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.bayes;
  
  import edu.cmu.tetrad.data.VariableSource;
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.Arrays;
  
  /**
   * Stores information for a variable source about evidence we have for each variable as
   * well as whether each variable has been manipulated.
   *
   * @author Joseph Ramsey
   */
  public final class Manipulation implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      private VariableSource variableSource;
  
      /**
       * An array indicating whether each variable in turn is manipulated.
       *
       * @serial Cannot be null.
       */
      private boolean[] manipulated;
  
      //===========================CONSTRUCTORS============================//
  
      /**
       * Constructs a container for evidence for the given Bayes IM.
       */
      public Manipulation(VariableSource variableSource) {
          if (variableSource == null) {
              throw new NullPointerException();
          }
  
          this.variableSource = variableSource;
          this.manipulated = new boolean[getNumNodes()];
      }
  
      /**
       * Copy constructor.
       */
      public Manipulation(Manipulation manipulation) {
          if (manipulation == null) {
              throw new NullPointerException();
          }
  
          if (manipulation.getVariableSource() == null) {
              throw new NullPointerException("Please reconstruct this part of the " +
                      "session; there was an error.");
          }
  
          this.variableSource = manipulation.getVariableSource();
  
          this.manipulated = new boolean[getNumNodes()];
  
          for (int i = 0; i < manipulated.length; i++) {
              this.manipulated[i] = manipulation.isManipulated(i);
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static Manipulation serializableInstance() {
          return new Manipulation(MlBayesIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
      public void setManipulated(int nodeIndex, boolean manipulated) {
          this.manipulated[nodeIndex] = manipulated;
      }
  
      public String toString() {
          StringBuilder buf = new StringBuilder();
  
          buf.append("\nManipulation:");
          buf.append("\n");
  
          for (int i = 0; i < getNumNodes(); i++) {
              buf.append(isManipulated(i) ? "(Man)" : "     ");
              buf.append("\t");
          }
  
          return buf.toString();
      }
  
      public boolean equals(Object o) {
          if (o == null) {
              return false;
          }
  
          if (!(o instanceof Manipulation)) {
              return false;
          }
  
          Manipulation evidence = (Manipulation) o;
  
          if (!(getVariableSource() == evidence.getVariableSource())) {
              return false;
          }
  
          for (int i = 0; i < manipulated.length; i++) {
              if (manipulated[i] != evidence.manipulated[i]) {
                  return false;
              }
          }
  
          return true;
      }
  
      public int hashCode() {
          int hashCode = 37;
          hashCode = 19 * hashCode + getVariableSource().hashCode();
          hashCode = 19 * hashCode + Arrays.hashCode(manipulated);
          return hashCode;
      }
  
      //===========================PRIVATE METHODS=========================//
  
      private int getNumNodes() {
          return getVariableSource().getVariables().size();
      }
  
      public boolean isManipulated(int nodeIndex) {
          return manipulated[nodeIndex];
      }
  
      /**
       * Adds semantic checks to the default deserialization method. This method
       * must have the standard signature for a readObject method, and the body of
       * the method must begin with "s.defaultReadObject();". Other than that, any
       * semantic checks can be specified and do not need to stay the same from
       * version to version. A readObject method of this form may be added to any
       * class, even if Tetrad sessions were previously saved out using a version
       * of the class that didn't include it. (That's what the
       * "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.
       *
       * @throws java.io.IOException
       * @throws ClassNotFoundException
       */
      private void readObject(ObjectInputStream s)
              throws IOException, ClassNotFoundException {
          s.defaultReadObject();
  
  //        if (variableSource == null) {
  //            throw new NullPointerException("Variable source must not be null.");
  //        }
      }
  
      private VariableSource getVariableSource() {
          return variableSource;
      }
  }
  
  
  
  
  
  
  