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.Arrays;
  import java.util.List;
  
  /**
   * Represents propositions over the variables of a particular BayesIm describing
   * an 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 Proposition implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * @serial Cannot be null.
       */
      private VariableSource variableSource;
  
      /**
       * @serial Cannot be null.
       */
      private boolean[][] allowedCategories;
  
      //===========================CONSTRUCTORS===========================//
  
      /**
       * Creates a new Proposition which allows all values.
       */
      private Proposition(VariableSource variableSource) {
          if (variableSource == null) {
              throw new NullPointerException();
          }
  
          this.variableSource = variableSource;
  
          List<Node> variables = this.variableSource.getVariables();
  
          for (Node variable : variables) {
              if (!(variable instanceof DiscreteVariable)) {
                  throw new IllegalArgumentException(
                          "Variables for Propositions " +
                                  "must be DiscreteVariables.");
              }
          }
  
          allowedCategories = new boolean[variables.size()][];
  
          for (int i = 0; i < variables.size(); i++) {
              DiscreteVariable discreteVariable =
                      (DiscreteVariable) variables.get(i);
              int numCategories = discreteVariable.getNumCategories();
              allowedCategories[i] = new boolean[numCategories];
          }
  
          setToTautology();
      }
  
      public static Proposition tautology(VariableSource variableSource) {
          return new Proposition(variableSource);
      }
  
      /**
       * Copies the info out of the old proposition into a new proposition for the
       * new BayesIm.
       */
      public Proposition(VariableSource variableSource, Proposition proposition) {
          this(variableSource);
  
          if (proposition == null) {
              throw new NullPointerException();
          }
  
          List<Node> variables = variableSource.getVariables();
          List<Node> oldVariables =
                  proposition.getVariableSource().getVariables();
  
          for (int i = 0; i < variables.size(); i++) {
              DiscreteVariable variable = (DiscreteVariable) variables.get(i);
              int oldIndex = -1;
  
              for (int j = 0; j < oldVariables.size(); j++) {
                  DiscreteVariable _variable =
                          (DiscreteVariable) oldVariables.get(j);
                  if (variable.equals(_variable)) {
                      oldIndex = j;
                      break;
                  }
              }
  
              if (oldIndex != -1) {
                  for (int j = 0; j < allowedCategories[i].length; j++) {
                      allowedCategories[i][j] =
                              proposition.isAllowed(oldIndex, j);
                  }
              }
          }
      }
  
      /**
       * Copies the info out of the old proposition into a new proposition for the
       * new BayesIm.
       */
      public Proposition(Proposition proposition) {
          this.variableSource = proposition.variableSource;
          this.allowedCategories =
                  new boolean[proposition.allowedCategories.length][];
  
          for (int i = 0; i < allowedCategories.length; i++) {
              this.allowedCategories[i] =
                      new boolean[proposition.allowedCategories[i].length];
  
              System.arraycopy(proposition.allowedCategories[i], 0,
                      allowedCategories[i], 0, allowedCategories[i].length);
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static Proposition serializableInstance() {
          return new Proposition(MlBayesIm.serializableInstance());
      }
  
      //===========================PUBLIC METHODS=========================//
  
      public int getNumAllowedCategories(int i) {
          int numAllowed = 0;
  
          for (int j = 0; j < getNumCategories(i); j++) {
              if (isAllowed(i, j)) {
                  numAllowed++;
              }
          }
  
          return numAllowed;
      }
  
      public void removeCategory(int variable, int category) {
          allowedCategories[variable][category] = false;
      }
  
      /**
       * Without changing the status of the specified category, disallows all
       * other categories for the given variable.
       */
      public void disallowComplement(int variable, int category) {
          for (int i = 0; i < allowedCategories[variable].length; i++) {
              if (i != category) {
                  allowedCategories[variable][i] = false;
              }
          }
      }
  
      /**
       * Sets the given value to true and all other values to false for the
       * given variable.
       */
      public void setCategory(int variable, int category) {
          setVariable(variable, false);
          addCategory(variable, category);
      }
  
      /**
       * @return true iff all categories for the given variable are allowed.
       */
      public boolean isUnconditioned(int variable) {
          return !isConditioned(variable);
      }
  
      /**
       * @return true iff the given point is true for this proposition.
       */
      public boolean isPermissibleCombination(int[] point) {
          for (int i = 0; i < allowedCategories.length; i++) {
              if (!allowedCategories[i][point[i]]) {
                  return false;
              }
          }
  
          return true;
      }
  
      /**
       * @return true iff there is some combination of categories for all the
       * variables of the proposition that is allowed.
       */
      public boolean existsCombination() {
          loop:
          for (boolean[] allowedCategory : allowedCategories) {
              for (boolean anAllowedCategory : allowedCategory) {
                  if (anAllowedCategory) {
                      continue loop;
                  }
              }
  
              return false;
          }
  
          return true;
      }
  
      public int getNumAllowed(int variable) {
          int sum = 0;
  
          for (int i = 0; i < getNumCategories(variable); i++) {
              if (isAllowed(variable, i)) {
                  sum++;
              }
          }
  
          return sum;
      }
  
      /**
       * @return the single category selected for the given variable, or -1 if it
       * is not the case that a single value is selected.
       */
      public int getSingleCategory(int variable) {
          int count = 0;
          int lastEncountered = -1;
  
          for (int i = 0; i < allowedCategories[variable].length; i++) {
              if (allowedCategories[variable][i]) {
                  lastEncountered = i;
                  count++;
              }
          }
  
          if (count != 1) {
              return -1;
          } else {
              return lastEncountered;
          }
      }
  
      /**
       * Restricts this proposition to the categories for each variable that are
       * true in the given proposition.
       */
      public void restrictToProposition(Proposition proposition) {
          if (proposition.getVariableSource() != this.variableSource) {
              throw new IllegalArgumentException("Can only restrict to " +
                      "propositions for the same variable source.");
          }
  
          for (int i = 0; i < allowedCategories.length; i++) {
              for (int j = 0; j < allowedCategories[i].length; j++) {
                  if (!proposition.allowedCategories[i][j]) {
                      this.allowedCategories[i][j] = false;
                  }
              }
          }
      }
  
  //    /**
  //     * Restricts this proposition to the categories for the given variable that
  //     * are true in the given proposition.
  //     */
  //    public void restrictToProposition(Proposition proposition, int variable) {
  //        if (proposition.getVariableSource() != this.variableSource) {
  //            throw new IllegalArgumentException("Can only restrict to " +
  //                    "propositions for the same variable source.");
  //        }
  //
  //        for (int j = 0; j < allowedCategories[variable].length; j++) {
  //            if (!proposition.isAllowed(variable, j)) {
  //                removeCategory(variable, j);
  //            }
  //        }
  //    }
  
      /**
       * @return the index of the variable with the given name, or -1 if such a
       * variable does not exist.
       */
      public int getNodeIndex(String name) {
          List<Node> variables = getVariableSource().getVariables();
  
          for (int i = 0; i < variables.size(); i++) {
              Node variable = variables.get(i);
              if (variable.getName().equals(name)) {
                  return i;
              }
          }
  
          return -1;
      }
  
      public int getCategoryIndex(String nodeName, String category) {
          int index = getVariableSource().getVariableNames().indexOf(nodeName);
          DiscreteVariable variable = (DiscreteVariable) getVariableSource().getVariables().get(index);
          return variable.getCategories().indexOf(category);
      }
  
      public void addCategory(int variable, int category) {
          allowedCategories[variable][category] = true;
      }
  
      /**
       * @return the Bayes IM that this is a proposition for.
       */
      public VariableSource getVariableSource() {
          return this.variableSource;
      }
  
      /**
       * @return the number of variables for the proposition.
       */
      public int getNumVariables() {
          return allowedCategories.length;
      }
  
      /**
       * @return the number of categories for the given variable.
       */
      public int getNumCategories(int variable) {
          return allowedCategories[variable].length;
      }
  
      /**
       * Specifies that all categories for the given variable are either all
       * allowed (true) or all disallowed (false).
       */
      public void setVariable(int variable, boolean allowed) {
          for (int i = 0; i < allowedCategories[variable].length; i++) {
              allowedCategories[variable][i] = allowed;
          }
      }
  
      /**
       * Specifies that all variables in the proposition are either completely
       * allowed (true) or completely disallowed (false) for all of their
       * categories.
       */
      public void setToTautology() {
          for (int i = 0; i < allowedCategories.length; i++) {
              setVariable(i, true);
          }
      }
  
      /**
       * @return true iff the given category for the given variable is allowed.
       */
      public boolean isAllowed(int variable, int category) {
          return allowedCategories[variable][category];
      }
  
      /**
       * @return true iff some category for the given variable is disallowed.
       */
      public boolean isConditioned(int variable) {
          for (int j = 0; j < getNumCategories(variable); j++) {
              if (!isAllowed(variable, j)) {
                  return true;
              }
          }
  
          return false;
      }
  
      public boolean equals(Object o) {
          if (o == null) {
              return false;
          }
  
          if (!(o instanceof Proposition)) {
              return false;
          }
  
          Proposition proposition = (Proposition) o;
  
          if (!(variableSource == proposition.variableSource)) {
              return false;
          }
  
          for (int i = 0; i < allowedCategories.length; i++) {
              for (int j = 0; j < allowedCategories[i].length; j++) {
                  if (allowedCategories[i][j] !=
                          proposition.allowedCategories[i][j]) {
                      return false;
                  }
              }
          }
  
          return true;
      }
  
      public int hashCode() {
          int hashCode = 37;
          hashCode = 19 * hashCode + variableSource.hashCode();
          hashCode = 19 * hashCode + Arrays.deepHashCode(allowedCategories);
          return hashCode;
      }
  
      public String toString() {
          StringBuilder buf = new StringBuilder();
          List<Node> variables = getVariableSource().getVariables();
  
          buf.append("\n");
  
          for (int i = 0; i < getNumVariables(); i++) {
              DiscreteVariable variable = (DiscreteVariable) variables.get(i);
              String name = variable.getName();
              buf.append(name);
  
              for (int j = name.length(); j < 5; j++) {
                  buf.append(" ");
              }
  
              buf.append("\t");
          }
  
          for (int i = 0; i < getMaxNumCategories(); i++) {
              buf.append("\n");
  
              for (int j = 0; j < getNumVariables(); j++) {
                  if (i < getNumCategories(j)) {
                      boolean allowed = isAllowed(j, i);
                      buf.append(allowed ? "true" : "*   ").append("\t");
                  } else {
                      buf.append("    \t");
                  }
              }
          }
  
          return buf.toString();
      }
  
      //=============================PRIVATE METHODS=======================//
  
      private int getMaxNumCategories() {
          int max = 0;
  
          for (int i = 0; i < getNumVariables(); i++) {
              if (getNumCategories(i) > max) {
                  max = getNumCategories(i);
              }
          }
  
          return max;
      }
  
      /**
       * 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();
          }
  
          if (allowedCategories == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  