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 java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * <p>Implements a linear update function, Gi.0 = L(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 LinearFunction implements UpdateFunction {
      static final long serialVersionUID = 23L;
  
      /**
       * The wrapped polynomial function that's doing all the work.
       *
       * @serial
       */
      private PolynomialFunction polynomialFunction;
  
      //=========================CONSTRUCTORS=============================//
  
      /**
       * Constructs a polyomial function where each factor is given a zero
       * polynomial.
       */
      public LinearFunction(LagGraph lagGraph) {
          if (lagGraph == null) {
              throw new NullPointerException("Lag graph must not be null.");
          }
  
          this.polynomialFunction = new PolynomialFunction(lagGraph);
          IndexedLagGraph connectivity = polynomialFunction.getIndexedLagGraph();
  
          for (int i = 0; i < connectivity.getNumFactors(); i++) {
              List terms = new ArrayList();
  
              // Intercept.
              terms.add(new PolynomialTerm(0.0, new int[0]));
  
              int numParents = connectivity.getNumParents(i);
              for (int j = 0; j < numParents; j++) {
  
                  int[] vars = new int[]{j};
                  terms.add(new PolynomialTerm(1.0 / (double) numParents, vars));
              }
              Polynomial p = new Polynomial(terms);
              polynomialFunction.setPolynomial(i, p);
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static LinearFunction serializableInstance() {
          return new LinearFunction(BasicLagGraph.serializableInstance());
      }
  
      //============================PUBLIC METHODS==========================//
  
      /**
       * Returns the value of the function.
       */
      public double getValue(int factorIndex, double[][] history) {
          return this.polynomialFunction.getValue(factorIndex, history);
      }
  
      /**
       * Returns the indexed connectivity.
       */
      public IndexedLagGraph getIndexedLagGraph() {
          return this.polynomialFunction.getIndexedLagGraph();
      }
  
      /**
       * Sets the intercept for the given factor.
       */
      public boolean setIntercept(String factor, double intercept) {
          IndexedLagGraph connectivity =
                  this.polynomialFunction.getIndexedLagGraph();
  
          int factorIndex = connectivity.getIndex(factor);
  
          return setIntercept(factorIndex, intercept);
      }
  
      /**
       * Sets the intercept for the given factor.
       */
      public boolean setIntercept(int factor, double intercept) {
          Polynomial p = this.polynomialFunction.getPolynomial(factor);
          PolynomialTerm term = p.findTerm(new int[0]);
          if (term == null) {
              return false;
          }
  
          term.setCoefficient(intercept);
          return true;
      }
  
      /**
       * Sets the intercept for the given factor.
       */
      public boolean setCoefficient(String factor, LaggedFactor parent,
                                    double intercept) {
          IndexedLagGraph connectivity = polynomialFunction.getIndexedLagGraph();
  
          int factorIndex = connectivity.getIndex(factor);
          int parentIndex = connectivity.getIndex(factor, parent);
  
          return setCoefficient(factorIndex, parentIndex, intercept);
      }
  
      /**
       * Sets the coefficient for the given parent of the given factor.
       */
      public boolean setCoefficient(int factor, int parent, double coefficient) {
  
          Polynomial p = this.polynomialFunction.getPolynomial(factor);
          PolynomialTerm term = p.findTerm(new int[]{parent});
  
          if (term == null) {
              return false;
          }
  
          term.setCoefficient(coefficient);
          return true;
      }
  
      /**
       * Method setIntenalNoiseModel
       *
       * @param factor
       * @param distribution
       */
      public void setErrorDistribution(int factor, Distribution distribution) {
          this.polynomialFunction.setErrorDistribution(factor, distribution);
      }
  
      /**
       * 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.polynomialFunction.getErrorDistribution(factor);
      }
  
      /**
       * Prints out the linear function of each factor of its parents.
       */
      public String toString() {
          StringBuilder buf = new StringBuilder();
          IndexedLagGraph connectivity = polynomialFunction.getIndexedLagGraph();
          buf.append("\n\nLinear Function:");
          for (int i = 0; i < connectivity.getNumFactors(); i++) {
              buf.append("\n\tFactor " + connectivity.getFactor(i) + " --> " +
                      this.polynomialFunction.getPolynomial(i));
          }
          return buf.toString();
      }
  
      /**
       * Returns the number of factors in the history. This is used to set up the
       * initial history array.
       */
      public int getNumFactors() {
          return this.polynomialFunction.getNumFactors();
      }
  
      /**
       * Returns the max lag of the history. This is used to set up the initial
       * history array.
       */
      public int getMaxLag() {
          return this.polynomialFunction.getMaxLag();
      }
  
      /**
       * 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 (polynomialFunction == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  