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 edu.cmu.tetrad.util.dist.Distribution;
  import edu.cmu.tetrad.util.dist.Normal;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  
  //import edu.cmu.tetrad.gene.history.function.BooleanGlassFunction;
  
  /**
   * Initializes a history array by setting the value of each variable to basal
   * if it is unregulated (has no parents other than itself one time step back)
   * and to a random value chosen from a N(basal, initStDev) distribution
   * otherwise.
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class BasalInitializer implements Initializer, TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The update function this is initializing for.
       *
       * @serial
       */
      private UpdateFunction updateFunction;
  
      /**
       * The average expression level that all unregulated genes are initialized
       * to.
       *
       * @serial
       */
      private double basalExpression;
  
      /**
       * The standard deviation of a normal distribution N(basalExpression,
       * sem.D.) that random initial values for unregulated genes are set to.
       *
       * @serial
       */
      private double initStDev;
  
      //============================CONSTRUCTORS===========================//
  
      /**
       * Constructs a new history that will initialize genes using the given basal
       * expression and initial standard deviation.
       */
      public BasalInitializer(UpdateFunction updateFunction,
                              double basalExpression, double initStDev) {
          if (updateFunction == null) {
              throw new NullPointerException(
                      "Update function must not be " + "null");
          }
  
          if (initStDev <= 0) {
              throw new IllegalArgumentException("The initialization standard " +
                      "deviation must be positive");
          }
  
          this.updateFunction = updateFunction;
          this.basalExpression = basalExpression;
          this.initStDev = initStDev;
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static BasalInitializer serializableInstance() {
          return new BasalInitializer(BooleanGlassFunction.serializableInstance(),
                  0.0, 1.0);
      }
  
      //============================PUBLIC METHODS==========================//
  
      /**
       * Sets the expression of each unregulated gene in the given history at time
       * step 0 to a random value drawn from N(basalExpression, initStDev),
       * sets the expression level at time step 0 of each regulated gene to zero,
       * and then copies the values at history[0][j] to history[i][j] for all i >
       * 0 less than the maximum time lag.
       *
       * @param history the 2D double array to randomize.
       */
      public void initialize(double[][] history) {
  
          Distribution initDistribution =
                  new Normal(this.basalExpression, this.initStDev);
  
          // TODO: Make sure normal dist gets nextGaussian, multiplies
          // by st.dev. and adds mean.
  
          // Modification 10/11/01: If a factor has no parents other
          // than itself, then it is initialized to mean of the
          // initialization distribution. The rationale for this is that
          // these "unregulated genes" will settle to zero anyway under
          // Glass updating, and this lets us avoid waiting for them to
          // settle (an unknown number of time steps). jdramsey
          for (int j = 0; j < history[0].length; j++) {
  
              IndexedLagGraph connectivity =
                      this.updateFunction.getIndexedLagGraph();
  
              if (connectivity.getNumParents(j) == 0) {
                  history[0][j] = this.basalExpression;
              } else {
                  history[0][j] = initDistribution.nextRandom();
              }
          }
  
          for (int i = 1; i < history.length; i++) {
              System.arraycopy(history[0], 0, history[i], 0, history[0].length);
          }
      }
  
      /**
       * 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 (updateFunction == null) {
              throw new NullPointerException();
          }
  
          if (initStDev <= 0.0) {
              throw new IllegalStateException();
          }
      }
  }
  
  
  
  
  
  