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.search;
  
  import edu.cmu.tetrad.data.Clusters;
  import edu.cmu.tetrad.graph.*;
  
  import java.rmi.MarshalledObject;
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.List;
  import java.util.Set;
  
  /**
   * Holds some utility methods for Purify, Build Clusters, and Mimbuild.
   *
   * @author Joseph Ramsey
   */
  public final class MimUtils {
  
      public static Clusters convertToClusters(Graph clusterGraph) {
          List<Node> measuredVariables = new ArrayList<>();
  
          for (Node node : clusterGraph.getNodes()) {
              if (node.getNodeType() != NodeType.LATENT) {
                  measuredVariables.add(node);
              }
          }
  
          return convertToClusters(clusterGraph, measuredVariables);
      }
  
      public static List<List<Node>> convertToClusters2(Graph clusterGraph) {
          Clusters clusters = convertToClusters(clusterGraph);
  
          List<List<Node>> _clusters = new ArrayList<>();
  
          for (int i = 0; i < clusters.getNumClusters(); i++) {
              List<Node> cluster = new ArrayList<>();
              List<String> cluster1 = clusters.getCluster(i);
  
              for (int j = 0; j < cluster1.size(); j++) {
                  cluster.add(clusterGraph.getNode(cluster1.get(j)));
              }
  
              _clusters.add(cluster);
          }
  
          return _clusters;
      }
  
      /**
       * Converts a disconnected multiple indicator model into a set of clusters. Assumes the given graph contains a
       * number of latents Li, i = 0,...,n-1, for each of which there is a list of indicators Wj, j = 0,...,m_i-1, such
       * that , Li-->Wj. Returns a Clusters object mapping i to Wj. The name for cluster i is set to Li.
       */
      public static Clusters convertToClusters(Graph clusterGraph, List<Node> measuredVariables) {
          List<String> latents = new ArrayList<>();
          Clusters clusters = new Clusters();
          clusterGraph = GraphUtils.replaceNodes(clusterGraph, measuredVariables);
  
          for (Node node : clusterGraph.getNodes()) {
              if (!measuredVariables.contains(node)) {
                  latents.add(node.getName());
              }
          }
  
          Collections.sort(latents);
  
          for (int i = 0; i < latents.size(); i++) {
              String name = latents.get(i);
              clusters.setClusterName(i, name);
              Node latent = clusterGraph.getNode(name);
              List<Node> measured =
                      clusterGraph.getNodesOutTo(latent, Endpoint.ARROW);
  
              for (Node _node : measured) {
                  if (measuredVariables.contains(_node)) {
                      clusters.addToCluster(i, _node.getName());
                  }
              }
          }
  
          return clusters;
      }
  
      /**
       * @throws Exception if the graph cannot be cloned properly due to a serialization problem.
       */
      public static Graph extractStructureGraph(Graph clusterGraph)
              throws Exception {
          Set<Edge> edges = clusterGraph.getEdges();
          Graph structureGraph = new EdgeListGraph();
  
          for (Edge edge : edges) {
              Node node1 = edge.getNode1();
              Node node2 = edge.getNode2();
  
              if (node1.getNodeType() == NodeType.LATENT) {
                  if (!structureGraph.containsNode(node1)) {
                      structureGraph.addNode(node1);
                  }
              }
  
              if (node2.getNodeType() == NodeType.LATENT) {
                  if (!structureGraph.containsNode(node2)) {
                      structureGraph.addNode(node2);
                  }
              }
  
              if (node1.getNodeType() == NodeType.LATENT &&
                      node2.getNodeType() == NodeType.LATENT) {
                  structureGraph.addEdge(edge);
              }
          }
  
          Graph clone = (Graph) new MarshalledObject(structureGraph).get();
          GraphUtils.circleLayout(clone, 200, 200, 150);
          GraphUtils.fruchtermanReingoldLayout(clone);
          return clone;
      }
  }
  
  
  
  
  
  