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;
  
  /**
   * Models the manner in which gene models are initialized differentially
   * depending on the dishes that the cells are in. The basic idea of the model is
   * that cells are grown in different dishes, and as a result may be initialized
   * differently. (They may also grow differently, although that is not being
   * modelled currently.) Causes of differentiation may be nutrition, temperature,
   * etc.
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class DishModel implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The number of the getModel dish.
       *
       * @serial
       */
      private int dishNumber = 0;
  
      /**
       * The standard deviation of the normal distribution from which dish bump
       * values are drawn, in percent. The distribution has a mean of 100%.
       *
       * @serial
       */
      private double dishBumpStDev = 10.0;
  
      /**
       * An array of dish bumps for each dish.
       *
       * @serial
       */
      private double[] dishBumps;
  
      //===============================CONSTRUCTORS========================//
  
      public DishModel(int numDishes, double dishBumpStDev) {
  
          if (numDishes < 1) {
              throw new IllegalArgumentException(
                      "There must be at least one dish");
          }
  
          if (dishBumpStDev < 0.0) {
              throw new IllegalArgumentException(
                      "The stdev must be non-negative");
          }
  
          // numDishes is not stored at the class level, because the
          // length of dishBumps[] already contains that information.
          this.dishBumps = new double[numDishes];
          this.setDishBumpStDev(dishBumpStDev);
  
          Distribution distribution =
                  new Normal(100.0, dishBumpStDev);
  
          for (int i = 0; i < numDishes; i++) {
              this.dishBumps[i] = distribution.nextRandom();
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static DishModel serializableInstance() {
          return new DishModel(1, 1.0);
      }
  
      //===============================PUBLIC METHODS======================//
  
      /**
       * Returns the number of the getModel dish.
       */
      public int getDishNumber() {
          return this.dishNumber;
      }
  
      /**
       * Sets the number of the getModel dish.
       */
      public void setDishNumber(int dishNumber) {
  
          if ((dishNumber >= 0) && (dishNumber < dishBumps.length)) {
              this.dishNumber = dishNumber;
          } else {
              throw new IllegalArgumentException(
                      "Invalid dish number: " + dishNumber);
          }
      }
  
      /**
       * Bumps the given expression value in the manner prescribed for the
       * getModel dish.
       */
      public double bumpInitialization(double expressionLevel) {
  
          //System.out.println(this.dishBumps[this.dishNumber]);
          return expressionLevel * this.dishBumps[this.dishNumber] / 100.0;
      }
  
      public double getDishBumpStDev() {
          return dishBumpStDev;
      }
  
      public void setDishBumpStDev(double dishBumpStDev) {
          this.dishBumpStDev = dishBumpStDev;
      }
  
      /**
       * 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 (dishBumps == null) {
              throw new NullPointerException();
          }
  
          if (dishBumpStDev < 0.0) {
              throw new IllegalStateException();
          }
  
          if (dishNumber < 0 || dishNumber >= dishBumps.length) {
              throw new IllegalStateException();
          }
      }
  
  }
  
  
  
  
  
  