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 java.io.IOException;
  import java.io.ObjectInputStream;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.SortedSet;
  
  /**
   * <p>Stores a "shapshot" of the indexedLagGraph of a lag graph, using indices
   * rather than Strings to refer to factors. Since lag graphs are dynamic, they
   * can't do this directly, as the indices might change from one time to the
   * next. However, for certain uses of lag graphs, the graph itself may be
   * assumed to be static, so this optimization is useful.</p>
   *
   * @author Joseph Ramsey jdramsey@andrew.cmu.edu
   */
  public class IndexedLagGraph implements TetradSerializable {
      static final long serialVersionUID = 23L;
  
      /**
       * The factors in the graph, in the order that they are used.
       *
       * @serial
       */
      private List<String> factors;
  
      /**
       * The graph that this "snapshot" of indexedLagGraph was taken from.
       *
       * @serial
       */
      private IndexedParent[][] parents;
  
      //===============================CONSTRUCTORS=========================//
  
      /**
       * Constructs an indexed lag graph for the getModel state of the given lag
       * graph, including all edges.
       */
      public IndexedLagGraph(LagGraph lagGraph) {
          this(lagGraph, false);
      }
  
      /**
       * Constructs an indexed lag graph for the getModel state of the given lag
       * graph.
       *
       * @param excludeSelfOneBack excludes from the lag graph any edge from a
       *                           gene one time step back to the same gene in the
       *                           getModel time step.
       */
      public IndexedLagGraph(LagGraph lagGraph, boolean excludeSelfOneBack) {
          if (lagGraph == null) {
              throw new NullPointerException("Lag graph must not be null.");
          }
  
          // Construct factor and parent lists in fixed order.
          this.factors = new ArrayList<>(lagGraph.getFactors());
          this.parents = new IndexedParent[this.factors.size()][];
  
          for (int i = 0; i < this.factors.size(); i++) {
              String factor = this.factors.get(i);
              SortedSet<LaggedFactor> factorParents = lagGraph.getParents(factor);
              List<IndexedParent> list = new ArrayList<>();
  
              for (LaggedFactor factorParent1 : factorParents) {
                  int index = this.factors.indexOf(factorParent1.getFactor());
                  int lag = factorParent1.getLag();
  
                  if (excludeSelfOneBack && index == i && lag == 1) {
                      continue;
                  }
  
                  IndexedParent parent = new IndexedParent(index, lag);
                  list.add(parent);
              }
  
              IndexedParent[] _parents = new IndexedParent[list.size()];
  
              for (int i2 = 0; i2 < list.size(); i2++) {
                  _parents[i2] = list.get(i2);
              }
  
              parents[i] = _parents;
          }
      }
  
      /**
       * Generates a simple exemplar of this class to test serialization.
       *
       * @see edu.cmu.TestSerialization
       * @see edu.cmu.tetradapp.util.TetradSerializableUtils
       */
      public static IndexedLagGraph serializableInstance() {
          return new IndexedLagGraph(BasicLagGraph.serializableInstance());
      }
  
      //===============================PUBLIC METHODS======================//
  
      /**
       * Returns the number of factors.
       */
      public int getNumFactors() {
          return this.factors.size();
      }
  
      /**
       * Returns the (string name of) the factor at the given index.
       */
      public String getFactor(int factor) {
          return this.factors.get(factor);
      }
  
      /**
       * Returns the index of the given String factor.
       */
      public int getIndex(String factor) {
          return this.factors.indexOf(factor);
      }
  
      /**
       * Returns the index of the given parent for the given factor.
       */
      public int getIndex(String factor, LaggedFactor parent) {
          int factorIndex = this.factors.indexOf(factor);
          int parentIndex = this.factors.indexOf(parent.getFactor());
          IndexedParent indexedParent =
                  new IndexedParent(parentIndex, parent.getLag());
          return getIndex(factorIndex, indexedParent);
      }
  
      /**
       * Returns the index of the parent of the given factor that is equal to the
       * given IndexedParent, or -1 if the given IndexedParent is not equal to any
       * parent.
       */
      public int getIndex(int factor, IndexedParent parent) {
          for (int i = 0; i < parents[factor].length; i++) {
              if (parent.equals(parents[factor][i])) {
                  return i;
              }
          }
          return -1;
      }
  
      /**
       * Returns the number of parents of the given factor. Each parent is a
       * factor at a given lag.
       */
      public int getNumParents(int factor) {
          return this.parents[factor].length;
      }
  
      /**
       * Returns the given parent as an IndexedParent.
       */
      public IndexedParent getParent(int factor, int parent) {
          return this.parents[factor][parent];
      }
  
      /**
       * Returns a string representation of the graph, indicating for each factor
       * which lagged factors map into it.
       *
       * @return this string.
       */
      public String toString() {
  
          StringBuilder buf = new StringBuilder();
  
          buf.append("\nIndexedLagGraph:\n");
  
          for (int i = 0; i < getNumFactors(); i++) {
              String factor = getFactor(i);
  
              buf.append("\n");
              buf.append(factor);
              buf.append("\t<-- ");
  
              for (int j = 0; j < getNumParents(i); j++) {
                  IndexedParent parent = getParent(i, j);
                  buf.append("\t");
                  buf.append(getFactor(parent.getIndex()));
                  buf.append(":");
                  buf.append(parent.getLag());
              }
          }
  
          buf.append("\n");
  
          return buf.toString();
      }
  
      /**
       * 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 (factors == null) {
              throw new NullPointerException();
          }
  
          if (parents == null) {
              throw new IllegalStateException();
          }
  
      }
  }
  
  
  
  
  
  
  