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 cern.colt.matrix.DoubleMatrix2D;
  
  import edu.cmu.tetrad.util.TetradMatrix;
  import edu.cmu.tetrad.util.TetradSerializable;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  
  /**
   * <p>Maps a parameter to the matrix element where its value is stored in the
   * model.</p>
   *
   * @author Frank Wimberly
   * @author Joe Ramsey
   */
  public class Mapping implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The SemIm for which this is a mapping.
       *
       * @serial Can't be null.
       */
      private ISemIm semIm;
  
      /**
       * The parameter this mapping maps.
       *
       * @serial Can't be null.
       */
      private Parameter parameter;
  
      /**
       * The 2D double array whose element at (i, j) to be manipulated.
       *
       * @serial Can't be null.
       */
      private TetradMatrix a;
  
      /**
       * The left-hand coordinate of a[i][j].
       *
       * @serial Any value.
       */
      private int i;
  
      /**
       * The right-hand coordinate of a[i][j].
       *
       * @serial Any value.
       */
      private int j;
  
      /**
       * Constructs matrix new mapping using the given freeParameters.
       *
       * @param parameter The parameter that this maps.
       * @param matrix    The array containing matrix[i][j], the element to be
       *                  manipulated.
       * @param i         Left coordinates of matrix[i][j].
       * @param j         Right coordinate of matrix[i][j].
       */
      public Mapping(ISemIm semIm, Parameter parameter, TetradMatrix matrix,
                     int i, int j) {
          if (semIm == null) {
              throw new NullPointerException("SemIm must not be null.");
          }
  
          if (parameter == null) {
              throw new NullPointerException("Parameter must not be null.");
          }
  
          if (matrix == null) {
              throw new NullPointerException("Supplied array must not be null.");
          }
  
          if (i < 0 || j < 0) {
              throw new IllegalArgumentException("Indices must be non-negative");
          }
  
          this.semIm = semIm;
          this.parameter = parameter;
          this.a = matrix;
          this.i = i;
          this.j = j;
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       */
      public static Mapping serializableInstance() {
          return new Mapping(SemIm.serializableInstance(),
                  Parameter.serializableInstance(), new TetradMatrix(0, 0),
                  1, 1);
      }
  
      /**
       * Sets the value of the array element at the stored coordinates (i, j).
       * If the array is symmetric sets two elements.
       */
      public void setValue(double x) {
          if (this.semIm.isParameterBoundsEnforced() &&
                  getParameter().getType() == ParamType.VAR && x < 0.0) {
              throw new IllegalArgumentException(
                      "Variances cannot " + "have values <= 0.0: " + x);
          }
  
          a.set(i, j, x);
  
          if (getParameter().getType() == ParamType.VAR ||
                  getParameter().getType() == ParamType.COVAR) {
              a.set(j, i, x);
              a.set(i, j, x);
          }
      }
  
      /**
       * @return the value of the array element at (i, j).
       */
      public double getValue() {
          return a.get(i, j);
      }
  
      /**
       * @return the paramter that this mapping maps.
       */
      public Parameter getParameter() {
          return this.parameter;
      }
  
      /**
       * @return a String containing information (array name and values of
       * subscripts) about the array element associated with this mapping.
       */
      public String toString() {
          return "<" + getParameter().getName() + " " + getParameter().getType() +
                  "[" + i + "][" + j + "]>";
      }
  
      /**
       * 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 (semIm == null) {
              throw new NullPointerException();
          }
  
          if (parameter == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  