0) {
                              _p = p2;
                              _v = v2;
                          }
                      } else {
                          if (p2 < _p) {
                              _p = p2;
                              _v = v2;
                          }
                      }
                  }
              }
          }
  
          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;
      }
  
      public void setReturnNullWhenIndep(boolean returnNullWhenIndep) {
          this.returnNullWhenIndep = returnNullWhenIndep;
      }
  
      public boolean isReturnNullWhenIndep() {
          return returnNullWhenIndep;
      }
  
      public List<Node> getSepset(Node a, Node y, Set<Node> inSet) {
          return getMinSepset(a, y, inSet);
      }
  
      private List<Node> getMinSepset(Node i, Node k, Set<Node> insSet) {
          double _p = Double.POSITIVE_INFINITY;
          List<Node> _v = null;
  
          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), Math.max(adji.size(), adjk.size())); d++) {
              if (d <= adji.size()) {
                  ChoiceGenerator gen = new ChoiceGenerator(adji.size(), d);
                  int[] choice;
  
                  while ((choice = gen.next()) != null) {
                      List<Node> v2 = GraphUtils.asList(choice, adji);
  
                      if (!insSet.containsAll(v2)) continue;
  
                      getIndependenceTest().isIndependent(i, k, v2);
                      double p2 = getIndependenceTest().getScore();
  
                      if (returnNullWhenIndep) {
                          if (p2 < _p && p2 < 0) {
                              _p = p2;
                              _v = v2;
                          }
                      } else {
                          if (p2 < _p) {
                              _p = p2;
                              _v = v2;
                          }
                      }
                  }
              }
  
              if (d <= adjk.size()) {
                  ChoiceGenerator gen = new ChoiceGenerator(adjk.size(), d);
                  int[] choice;
  
                  while ((choice = gen.next()) != null) {
                      List<Node> v2 = GraphUtils.asList(choice, adjk);
  
                      if (!insSet.containsAll(v2)) continue;
  
                      getIndependenceTest().isIndependent(i, k, v2);
                      double p2 = getIndependenceTest().getScore();
  
                      if (returnNullWhenIndep) {
                          if (p2 < _p && p2 < 0) {
                              _p = p2;
                              _v = v2;
                          }
                      } else {
                          if (p2 < _p) {
                              _p = p2;
                              _v = v2;
                          }
                      }
                  }
              }
          }
  
          this.p = _p;
          return _v;
      }
  }
  
  