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.ArrayList;
  import java.util.List;
  
  /**
   * Implements a polynomial as a sum of a list of terms whose variables are
   * identified as integers in the set {0, 1, 2, ...}.
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public final class Polynomial implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The terms of the polynomial.
       *
       * @serial
       */
      private List<PolynomialTerm> terms;
  
      //==============================CONSTRUCTOR===========================//
  
      /**
       * Constructs a polynomial from a list of terms.
       */
      public Polynomial(List<PolynomialTerm> terms) {
  
          if (terms == null) {
              throw new NullPointerException("Terms list cannot be null.");
          }
  
          this.terms = new ArrayList<>(terms);
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static Polynomial serializableInstance() {
          return new Polynomial(new ArrayList<PolynomialTerm>());
      }
  
      //==============================PUBLIC METHODS========================//
  
      /**
       * Returns the number of terms.
       */
      public int getNumTerms() {
          return this.terms.size();
      }
  
      /**
       * Returns the coefficient.
       */
      public PolynomialTerm getTerm(int index) {
          return this.terms.get(index);
      }
  
      /**
       * Finds the first term matching the given profile.
       */
      public PolynomialTerm findTerm(int[] variables) {
          for (PolynomialTerm term1 : this.terms) {
              if (term1.isVariableListEqual(variables)) {
                  return term1;
              }
          }
  
          return null;
      }
  
      /**
       * Returns the highest variable index in any term.
       */
      public int getMaxIndex() {
          int max = 0;
          for (PolynomialTerm term1 : this.terms) {
              int termMax = term1.getMaxIndex();
              if (termMax > max) {
                  max = termMax;
              }
          }
          return max;
      }
  
      /**
       * Evaluates the term.
       */
      public double evaluate(double[] values) {
          double sum = 0.0;
          for (PolynomialTerm term1 : this.terms) {
              sum += term1.evaluate(values);
          }
          return sum;
      }
  
      /**
       * Prints out a representation of the term.
       */
      public String toString() {
          StringBuilder buf = new StringBuilder();
          for (int i = 0; i < this.terms.size(); i++) {
              buf.append(this.terms.get(i));
              if (i < this.terms.size() - 1) {
                  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 (terms == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  