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.data.ICovarianceMatrix;
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.util.ProbUtils;
  import edu.cmu.tetrad.util.TetradLogger;
  import edu.cmu.tetrad.util.TetradMatrix;
  
  import java.util.*;
  
  /**
   * Pools together a set of independence tests using a specified methods
   *
   * @author Robert Tillman
   */
  public final class IndTestMulti implements IndependenceTest {
  
  
      /**
       * The variables of the covariance matrix, in order. (Unmodifiable list.)
       */
      private final List<Node> variables;
  
      /**
       * The independence test associated with each data set.
       */
      private List<IndependenceTest> independenceTests;
  
      /**
       * Pooling method
       */
      private ResolveSepsets.Method method;
      private double p = Double.NaN;
      private boolean verbose = false;
  
  //    private DataSet concatenatedData;
  
      //==========================CONSTRUCTORS=============================//
  
      public IndTestMulti(List<IndependenceTest> independenceTests, ResolveSepsets.Method method) {
          Set<String> nodeNames = new HashSet<>();
          for (IndependenceTest independenceTest : independenceTests) {
              nodeNames.addAll(independenceTest.getVariableNames());
          }
          if (independenceTests.get(0).getVariables().size() != nodeNames.size()) {
              throw new IllegalArgumentException("Data sets must have same variables.");
          }
          this.variables = independenceTests.get(0).getVariables();
          this.independenceTests = independenceTests;
          this.method = method;
  
          List<DataSet> dataSets = new ArrayList<>();
  
          for (IndependenceTest test : independenceTests) {
              dataSets.add((DataSet) test.getData());
          }
  
  //        this.concatenatedData = DataUtils.concatenate(dataSets);
      }
  
      //==========================PUBLIC METHODS=============================//
  
      public IndependenceTest indTestSubset(List<Node> vars) {
          throw new UnsupportedOperationException();
      }
  
      /**
       * Determines whether variable x is independent of variable y given a list of conditioning variables z.
       *
       * @param x the one variable being compared.
       * @param y the second variable being compared.
       * @param z the list of conditioning variables.
       * @return true iff x _||_ y | z.
       * @throws RuntimeException if a matrix singularity is encountered.
       */
      public boolean isIndependent(Node x, Node y, List<Node> z) {
          boolean independent = ResolveSepsets.isIndependentPooled(method, independenceTests, x, y, z);
  
  
          if (independent) {
              TetradLogger.getInstance().log("independencies", "In aggregate independent: " + SearchLogUtils.independenceFact(x, y, z));
          } else {
              TetradLogger.getInstance().log("dependencies", "In aggregate dependent: " + SearchLogUtils.independenceFact(x, y, z));
          }
  
          return independent;
      }
  
      public boolean isIndependentPooledFisher2(List<IndependenceTest> independenceTests, Node x, Node y, List<Node> condSet) {
          double alpha = independenceTests.get(0).getAlpha();
          List<Double> pValues = getAvailablePValues(independenceTests, x, y, condSet);
  
          double tf = 0.0;
          int numPValues = 0;
  
          for (double p : pValues) {
  //            if (p > 0) {
              tf += -2.0 * Math.log(p);
              numPValues++;
  //            }
          }
  
          double p = 1.0 - ProbUtils.chisqCdf(tf, 2 * numPValues);
          this.p = p;
  
          return (p > alpha);
      }
  
      private static List<Double> getAvailablePValues(List<IndependenceTest> independenceTests, Node x, Node y, List<Node> condSet) {
          List<Double> allPValues = new ArrayList<>();
  
          for (IndependenceTest test : independenceTests) {
              List<Node> localCondSet = new ArrayList<>();
              for (Node node : condSet) {
                  localCondSet.add(test.getVariable(node.getName()));
              }
  
              try {
                  test.isIndependent(test.getVariable(x.getName()), test.getVariable(y.getName()), localCondSet);
                  allPValues.add(test.getPValue());
              } catch (Exception e) {
                  // Skip that test.
              }
          }
  
          return allPValues;
      }
  
      public boolean isIndependent(Node x, Node y, Node... z) {
          List<Node> zList = Arrays.asList(z);
          return isIndependent(x, y, zList);
      }
  
      public boolean isDependent(Node x, Node y, List<Node> z) {
          return !isIndependent(x, y, z);
      }
  
      public boolean isDependent(Node x, Node y, Node... z) {
          List<Node> zList = Arrays.asList(z);
          return isDependent(x, y, zList);
      }
  
      /**
       * @throws UnsupportedOperationException
       */
      public double getPValue() {
          return p;
      }
  
      /**
       * @throws UnsupportedOperationException
       */
      public void setAlpha(double alpha) {
          throw new UnsupportedOperationException();
      }
  
      /**
       * Gets the getModel significance level.
       */
      public double getAlpha() {
          throw new UnsupportedOperationException();
      }
  
      /**
       * @return the list of variables over which this independence checker is capable of determinine independence
       * relations-- that is, all the variables in the given graph or the given data set.
       */
      public List<Node> getVariables() {
          return this.variables;
      }
  
      /**
       * @return the variable with the given name.
       */
      public Node getVariable(String name) {
          for (int i = 0; i < getVariables().size(); i++) {
              Node variable = getVariables().get(i);
              if (variable.getName().equals(name)) {
                  return variable;
              }
          }
  
          return null;
      }
  
      /**
       * @return the list of variable varNames.
       */
      public List<String> getVariableNames() {
          List<Node> variables = getVariables();
          List<String> variableNames = new ArrayList<>();
          for (Node variable1 : variables) {
              variableNames.add(variable1.getName());
          }
          return variableNames;
      }
  
      /**
       * @throws UnsupportedOperationException
       */
      public boolean determines(List z, Node x) throws UnsupportedOperationException {
          throw new UnsupportedOperationException();
      }
  
      /**
       * @throws UnsupportedOperationException
       */
      public DataSet getData() {
          throw new UnsupportedOperationException();
  //        return concatenatedData;
      }
  
      @Override
      public ICovarianceMatrix getCov() {
          return null;
      }
  
      @Override
      public List<DataSet> getDataSets() {
          return null;
      }
  
      @Override
      public int getSampleSize() {
          return 0;
      }
  
      @Override
      public List<TetradMatrix> getCovMatrices() {
          return null;
      }
  
      @Override
      public double getScore() {
          return getPValue();
      }
  
      /**
       * @return a string representation of this test.
       */
      public String toString() {
          return "Pooled Independence Test:  alpha = " + independenceTests.get(0).getAlpha();
      }
  
      @Override
      public boolean isVerbose() {
          return verbose;
      }
  
      @Override
      public void setVerbose(boolean verbose) {
          this.verbose = verbose;
      }
  }
  
  