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.sem;
  
  import edu.cmu.tetrad.graph.Node;
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.Arrays;
  import java.util.List;
  
  /**
   * Stores information for a BayesIm about evidence we have for each variable as
   * well as whether each variable has been manipulated.
   *
   * @author Joseph Ramsey
   */
  public final class SemManipulation implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * Bayes IM that this is evidence for.
       *
       * @serial Cannot be null.
       */
      private SemIm semIm;
  
      /**
       * 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 SemManipulation(SemIm semIm) {
          if (semIm == null) {
              throw new NullPointerException();
          }
  
          this.semIm = semIm;
          this.manipulated = new boolean[semIm.getVariableNodes().size()];
      }
  
  //    /**
  //     * Copy constructor.
  //     */
  //    public SemManipulation(SemManipulation evidence) {
  //        if (evidence == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        this.semIm = evidence.getSemIm();
  //        this.manipulated = new boolean[semIm.getVariableNodes().size()];
  //
  //        for (int i = 0; i < manipulated.length; i++) {
  //            this.manipulated[i] = evidence.isManipulated(i);
  //        }
  //    }
  
  //    public SemManipulation(SemManipulation evidence, SemIm semIm) {
  //        if (semIm == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        if (evidence == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        this.semIm = semIm;
  //        this.manipulated = new boolean[semIm.getVariableNodes().size()];
  //
  //        for (int i = 0; i < manipulated.length; i++) {
  //            this.manipulated[i] = evidence.isManipulated(i);
  //        }
  //    }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static SemManipulation serializableInstance() {
          return new SemManipulation(SemIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
  //    /**
  //     * @return the Bayes IM that this is evidence for.
  //     */
  //    private SemIm getSemIm() {
  //        return this.semIm;
  //    }
  
      public int getNodeIndex(String nodeName) {
          List nodes = semIm.getSemPm().getVariableNodes();
  
          for (int i = 0; i < nodes.size(); i++) {
              Node node = (Node) nodes.get(i);
  
              if (node.getName().equals(nodeName)) {
                  return i;
              }
          }
  
          return -1;
      }
  
      private int getNumNodes() {
          return semIm.getVariableNodes().size();
      }
  
      public Node getNode(int nodeIndex) {
          return semIm.getVariableNodes().get(nodeIndex);
      }
  
      public boolean isManipulated(int nodeIndex) {
          return manipulated[nodeIndex];
      }
  
      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 SemManipulation)) {
              throw new IllegalArgumentException();
          }
  
          SemManipulation evidence = (SemManipulation) o;
  
          if (!(semIm == evidence.semIm)) {
              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 + semIm.hashCode();
          hashCode = 19 * hashCode + Arrays.hashCode(manipulated);
          return hashCode;
      }
  
      /**
       * 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();
      }
  }
  
  
  
  
  
  
  