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.data.DataSet;
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.graph.NodeType;
  
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Implements Chickering and Meek's (2002) locally consistent score criterion.
   *
   * @author Joseph Ramsey
   */
  public class ScoredIndTest implements Score {
  
      private final IndependenceTest test;
  
      // The variables of the covariance matrix.
      private List<Node> variables;
  
      // True if verbose output should be sent to out.
      private boolean verbose = false;
  
      /**
       * Constructs the score using a covariance matrix.
       */
      public ScoredIndTest(IndependenceTest test) {
          this.variables = new ArrayList<>();
  
          for (Node node : test.getVariables()) {
              if (node.getNodeType() == NodeType.MEASURED) {
                  this.variables.add(node);
              }
          }
  
          this.test = test;
      }
  
      /**
       * Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model
       */
      public double localScore(int i, int[] parents) {
          throw new UnsupportedOperationException();
      }
  
      private List<Node> getVariableList(int[] indices) {
          List<Node> variables = new ArrayList<>();
          for (int i : indices) {
              variables.add(this.variables.get(i));
          }
          return variables;
      }
  
  
      @Override
      public double localScoreDiff(int x, int y, int[] z) {
          test.isIndependent(variables.get(x), variables.get(y), getVariableList(z));
          return test.getScore();
      }
  
      @Override
      public double localScoreDiff(int x, int y) {
          return localScoreDiff(x, y, new int[0]);
      }
  
  
      int[] append(int[] parents, int extra) {
          int[] all = new int[parents.length + 1];
          System.arraycopy(parents, 0, all, 0, parents.length);
          all[parents.length] = extra;
          return all;
      }
  
      /**
       * Specialized scoring method for a single parent. Used to speed up the effect edges search.
       */
  
      public double localScore(int i, int parent) {
          throw new UnsupportedOperationException();
      }
  
      /**
       * Specialized scoring method for no parents. Used to speed up the effect edges search.
       */
      public double localScore(int i) {
          throw new UnsupportedOperationException();
      }
  
      @Override
      public boolean isEffectEdge(double bump) {
          return true;
      }
  
      public DataSet getDataSet() {
          throw new UnsupportedOperationException();
      }
  
      public boolean isVerbose() {
          return verbose;
      }
  
      public void setVerbose(boolean verbose) {
          this.verbose = verbose;
      }
  
      @Override
      public List<Node> getVariables() {
          return variables;
      }
  
      public int getSampleSize() {
          return 0;
      }
  
      public boolean getAlternativePenalty() {
          return false;
      }
  
      @Override
      public Node getVariable(String targetName) {
          for (Node node : variables) {
              if (node.getName().equals(targetName)) {
                  return node;
              }
          }
  
          return null;
      }
  
      @Override
      public int getMaxDegree() {
          return 1000;
      }
  
      @Override
      public boolean determines(List<Node> z, Node y) {
          return false;
      }
  
  }
  
  
  
  