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.bayes;
  
  import edu.cmu.tetrad.graph.*;
  
  import java.util.LinkedList;
  import java.util.List;
  import java.util.Set;
  
  /**
   * Provides static methods for generating variants of an input graph. For
   * example, the first method generates all 1 step modifications of the graph.
   *
   * @author Frank Wimberly
   */
  public final class ModelGenerator {
  
      /**
       * This method takes an acyclic graph as input and returns a list of graphs
       * each of which is a modification of the original graph with either an edge
       * deleted, added or reversed.  Edges are not added or reversed if a cycle
       * would result.
       */
      public static List<Graph> generate(Graph graph) {
  
          //Make sure the argument contains no cycles.
          if (graph.existsDirectedCycle()) {
              throw new IllegalArgumentException(
                      "Input must not contain cycles.");
          }
  
          List<Graph> graphs = new LinkedList<>();
  
          Set<Edge> allEdges = graph.getEdges();
          List<Node> allNodes = graph.getNodes();
  
          //Add those graphs in which each edge is removed in turn.
          for (Edge allEdge1 : allEdges) {
              Graph toAdd = new EdgeListGraph(graph);
              toAdd.removeEdge(allEdge1);
              graphs.add(toAdd);
          }
  
          //Add those graphs in which each edge is reversed
          for (Edge allEdge : allEdges) {
              Graph toAdd = new EdgeListGraph(graph);
  
              Endpoint e1 = allEdge.getEndpoint1();
              Endpoint e2 = allEdge.getEndpoint2();
  
              Node n1 = allEdge.getNode1();
              Node n2 = allEdge.getNode2();
  
              Edge newEdge = new Edge(n1, n2, e2, e1);
  
              toAdd.removeEdge(allEdge);
              if (!toAdd.existsDirectedPathFromTo(n1, n2)) {
                  toAdd.addEdge(newEdge);
                  graphs.add(toAdd);
              }
  
          }
  
          //For each pair of nodes which are not adjacent, add the two graphs produced by
          //adding a directed edge in each direction provided no cycles are introduced.
          //for(Iterator itn1 = allNodes.iterator(); itn1.hasNext(); ) {
          //    Node node1 = (Node) itn1.next();
  
          for (int i = 0; i < allNodes.size(); i++) {
              Node node1 = allNodes.get(i);
  
              //for(Iterator itn2 = allNodes.iterator(); itn2.hasNext(); ) {
              //    Node node2 = (Node) itn2.next();
              for (int j = i + 1; j < allNodes.size(); j++) {
                  Node node2 = allNodes.get(j);
  
                  //if(node1 == node2) continue;
  
                  //If there is no edge between node1 and node2
                  if (!graph.isParentOf(node1, node2) &&
                          !graph.isParentOf(node2, node1)) {
  
                      Graph toAdd1 = new EdgeListGraph(graph);
                      //Make sure adding this edge won't introduce a cycle.
                      if (!toAdd1.existsDirectedPathFromTo(node1, node2)) {  //
                          Edge newN2N1 = new Edge(node2, node1, Endpoint.TAIL,
                                  Endpoint.ARROW);
                          toAdd1.addEdge(newN2N1);
                          graphs.add(toAdd1);
                      }
  
                      //Now create the graph with the edge added in the other direction
                      Graph toAdd2 = new EdgeListGraph(graph);
                      //Make sure adding this edge won't introduce a cycle.
                      if (!toAdd2.existsDirectedPathFromTo(node2, node1)) {
                          Edge newN1N2 = new Edge(node1, node2, Endpoint.TAIL,
                                  Endpoint.ARROW);
                          toAdd2.addEdge(newN1N2);
                          graphs.add(toAdd2);
                      }
  
                  }
  
              }
          }
  
          return graphs;
      }
  }
  
  
  
  
  
  