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;
  
  /**
   * Represents propositions over the variables of a particular BayesIm describing
   * and event of a fairly general sort--namely, conjunctions of propositions that
   * particular variables take on values from a particular disjunctive list of
   * categories. For example, X1 = 1 or 2 & X2 = 3 & X3 = 1 or 3 & X4 = 2 or 3 or
   * 5. The proposition is created by allowing or disallowing particular
   * categories. Notice that "knowing nothing" about a variable is the same as
   * saying that all categories for that variable are allowed, so the proposition
   * by default allows all categories for all variables--i.e. it is a tautology.
   *
   * @author Joseph Ramsey
   */
  public final class SemProposition implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * @serial Cannot be null.
       */
      private SemIm semIm;
  
      /**
       * @serial Cannot be null.
       */
      private double[] values;
  
      //===========================CONSTRUCTORS===========================//
  
      /**
       * Creates a new Proposition which allows all values.
       */
      private SemProposition(SemIm semIm) {
          if (semIm == null) {
              throw new NullPointerException();
          }
  
          this.semIm = semIm;
          this.values = new double[semIm.getVariableNodes().size()];
  
          for (int i = 0; i < values.length; i++) {
              values[i] = Double.NaN;
          }
      }
  
      public static SemProposition tautology(SemIm semIm) {
          return new SemProposition(semIm);
      }
  
  //    /**
  //     * Copies the info out of the old proposition into a new proposition for the
  //     * new BayesIm.
  //     */
  //    public SemProposition(SemIm semIm, SemProposition proposition) {
  //        this(semIm);
  //
  //        if (proposition == null) {
  //            throw new NullPointerException();
  //        }
  //    }
  
  //    /**
  //     * Copies the info out of the old proposition into a new proposition for the
  //     * new BayesIm.
  //     */
  //    public SemProposition(SemProposition proposition) {
  //        this.semIm = proposition.semIm;
  //        this.values = new double[proposition.values.length];
  //        System.arraycopy(proposition.values, 0, this.values, 0, values.length);
  //    }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static SemProposition serializableInstance() {
          return new SemProposition(SemIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
      /**
       * @return the Bayes IM that this is a proposition for.
       */
      public SemIm getSemIm() {
          return this.semIm;
      }
  
      /**
       * @return the number of variables for the proposition.
       */
      public int getNumVariables() {
          return values.length;
      }
  
      /**
       * @return the index of the variable with the given name, or -1 if such a
       * variable does not exist.
       */
      public int getNodeIndex() {
  
          return -1;
      }
  
      public boolean equals(Object o) {
          if (o == null) {
              return false;
          }
  
          if (!(o instanceof SemProposition)) {
              throw new IllegalArgumentException();
          }
  
          SemProposition proposition = (SemProposition) o;
  
          if (!(semIm == proposition.semIm)) {
              return false;
          }
  
          for (int i = 0; i < values.length; i++) {
              if (!(Double.isNaN(values[i]) && Double.isNaN(proposition.values[i]))) {
                  if (values[i] != proposition.values[i]) {
                      return false;
                  }
              }
          }
  
          return true;
      }
  
      public int hashCode() {
          int hashCode = 37;
          hashCode = 19 * hashCode + semIm.hashCode();
          hashCode = 19 * hashCode + Arrays.hashCode(values);
          return hashCode;
      }
  
      public String toString() {
          List nodes = semIm.getVariableNodes();
          StringBuilder buf = new StringBuilder();
          buf.append("\nProposition: ");
  
          for (int i = 0; i < nodes.size(); i++) {
              Node node = (Node) nodes.get(i);
              buf.append("\n").append(node).append(" = ").append(values[i]);
          }
  
          return buf.toString();
      }
  
      /**
       * 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();
      }
  
      public double getValue(int i) {
          return values[i];
      }
  
      public void setValue(int i, double value) {
          values[i] = value;
      }
  
      public double getValue(Node node) {
          List nodes = semIm.getVariableNodes();
          return values[nodes.indexOf(node)];
      }
  
      public void setValue(Node node, double value) {
          List nodes = semIm.getVariableNodes();
          values[nodes.indexOf(node)] = value;
      }
  }
  
  
  
  
  
  