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.dist.Distribution;
  import edu.cmu.tetrad.util.dist.Normal;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.ArrayList;
  
  /**
   * <p>Implements a polynomial update function, Gi.0 = P(Parents(G0.0)) + ei,
   * where P is a polynomial function and ei is a random noise term.</p>
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class PolynomialFunction implements UpdateFunction {
      static final long serialVersionUID = 23L;
  
      /**
       * The "snapshot" indexed connectivity of the initial lag graph.
       *
       * @serial
       */
      private IndexedLagGraph connectivity;
  
      /**
       * The polynomials of each factor given its parents.
       *
       * @serial
       */
      private Polynomial[] polynomials;
  
      /**
       * Error distributions from which errors are drawn for each of the factors.
       *
       * @serial
       */
      private Distribution[] errorDistributions;
  
      //=============================CONSTRUCTORS===========================//
  
      /**
       * Constructs a polyomial function where each factor is given a zero
       * polynomial.
       */
      public PolynomialFunction(LagGraph lagGraph) {
  
          if (lagGraph == null) {
              throw new NullPointerException("Lag graph must not be null.");
          }
  
          // Construct the "snapshot" indexed connectivity.
          this.connectivity = new IndexedLagGraph(lagGraph);
          int numFactors = this.connectivity.getNumFactors();
  
          // Give each factor a zero polynomial.
          this.polynomials = new Polynomial[numFactors];
  
          for (int i = 0; i < numFactors; i++) {
              this.polynomials[i] = new Polynomial(new ArrayList());
          }
  
          // Set up error distributions.
          errorDistributions = new Distribution[numFactors];
  
          for (int i = 0; i < errorDistributions.length; i++) {
              errorDistributions[i] = new Normal(0.0, 0.05);
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static PolynomialFunction serializableInstance() {
          return new PolynomialFunction(BasicLagGraph.serializableInstance());
      }
  
      //===============================PUBLIC METHODS=======================//
  
      /**
       * Returns the value of the function.
       */
      public double getValue(int factorIndex, double[][] history) {
  
          int numParents = this.connectivity.getNumParents(factorIndex);
          double[] values = new double[numParents];
          for (int i = 0; i < numParents; i++) {
              IndexedParent parent = this.connectivity.getParent(factorIndex, i);
              values[i] = history[parent.getLag()][parent.getIndex()];
          }
          return polynomials[factorIndex].evaluate(values) +
                  errorDistributions[factorIndex].nextRandom();
      }
  
      /**
       * Returns the indexed connectivity.
       */
      public IndexedLagGraph getIndexedLagGraph() {
          return this.connectivity;
      }
  
      /**
       * Method setIntenalNoiseModel
       *
       * @param factor
       * @param distribution
       */
      public void setErrorDistribution(int factor, Distribution distribution) {
          if (distribution != null) {
              this.errorDistributions[factor] = distribution;
          } else {
              throw new NullPointerException();
          }
      }
  
      /**
       * Returns the error distribution for the <code>factor</code>'th factor.
       *
       * @param factor the factor in question.
       * @return the error distribution for <code>factor</code>.
       */
      public Distribution getErrorDistribution(int factor) {
          return this.errorDistributions[factor];
      }
  
      /**
       * Sets the polynomial for the given factor.
       */
      public void setPolynomial(int factor, Polynomial polynomial) {
  
          if (polynomial == null) {
              throw new NullPointerException("Polynomial must not be null.");
          }
  
          this.polynomials[factor] = polynomial;
      }
  
      /**
       * Returns the polynomial for the given factor.
       */
      public Polynomial getPolynomial(int factor) {
          return this.polynomials[factor];
      }
  
      /**
       * Returns the number of factors in the history. This is used to set up the
       * initial history array.
       */
      public int getNumFactors() {
          return this.connectivity.getNumFactors();
      }
  
      /**
       * Returns the max lag of the history. This is used to set up the initial
       * history array.
       */
      public int getMaxLag() {
          int maxLag = 0;
          for (int i = 0; i < this.connectivity.getNumFactors(); i++) {
              for (int j = 0; j < this.connectivity.getNumParents(i); j++) {
                  IndexedParent parent = this.connectivity.getParent(i, j);
                  if (parent.getLag() > maxLag) {
                      maxLag = parent.getLag();
                  }
              }
          }
          return maxLag;
      }
  
      /**
       * 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 (connectivity == null) {
              throw new NullPointerException();
          }
  
          if (polynomials == null) {
              throw new NullPointerException();
          }
  
          if (errorDistributions == null) {
              throw new NullPointerException();
          }
  
      }
  }
  
  
  
  
  
  