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.gene.tetrad.gene.history;
  
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.Arrays;
  
  /**
   * <p>Implements a term in a polymonial whose variables are mapped to indices in
   * in the set {0, 1, 2, ...}. The term has a coefficient and a freely generated
   * list of variables. For example, if "x" -> 0, "y" -> 1, "z" -> 2, then the
   * following terms are represented as follows, where "Vi" stands for the
   * variable mapped to index i:</p> </p> <ol> <li> 2.5x -> 2.5*(V0)(V0) <li>
   * 1.7xyz^2 -> 1.7*(V0)(V1)(V2)(V2) <li> -5.0z^3y^2 -> -5.0*(V2)(V2)(V2)(V1)(V1)
   * </ol>
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class PolynomialTerm implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The coefficient of the term.
       *
       * @serial
       */
      private double coefficient;
  
      /**
       * The variables of the term.
       *
       * @serial
       */
      private int[] variables;
  
      //=================================CONSTRUCTORS========================//
  
      /**
       * Constructs a term.
       */
      public PolynomialTerm(double coefficient, int[] variables) {
          if (variables == null) {
              throw new NullPointerException("Variables cannot be null.");
          }
  
          this.variables = new int[variables.length];
          System.arraycopy(variables, 0, this.variables, 0, variables.length);
  
          this.coefficient = coefficient;
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static PolynomialTerm serializableInstance() {
          return new PolynomialTerm(0.0, new int[0]);
      }
  
      //==================================PUBLIC METHODS=====================//
  
      /**
       * Returns the coefficient.
       */
      public double getCoefficient() {
          return this.coefficient;
      }
  
      /**
       * Sets the coefficient.
       */
      public void setCoefficient(double coefficient) {
          this.coefficient = coefficient;
      }
  
      /**
       * Returns the number of variables in this term.
       */
      public int getNumVariables() {
          return this.variables.length;
      }
  
      /**
       * Returns the index'th variable.
       */
      public int getVariable(int index) {
          return this.variables[index];
      }
  
      /**
       * Returns true iff the given variable list is equal to the variable list of
       * this term.
       */
      public boolean isVariableListEqual(int[] variables) {
          return Arrays.equals(variables, this.variables);
      }
  
      /**
       * Returns the highest variable index in this term.
       */
      public int getMaxIndex() {
          int max = 0;
          for (int variable : variables) {
              if (variable > max) {
                  max = variable;
              }
          }
          return max;
      }
  
      /**
       * Evaluates the term.
       */
      public double evaluate(double[] values) {
          double product = this.coefficient;
          for (int variable : this.variables) {
              product *= values[variable];
          }
          return product;
      }
  
      /**
       * Prints out a representation of the term.
       */
      public String toString() {
          StringBuilder buf = new StringBuilder();
          buf.append(this.coefficient);
          if (this.variables.length > 0) {
              buf.append("*");
          }
          for (int variable : this.variables) {
              buf.append("(V");
              buf.append(variable);
              buf.append(")");
          }
          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();
  
          if (variables == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  