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.DiscreteVariable;
  import edu.cmu.tetrad.data.VariableSource;
  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 variable source about evidence we have for each variable as
   * well as whether each variable has been manipulated.
   *
   * @author Joseph Ramsey
   */
  public final class Evidence implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * A proposition stating what we know for each variable.
       *
       * @serial Cannot be null.
       */
      private Proposition proposition;
  
      /**
       * A manipulation indicating how the bayes Im should be manipulated before
       * updating.
       *
       * @serial
       */
      private Manipulation manipulation;
  
      //=============================CONSTRUCTORS=========================//
  
      /**
       * Tautology constructor--use Evidence.tautology() instead.
       */
      private Evidence(VariableSource variableSource) {
          if (variableSource == null) {
              throw new NullPointerException();
          }
  
          this.proposition = Proposition.tautology(variableSource);
          this.manipulation = new Manipulation(variableSource);
      }
  
      /**
       * Copy constructor.
       */
      public Evidence(Evidence evidence) {
          if (evidence == null) {
              throw new NullPointerException();
          }
  
          this.proposition = new Proposition(evidence.getVariableSource(),
                  evidence.getProposition());
          this.manipulation = new Manipulation(evidence.manipulation);
      }
  
      /**
       * Wraps the proposition. The Bayes IM and manipulation will be null.
       */
      public Evidence(Proposition proposition) {
          if (proposition == null) {
              throw new NullPointerException();
          }
  
          this.proposition = new Proposition(proposition);
      }
  
      public Evidence(Evidence evidence, VariableSource variableSource) {
          if (variableSource == null) {
              throw new NullPointerException();
          }
  
          if (evidence == null) {
              throw new NullPointerException();
          }
  
          this.proposition = new Proposition(variableSource, evidence.getProposition());
          this.manipulation = new Manipulation(evidence.manipulation);
      }
  
      public static Evidence tautology(VariableSource variableSource) {
          return new Evidence(variableSource);
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static Evidence serializableInstance() {
          return new Evidence(MlBayesIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
      /**
       * @return the Bayes IM that this is evidence for.
       */
      public VariableSource getVariableSource() {
          return proposition.getVariableSource();
      }
  
      public int getNodeIndex(String nodeName) {
          return proposition.getNodeIndex(nodeName);
      }
  
      public int getCategoryIndex(String nodeName, String category) {
          return proposition.getCategoryIndex(nodeName, category);
      }
  
      public int getNumNodes() {
          return proposition.getVariableSource().getVariables().size();
      }
  
      public Node getNode(int nodeIndex) {
          return proposition.getVariableSource().getVariables().get(nodeIndex);
      }
  
      public DiscreteVariable getVariable(String nodeName) {
          int index = proposition.getVariableSource().getVariableNames().indexOf(nodeName);
          return (DiscreteVariable) proposition.getVariableSource().getVariables().get(index);
      }
  
      public int getNumCategories(int variable) {
          return proposition.getNumCategories(variable);
      }
  
      public Proposition 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() {
          StringBuilder buf = new StringBuilder();
  
          buf.append("\nEvidence:");
          buf.append(getProposition());
          buf.append("\n");
  
          for (int i = 0; i < getNumNodes(); i++) {
              buf.append(isManipulated(i) ? "(Man)" : "     ");
              buf.append("\t");
          }
  
          return buf.toString();
      }
  
      public boolean hasNoEvidence(int variable) {
          for (int i = 0; i < proposition.getNumCategories(variable); i++) {
              if (!proposition.isAllowed(variable, i)) {
                  return false;
              }
          }
  
          return true;
      }
  
      /**
       * @return the variable for which there is evidence.
       */
      public List<Node> getVariablesInEvidence() {
          List<Node> nodes = new ArrayList<>();
          for (int i = 0; i < getNumNodes(); i++) {
              if (proposition.getSingleCategory(i) != -1) {
                  nodes.add(getNode(i));
              }
          }
  
          return nodes;
      }
  
      public String getCategory(Node node, int j) {
          DiscreteVariable variable = (DiscreteVariable) node;
          return variable.getCategory(j);
      }
  
      /**
       * Returna true just in case this evidence has a list of variables
       * equal to those of the given variable source.
       */
      public boolean isIncompatibleWith(VariableSource variableSource) {
          List<Node> variables1 = getVariableSource().getVariables();
          List<Node> variables2 = variableSource.getVariables();
  
          return !variables1.equals(variables2);
      }
  
      public boolean equals(Object o) {
          if (o == null) {
              return false;
          }
  
          if (!(o instanceof Evidence)) {
              return false;
          }
  
          Evidence evidence = (Evidence) o;
  
          return proposition.equals(evidence.proposition) && manipulation.equals(evidence.manipulation);
  
      }
  
      public int hashCode() {
          int hashCode = 37;
          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();
          }
      }
  }
  
  
  
  
  
  
  