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.graph;
  
  import edu.cmu.tetrad.util.NamingProtocol;
  import edu.cmu.tetrad.util.PointXy;
  import edu.cmu.tetrad.gene.tetrad.gene.history.BasicLagGraph;
  import edu.cmu.tetrad.gene.tetrad.gene.history.LagGraph;
  import edu.cmu.tetrad.gene.tetrad.gene.history.LaggedFactor;
  
  import java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.Iterator;
  import java.util.Map;
  import java.util.SortedMap;
  import java.util.SortedSet;
  
  /**
   * Constructs as a (manual) update graph.
   */
  public final class ManualLagGraph implements LagGraph {
      static final long serialVersionUID = 23L;
  
      /**
       * @serial
       */
      private final BasicLagGraph lagGraph = new BasicLagGraph();
  
      //============================CONSTRUCTORS========================//
  
      /**
       * Using the given parameters, constructs an BasicLagGraph.
       *
       * @param params an LagGraphParams object.
       */
      public ManualLagGraph(ManualLagGraphParams params) {
          addFactors("G", params.getVarsPerInd());
          setMaxLagAllowable(params.getMlag());
  
          // Add edges one time step back.
          for (Iterator it = getFactors().iterator(); it.hasNext();) {
              String factor = (String) it.next();
              LaggedFactor laggedFactor = new LaggedFactor(factor, 1);
              addEdge(factor, laggedFactor);
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static ManualLagGraph serializableInstance() {
          return new ManualLagGraph(ManualLagGraphParams.serializableInstance());
      }
  
      //=============================PUBLIC METHODS=======================//
  
      public void addEdge(String factor, LaggedFactor laggedFactor)
              throws IllegalArgumentException {
          lagGraph.addEdge(factor, laggedFactor);
      }
  
      public void clearEdges() {
          lagGraph.clearEdges();
      }
  
      public void addFactor(String factor) {
          if (!NamingProtocol.isLegalName(factor)) {
              throw new IllegalArgumentException(
                      NamingProtocol.getProtocolDescription());
          }
  
          lagGraph.addFactor(factor);
      }
  
      public boolean existsFactor(String factor) {
          return lagGraph.existsFactor(factor);
      }
  
      public boolean existsEdge(String factor, LaggedFactor laggedFactor) {
          return lagGraph.existsEdge(factor, laggedFactor);
      }
  
      public SortedSet getParents(String factor) {
          return lagGraph.getParents(factor);
      }
  
      public void removeEdge(String factor, LaggedFactor laggedFactor) {
          lagGraph.removeEdge(factor, laggedFactor);
      }
  
      public int getMaxLagAllowable() {
          return lagGraph.getMaxLagAllowable();
      }
  
      public void setMaxLagAllowable(int maxLagAllowable) {
          lagGraph.setMaxLagAllowable(maxLagAllowable);
      }
  
      public int getMaxLag() {
          return lagGraph.getMaxLag();
      }
  
      public void removeFactor(String factor) {
          lagGraph.removeFactor(factor);
      }
  
      public SortedMap getConnectivity() {
          return lagGraph.getConnectivity();
      }
  
      public void renameFactor(String oldName, String newName) {
          lagGraph.renameFactor(oldName, newName);
      }
  
      public int getNumFactors() {
          return lagGraph.getNumFactors();
      }
  
      public SortedSet getFactors() {
          return lagGraph.getFactors();
      }
  
      public String toString() {
          return lagGraph.toString();
      }
  
      public void addFactors(String base, int numFactors) {
          lagGraph.addFactors(base, numFactors);
      }
  
      public void setLocation(String factor, PointXy point) {
          lagGraph.setLocation(factor, point);
      }
  
      public PointXy getLocation(String factor) {
          return lagGraph.getLocation(factor);
      }
  
      public Map getLocations() {
          return lagGraph.getLocations();
      }
  
      /**
       * 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 (lagGraph == null) {
              throw new NullPointerException();
          }
      }
  }
  
  
  
  
  
  