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.sem;
  
  import edu.cmu.tetrad.graph.GraphNode;
  import edu.cmu.tetrad.graph.SemGraph;
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  
  /**
   * Stores the freeParameters for an instance of a SemEstimatorGibbs.
   *
   * @author Frank Wimberly
   */
  public final class SemEstimatorGibbsParams implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      private SemIm startIm;
      private boolean flatPrior;
      private int numIterations;
      private double stretch;
  
      private double tolerance;
  
      //=============================CONSTRUCTORS============================//
  
      /**
       *
       */
      private SemEstimatorGibbsParams(SemIm startIm, boolean flatPrior,
                                      double stretch, int numIterations) {
  
          // note that seed is never used... just as well to get rid of it?
  
          this.startIm = startIm;
          this.flatPrior = flatPrior;
          this.stretch = stretch;
          this.numIterations = numIterations;
  
          this.tolerance = 0.0001;
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static SemEstimatorGibbsParams serializableInstance() {
          SemGraph graph = new SemGraph();
          graph.addNode(new GraphNode("X"));
          return new SemEstimatorGibbsParams(new SemIm(new SemPm(graph)), false,
                  0.0d, 1);
      }
  
      public SemIm getStartIm() {
          return startIm;
      }
  
      public void setStartIm(SemIm startIm) {
          this.startIm = startIm;
      }
  
      public double getStretch() {
          return stretch;
      }
  
      public void setStretch(double stretch) {
          this.stretch = stretch;
      }
  
      public double getTolerance() {
          return tolerance;
      }
  
      public int getNumIterations() {
          return numIterations;
      }
  
      public void setNumIterations(int numIterations) {
          this.numIterations = numIterations;
      }
  
      public void setFlatPrior(boolean flatPrior) {
          this.flatPrior = flatPrior;
      }
  
      public boolean isFlatPrior() {
          return flatPrior;
      }
  
  
      /**
       * 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();
      }
  }
  
  
  