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.ArrayList;
  import java.util.List;
  
  /**
   * Stores information for a SemIm about evidence we have for each variable as
   * well as whether each variable has been manipulated.
   *
   * @author Joseph Ramsey
   */
  public final class SemEvidence implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * Bayes IM that this is evidence for.
       *
       * @serial
       */
      private SemIm semIm;
  
      /**
       * A proposition stating what we know for each variable.
       *
       * @serial Cannot be null.
       */
      private SemProposition proposition;
  
      /**
       * A manipulation indicating how the bayes Im should be manipulated before
       * updating.
       *
       * @serial
       */
      private SemManipulation manipulation;
  
      //=============================CONSTRUCTORS=========================//
  
      /**
       * Constructs a container for evidence for the given Bayes IM.
       */
      public SemEvidence(SemIm semIm) {
          if (semIm == null) {
              throw new NullPointerException();
          }
  
          this.semIm = semIm;
          this.proposition = SemProposition.tautology(semIm);
          this.manipulation = new SemManipulation(semIm);
      }
  
  //    /**
  //     * Copy constructor.
  //     */
  //    public SemEvidence(SemEvidence evidence) {
  //        if (evidence == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        this.semIm = evidence.getSemIm();
  //        this.proposition = new SemProposition(semIm, evidence.getProposition());
  //        this.manipulation = new SemManipulation(evidence.manipulation);
  //    }
  
  //    /**
  //     * Wraps the proposition. The Bayes IM and manipulation will be null.
  //     */
  //    public SemEvidence(SemProposition proposition) {
  //        if (proposition == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        this.semIm = proposition.getSemIm();
  //        this.proposition = new SemProposition(proposition);
  //        this.manipulation = new SemManipulation(semIm);
  //    }
  
  //    public SemEvidence(SemEvidence evidence, SemIm semIm) {
  //        if (semIm == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        if (evidence == null) {
  //            throw new NullPointerException();
  //        }
  //
  //        this.semIm = semIm;
  //        this.proposition = new SemProposition(semIm, evidence.getProposition());
  //        this.manipulation = new SemManipulation(evidence.manipulation);
  //    }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static SemEvidence serializableInstance() {
          return new SemEvidence(SemIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
      /**
       * @return the Bayes IM that this is evidence for.
       */
      public SemIm getSemIm() {
          return this.semIm;
      }
  
      public int getNodeIndex(String nodeName) {
          List<Node> nodes = semIm.getSemPm().getVariableNodes();
  
          for (int i = 0; i < nodes.size(); i++) {
              Node node = nodes.get(i);
  
              if (node.getName().equals(nodeName)) {
                  return i;
              }
          }
  
          return -1;
      }
  
      public int getNodeIndex(Node node) {
          List<Node> nodes = semIm.getSemPm().getVariableNodes();
  
          for (int i = 0; i < nodes.size(); i++) {
              Node _node = nodes.get(i);
  
              if (node == _node) {
                  return i;
              }
          }
  
          return -1;
      }
  
      public int getNumNodes() {
          return semIm.getVariableNodes().size();
      }
  
      public Node getNode(int nodeIndex) {
          return semIm.getVariableNodes().get(nodeIndex);
      }
  
      public SemProposition getProposition() {
          return this.proposition;
      }
  
      public boolean isManipulated(int nodeIndex) {
          return manipulation.isManipulated(nodeIndex);
      }
  
      public void setManipulated(int nodeIndex, boolean manipulated) {
          manipulation.setManipulated(nodeIndex, manipulated);
      }
  
      public String toString() {
          List<Node> nodes = semIm.getVariableNodes();
          StringBuilder buf = new StringBuilder();
          buf.append("\nEvidence: ");
  
          for (int i = 0; i < nodes.size(); i++) {
              Node node = nodes.get(i);
              buf.append("\n").append(node).append(" = ")
                      .append(proposition.getValue(i));
  
              if (isManipulated(i)) {
                  buf.append("\tManipulated");
              }
          }
  
          return buf.toString();
      }
  
      /**
       * @return the variable for which there is evidence.
       */
      public List<Node> getNodesInEvidence() {
          List<Node> nodes = semIm.getVariableNodes();
          List<Node> nodesInEvidence = new ArrayList<>();
  
          for (int i = 0; i < nodes.size(); i++) {
              if (!Double.isNaN(proposition.getValue(i))) {
                  nodesInEvidence.add(nodes.get(i));
              }
          }
  
          return nodesInEvidence;
      }
  
      public boolean equals(Object o) {
          if (o == null) {
              return false;
          }
  
          if (!(o instanceof SemEvidence)) {
              throw new IllegalArgumentException();
          }
  
          SemEvidence evidence = (SemEvidence) o;
  
          return semIm == evidence.semIm && proposition.equals(evidence.proposition) && manipulation.equals(evidence.manipulation);
  
      }
  
      public int hashCode() {
          int hashCode = 37;
          hashCode = 19 * hashCode + semIm.hashCode();
          hashCode = 19 * hashCode + proposition.hashCode();
          hashCode = 19 * hashCode + manipulation.hashCode();
          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();
  
          if (proposition == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  
  