gt:         for (Node node : latents) {
context: ///////////////////////////////////////////////////////////////////////////////
  // 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.test;
  
  import edu.cmu.tetrad.data.*;
  import edu.cmu.tetrad.graph.*;
  import edu.cmu.tetrad.search.*;
  import edu.cmu.tetrad.sem.SemIm;
  import edu.cmu.tetrad.sem.SemPm;
  import edu.cmu.tetrad.search.Mimbuild2;
  import edu.cmu.tetrad.util.RandomUtil;
  import org.junit.Test;
  
  import java.util.ArrayList;
  import java.util.List;
  
  import static org.junit.Assert.assertEquals;
  
  /**
   * @author Joseph Ramsey
   */
  public class TestPurify {
  
      @Test
      public void test1() {
          RandomUtil.getInstance().setSeed(48290483L);
  
          SemGraph graph = new SemGraph();
  
          Node l1 = new GraphNode("L1");
          l1.setNodeType(NodeType.LATENT);
  
          Node l2 = new GraphNode("L2");
          l2.setNodeType(NodeType.LATENT);
  
          Node l3 = new GraphNode("L3");
          l3.setNodeType(NodeType.LATENT);
  
          Node x1 = new GraphNode("X1");
          Node x2 = new GraphNode("X2");
          Node x3 = new GraphNode("X3");
          Node x4 = new GraphNode("X4");
          Node x4b = new GraphNode("X4b");
  
          Node x5 = new GraphNode("X5");
          Node x6 = new GraphNode("X6");
          Node x7 = new GraphNode("X7");
          Node x8 = new GraphNode("X8");
          Node x8b = new GraphNode("X8b");
  
          Node x9 = new GraphNode("X9");
          Node x10 = new GraphNode("X10");
          Node x11 = new GraphNode("X11");
          Node x12 = new GraphNode("X12");
          Node x12b = new GraphNode("X12b");
  
          graph.addNode(l1);
          graph.addNode(l2);
          graph.addNode(l3);
  
          graph.addNode(x1);
          graph.addNode(x2);
          graph.addNode(x3);
          graph.addNode(x4);
          graph.addNode(x4b);
  
          graph.addNode(x5);
          graph.addNode(x6);
          graph.addNode(x7);
          graph.addNode(x8);
          graph.addNode(x8b);
  
          graph.addNode(x9);
          graph.addNode(x10);
          graph.addNode(x11);
          graph.addNode(x12);
          graph.addNode(x12b);
  
          graph.addDirectedEdge(l1, x1);
          graph.addDirectedEdge(l1, x2);
          graph.addDirectedEdge(l1, x3);
          graph.addDirectedEdge(l1, x4);
          graph.addDirectedEdge(l1, x4b);
          graph.addDirectedEdge(l1, x5);
  
          graph.addDirectedEdge(l2, x5);
          graph.addDirectedEdge(l2, x6);
          graph.addDirectedEdge(l2, x7);
          graph.addDirectedEdge(l2, x8);
          graph.addDirectedEdge(l2, x8b);
  
          graph.addDirectedEdge(l3, x9);
          graph.addDirectedEdge(l3, x10);
          graph.addDirectedEdge(l3, x11);
          graph.addDirectedEdge(l3, x12);
          graph.addDirectedEdge(l3, x12b);
  
          graph.addDirectedEdge(x1, x4);
  
          SemPm pm = new SemPm(graph);
          SemIm im = new SemIm(pm);
          DataSet data = im.simulateData(1000, false);
  
          List<List<Node>> partition = new ArrayList<>();
  
          List<Node> cluster1 = new ArrayList<>();
          cluster1.add(x1);
          cluster1.add(x2);
          cluster1.add(x3);
          cluster1.add(x4);
          cluster1.add(x4b);
          cluster1.add(x5);
  
          List<Node> cluster2 = new ArrayList<>();
          cluster2.add(x5);
          cluster2.add(x6);
          cluster2.add(x7);
          cluster2.add(x8);
          cluster2.add(x8b);
  
          List<Node> cluster3 = new ArrayList<>();
          cluster3.add(x9);
          cluster3.add(x10);
          cluster3.add(x11);
          cluster3.add(x12);
          cluster3.add(x12b);
  
          partition.add(cluster1);
          partition.add(cluster2);
          partition.add(cluster3);
  
          TetradTest test = new ContinuousTetradTest(data, TestType.TETRAD_WISHART, 0.05);
          IPurify purify = new PurifyTetradBased2(test);
          purify.setTrueGraph(graph);
  
          List<List<Node>> partition2 = purify.purify(partition);
  
          assertEquals(3, partition2.get(0).size());
          assertEquals(2, partition2.get(1).size());
          assertEquals(5, partition2.get(2).size());
      }
  
      @Test
      public void test1b() {
          RandomUtil.getInstance().setSeed(48290483L);
  
          SemGraph graph = new SemGraph();
  
          Node l1 = new GraphNode("L1");
          l1.setNodeType(NodeType.LATENT);
  
          Node l2 = new GraphNode("L2");
          l2.setNodeType(NodeType.LATENT);
  
          Node x1 = new GraphNode("X1");
          Node x2 = new GraphNode("X2");
          Node x3 = new GraphNode("X3");
          Node x4 = new GraphNode("X4");
          Node x5 = new GraphNode("X5");
          Node x6 = new GraphNode("X6");
  
          Node x7 = new GraphNode("X7");
          Node x8 = new GraphNode("X8");
          Node x9 = new GraphNode("X9");
          Node x10 = new GraphNode("X10");
          Node x11 = new GraphNode("X11");
          Node x12 = new GraphNode("X12");
  
          graph.addNode(l1);
          graph.addNode(l2);
  
          graph.addNode(x1);
          graph.addNode(x2);
          graph.addNode(x3);
          graph.addNode(x4);
          graph.addNode(x5);
          graph.addNode(x6);
  
          graph.addNode(x7);
          graph.addNode(x8);
          graph.addNode(x9);
          graph.addNode(x10);
          graph.addNode(x11);
          graph.addNode(x12);
  
          graph.addDirectedEdge(l1, x1);
          graph.addDirectedEdge(l1, x2);
          graph.addDirectedEdge(l1, x3);
          graph.addDirectedEdge(l1, x4);
          graph.addDirectedEdge(l1, x5);
          graph.addDirectedEdge(l1, x5);
          graph.addDirectedEdge(l1, x6);
  
          graph.addDirectedEdge(l2, x6);
          graph.addDirectedEdge(l2, x7);
          graph.addDirectedEdge(l2, x8);
          graph.addDirectedEdge(l2, x9);
          graph.addDirectedEdge(l2, x10);
          graph.addDirectedEdge(l2, x11);
          graph.addDirectedEdge(l2, x12);
  
          graph.addDirectedEdge(x3, x4);
          graph.addDirectedEdge(x9, x10);
  
          SemPm pm = new SemPm(graph);
          SemIm im = new SemIm(pm);
          DataSet data = im.simulateData(3000, false);
  
          List<List<Node>> partition = new ArrayList<>();
  
          List<Node> cluster1 = new ArrayList<>();
          cluster1.add(x1);
          cluster1.add(x2);
          cluster1.add(x3);
          cluster1.add(x4);
          cluster1.add(x5);
  
          List<Node> cluster2 = new ArrayList<>();
          cluster2.add(x7);
          cluster2.add(x8);
          cluster2.add(x9);
          cluster2.add(x10);
          cluster2.add(x11);
          cluster2.add(x12);
  
          partition.add(cluster1);
          partition.add(cluster2);
  
          TetradTest test = new ContinuousTetradTest(data, TestType.TETRAD_WISHART, 0.0001);
          IPurify purify = new PurifyTetradBased2(test);
          purify.setTrueGraph(graph);
  
          List<List<Node>> clustering = purify.purify(partition);
  
          assertEquals(4, clustering.get(0).size());
          assertEquals(5, clustering.get(1).size());
  
      }
  
      @Test
      public void test2() {
          RandomUtil.getInstance().setSeed(48290483L);
  
          Graph graph = new EdgeListGraph(DataGraphUtils.randomSingleFactorModel(3, 3, 5, 0, 0, 0));
  
          SemPm pm = new SemPm(graph);
          SemIm im = new SemIm(pm);
          DataSet data = im.simulateData(1000, false);
  
          List<Node> latents = new ArrayList<>();
  
          for (Node node : graph.getNodes()) {
              if (node.getNodeType() == NodeType.LATENT) latents.add(node);
          }
  
          Graph structuralGraph = graph.subgraph(latents);
  
          List<List<Node>> clustering = new ArrayList<>();
  
  