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.tetradapp.model;
  
  import edu.cmu.tetrad.gene.tetrad.gene.history.BasalInitializer;
  import edu.cmu.tetrad.gene.tetrad.gene.history.BooleanGlassFunction;
  import edu.cmu.tetrad.gene.tetrad.gene.history.GeneHistory;
  import edu.cmu.tetrad.gene.tetrad.gene.simulation.MeasurementSimulator;
  import edu.cmu.tetrad.util.Parameters;
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  
  /**
   * Wraps MeasurementSimulator so that it may be used as a parameter object.
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class MeasurementSimulatorParams implements TetradSerializable{
      static final long serialVersionUID = 23L;
  
      /**
       * @serial Cannot be null.
       */
      private MeasurementSimulator simulator;
      private boolean includeDishAndChipVariables;
  
      //==============================CONSTRUCTORS=========================//
  
      /**
       * Constructs a measurement simulator using the given history. The history
       * will be used to do the simulation of each cell.
       *
       * @throws NullPointerException if the history argument is null.
       */
      public MeasurementSimulatorParams(Parameters parameters) {
          simulator = new MeasurementSimulator(parameters);
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static MeasurementSimulatorParams serializableInstance() {
          MeasurementSimulatorParams params = new MeasurementSimulatorParams(new Parameters());
          params.setHistory(new GeneHistory(
                  BasalInitializer.serializableInstance(),
                  BooleanGlassFunction.serializableInstance()));
          return params;
      }
  
      //==============================PUBLIC METHODS======================//
  
      public void setHistory(GeneHistory history) {
          getSimulator().setHistory(history);
      }
  
      public double getDishDishVariability() {
          return getSimulator().getDishDishVariability();
      }
  
      public void setDishDishVariability(double value) {
          getSimulator().setDishDishVariability(value);
      }
  
      public double getSampleSampleVariability() {
          return getSimulator().getSampleSampleVariability();
      }
  
      public void setSampleSampleVariability(double value) {
          getSimulator().setSampleSampleVariability(value);
      }
  
      public double getChipChipVariability() {
          return getSimulator().getChipChipVariability();
      }
  
      public void setChipChipVariability(double value) {
          getSimulator().setChipChipVariability(value);
      }
  
      public double getPixelDigitalization() {
          return getSimulator().getPixelDigitalization();
      }
  
      public void setPixelDigitalization(double value) {
          getSimulator().setPixelDigitalization(value);
      }
  
      public int getNumDishes() {
          return getSimulator().getNumDishes();
      }
  
      public void setNumDishes(int value) {
          getSimulator().setNumDishes(value);
      }
  
      public int getNumCellsPerDish() {
          return getSimulator().getNumCellsPerDish();
      }
  
      public void setNumCellsPerDish(int value) {
          getSimulator().setNumCellsPerDish(value);
      }
  
      public int getNumSamplesPerDish() {
          return getSimulator().getNumSamplesPerDish();
      }
  
      public void setNumSamplesPerDish(int value) {
          getSimulator().setNumSamplesPerDish(value);
      }
  
      public int getStepsGenerated() {
          return getSimulator().getStepsGenerated();
      }
  
      public void setStepsGenerated(int value) {
          getSimulator().setStepsGenerated(value);
      }
  
      public int getFirstStepStored() {
          return getSimulator().getFirstStepStored();
      }
  
      public void setFirstStepStored(int value) {
          getSimulator().setFirstStepStored(value);
      }
  
      public int getInterval() {
          return getSimulator().getInterval();
      }
  
      public void setInterval(int value) {
          getSimulator().setInterval(value);
      }
  
      public boolean isInitSync() {
          return getSimulator().isInitSync();
      }
  
      public void setInitSync(boolean selected) {
          getSimulator().setInitSync(selected);
      }
  
      public boolean isRawDataSaved() {
          return getSimulator().isRawDataSaved();
      }
  
      public void setRawDataSaved(boolean selected) {
          getSimulator().setRawDataSaved(selected);
      }
  
      public boolean isAntilogCalculated() {
          return getSimulator().isAntilogCalculated();
      }
  
      public void setAntilogCalculated(boolean selected) {
          getSimulator().setAntilogCalculated(selected);
      }
  
      public MeasurementSimulator getSimulator() {
          return simulator;
      }
  
      public void simulate(GeneHistory history) {
          getSimulator().simulate(history);
      }
  
      public double[][][] getMeasuredData() {
          return getSimulator().getMeasuredData();
      }
  
      public int[] getTimeSteps() {
          return getSimulator().getTimeSteps();
      }
  
      public double[][][] getRawData() {
          return getSimulator().getRawData();
      }
  
      /**
       * 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 (simulator == null) {
              throw new NullPointerException();
          }
      }
  
      public boolean isIncludeDishAndChipVariables() {
          return getSimulator().isIncludeDishAndChipColumns();
      }
  
      public void setIncludeDishAndChipVariables(boolean includeDishAndChipVariables) {
          getSimulator().setIncludeDishAndChipColumns(includeDishAndChipVariables);
      }
  }
  
  
  
  
  
  