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.IKnowledge;
  import edu.cmu.tetrad.data.Knowledge2;
  import edu.cmu.tetrad.graph.*;
  import edu.cmu.tetrad.util.ChoiceGenerator;
  import edu.cmu.tetrad.util.TetradLogger;
  
  import java.util.HashSet;
  import java.util.List;
  import java.util.Set;
  
  /**
   * Implements a convervative version of PC, in which the Markov condition is assumed but faithfulness is tested
   * locally.
   *
   * @author Joseph Ramsey (this version).
   */
  public final class TimeSeriesLagSearch implements GraphSearch {
  
      /**
       * The independence test used for the PC search.
       */
      private IndependenceTest independenceTest;
  
      /**
       * Forbidden and required edges for the search.
       */
      private IKnowledge knowledge = new Knowledge2();
  
      /**
       * The maximum number of nodes conditioned on in the search.
       */
      private int depth = 0;
  
      /**
       * The graph that's constructed during the search.
       */
      private Graph graph;
  
      /**
       * Elapsed time of last search.
       */
      private long elapsedTime;
  
      /**
       * The list of all unshielded triples.
       */
      private Set<Triple> allTriples;
  
      /**
       * Set of unshielded colliders from the triple orientation step.
       */
      private Set<Triple> colliderTriples;
  
      /**
       * Set of unshielded noncolliders from the triple orientation step.
       */
      private Set<Triple> noncolliderTriples;
  
      /**
       * Set of ambiguous unshielded triples.
       */
      private Set<Triple> ambiguousTriples;
  
      /**
       * True if cycles are to be aggressively prevented. May be expensive for large graphs (but also useful for large
       * graphs).
       */
      private boolean aggressivelyPreventCycles = false;
  
      //=============================CONSTRUCTORS==========================//
  
      /**
       * Constructs a CPC algorithm that uses the given independence test as oracle. This does not make a copy of the
       * independence test, for fear of duplicating the data set!
       */
      public TimeSeriesLagSearch(IndependenceTest independenceTest) {
          if (independenceTest == null) {
              throw new NullPointerException();
          }
  
          this.independenceTest = independenceTest;
      }
  
      //==============================PUBLIC METHODS========================//
  
      /**
       * @return true just in case edges will not be added if they would create cycles.
       */
      public boolean isAggressivelyPreventCycles() {
          return this.aggressivelyPreventCycles;
      }
  
      /**
       * Sets to true just in case edges will not be added if they would create cycles.
       */
      public void setAggressivelyPreventCycles(boolean aggressivelyPreventCycles) {
          this.aggressivelyPreventCycles = aggressivelyPreventCycles;
      }
  
  //    /**
  //     * Sets the maximum number of variables conditioned on in any conditional
  //     * independence test. If set to -1, the value of 1000 will be used. May
  //     * not be set to Integer.MAX_VALUE, due to a Java bug on multi-core systems.
  //     */
  //    public final void setMaxIndegree(int depth) {
  //        if (depth < -1) {
  //            throw new IllegalArgumentException("Depth must be -1 or >= 0: "  + depth);
  //        }
  //
  //        if (depth == Integer.MAX_VALUE) {
  //            throw new IllegalArgumentException("Depth must not be Integer.MAX_VALUE, " +
  //                    "due to a known bug.");
  //        }
  //
  //        this.depth = depth;
  //    }
  
      /**
       * @return the elapsed time of search in milliseconds, after <code>search()</code> has been run.
       */
      public final long getElapsedTime() {
          return this.elapsedTime;
      }
  
      /**
       * @return the knowledge specification used in the search. Non-null.
       */
      public IKnowledge getKnowledge() {
          return knowledge;
      }
  
      /**
       * Sets the knowledge specification used in the search. Non-null.
       */
      public void setKnowledge(IKnowledge knowledge) {
          this.knowledge = knowledge;
      }
  
      /**
       * @return the independence test used in the search, set in the constructor. This is not returning a copy, for fear
       * of duplicating the data set!
       */
      public IndependenceTest getIndependenceTest() {
          return independenceTest;
      }
  
      /**
       * @return the depth of the search--that is, the maximum number of variables conditioned on in any conditional
       * independence test.
       */
      public int getDepth() {
          return depth;
      }
  
      /**
       * @return the set of ambiguous triples found during the most recent run of the algorithm. Non-null after a call to
       * <code>search()</code>.
       */
      public Set<Triple> getAmbiguousTriples() {
          return new HashSet<>(ambiguousTriples);
      }
  
      /**
       * @return the set of collider triples found during the most recent run of the algorithm. Non-null after a call to
       * <code>search()</code>.
       */
      public Set<Triple> getColliderTriples() {
          return new HashSet<>(colliderTriples);
      }
  
      /**
       * @return the set of noncollider triples found during the most recent run of the algorithm. Non-null after a call
       * to <code>search()</code>.
       */
      public Set<Triple> getNoncolliderTriples() {
          return new HashSet<>(noncolliderTriples);
      }
  
      /**
       * @return the set of all triples found during the most recent run of the algorithm. Non-null after a call to
       * <code>search()</code>.
       */
      public Set<Triple> getAllTriples() {
          return new HashSet<>(allTriples);
      }
  
      /**
       * Runs PC starting with a fully connected graph over all of the variables in the domain of the independence test.
       * See PC for caveats. The number of possible cycles and bidirected edges is far less with CPC than with PC.
       */
      public final Graph search() {
          return search(independenceTest.getVariables());
      }
  
      /**
       * Runs PC on just the given variable, all of which must be in the domain of the independence test. See PC for
       * caveats. The number of possible cycles and bidirected edges is far less with CPC than with PC.
       */
      public Graph search(List<Node> nodes) {
          TetradLogger.getInstance().log("info", "Starting TimeSeriesLagSearch.");
          TetradLogger.getInstance().log("info", "Independence test = " + independenceTest + ".");
          long startTime = System.currentTimeMillis();
          this.allTriples = new HashSet<>();
          this.ambiguousTriples = new HashSet<>();
          this.colliderTriples = new HashSet<>();
          this.noncolliderTriples = new HashSet<>();
  
          if (getIndependenceTest() == null) {
              throw new NullPointerException();
          }
  
          List<Node> allNodes = getIndependenceTest().getVariables();
          if (!allNodes.containsAll(nodes)) {
              throw new IllegalArgumentException("All of the given nodes must " +
                      "be in the domain of the independence test provided.");
          }
  
          graph = new EdgeListGraph(nodes);
          graph.fullyConnect(Endpoint.TAIL);
  
          Fas fas = new Fas(graph, getIndependenceTest());
          fas.setKnowledge(getKnowledge());
          fas.setDepth(0);
  
          // Note that we are ignoring the sepset map returned by this method
          // on purpose; it is not used in this search.
          fas.search();
  
  //        SearchGraphUtils.pcOrientbk(knowledge, graph, nodes);
          orientUnshieldedTriples(knowledge, getIndependenceTest(), 3);
  //        MeekRules meekRules = new MeekRules();
  //
  //        meekRules.setAggressivelyPreventCycles(this.aggressivelyPreventCycles);
  //        meekRules.setKnowledge(knowledge);
  //
  //        meekRules.orientImplied(graph);
  
          TetradLogger.getInstance().log("graph", "\nReturning this graph: " + graph);
  
          long endTime = System.currentTimeMillis();
          this.elapsedTime = endTime - startTime;
  
          TetradLogger.getInstance().log("info", "Elapsed time = " + (elapsedTime) / 1000. + " s");
          TetradLogger.getInstance().log("info", "Finishing CPC algorithm.");
  
          logTriples();
  
          TetradLogger.getInstance().flush();
  //        SearchGraphUtils.verifySepsetIntegrity(sepsetMap, graph);
          return graph;
      }
  
      /**
       * Orients the given graph using CPC orientation with the conditional independence test provided in the
       * constructor.
       */
      public final Graph orientationForGraph(Dag trueGraph) {
          Graph graph = new EdgeListGraph(independenceTest.getVariables());
  
          for (Edge edge : trueGraph.getEdges()) {
              Node nodeA = edge.getNode1();
              Node nodeB = edge.getNode2();
  
              Node _nodeA = independenceTest.getVariable(nodeA.getName());
              Node _nodeB = independenceTest.getVariable(nodeB.getName());
  
              graph.addUndirectedEdge(_nodeA, _nodeB);
          }
  
          SearchGraphUtils.pcOrientbk(knowledge, graph, graph.getNodes());
          orientUnshieldedTriples(knowledge, getIndependenceTest(), depth);
          MeekRules meekRules = new MeekRules();
          meekRules.setAggressivelyPreventCycles(this.aggressivelyPreventCycles);
          meekRules.setKnowledge(knowledge);
          meekRules.orientImplied(graph);
  
          return graph;
      }
  
      //==========================PRIVATE METHODS===========================//
  
      private void logTriples() {
          TetradLogger.getInstance().log("info", "\nCollider triples judged from sepsets:");
  
          for (Triple triple : colliderTriples) {
              TetradLogger.getInstance().log("info", "Collider: " + triple);
          }
  
          TetradLogger.getInstance().log("info", "\nNoncollider triples judged from sepsets:");
  
          for (Triple triple : noncolliderTriples) {
              TetradLogger.getInstance().log("info", "Noncollider: " + triple);
          }
  
          TetradLogger.getInstance().log("info", "\nAmbiguous triples judged from sepsets (i.e. list of triples for which " +
                  "\nthere is ambiguous data about whether they are colliders or not):");
  
          for (Triple triple : getAmbiguousTriples()) {
              TetradLogger.getInstance().log("info", "Ambiguous: " + triple);
          }
      }
  
      private void orientUnshieldedTriples(IKnowledge knowledge,
                                           IndependenceTest test, int depth) {
          TetradLogger.getInstance().log("info", "Starting Collider Orientation:");
  
  //        System.out.println("orientUnshieldedTriples 1");
  
          colliderTriples = new HashSet<>();
          noncolliderTriples = new HashSet<>();
          ambiguousTriples = new HashSet<>();
  
          for (Node y : graph.getNodes()) {
  //            System.out.println("orientUnshieldedTriples 2");
  
              List<Node> adjacentNodes = graph.getAdjacentNodes(y);
  
              if (adjacentNodes.size() < 2) {
                  continue;
              }
  
              ChoiceGenerator cg = new ChoiceGenerator(adjacentNodes.size(), 2);
              int[] combination;
  
              while ((combination = cg.next()) != null) {
  //                System.out.println("orientUnshieldedTriples 3");
  
                  Node x = adjacentNodes.get(combination[0]);
                  Node z = adjacentNodes.get(combination[1]);
  
                  if (this.graph.isAdjacentTo(x, z)) {
                      continue;
                  }
  
                  getAllTriples().add(new Triple(x, y, z));
  
  //                System.out.println("orientUnshieldedTriples 4");
  
                  SearchGraphUtils.CpcTripleType type = SearchGraphUtils.getCpcTripleType(x, y, z, test, depth, graph, false);
  
  //                System.out.println("orientUnshieldedTriples 5");
  
                  if (type == SearchGraphUtils.CpcTripleType.COLLIDER) {
  //                    System.out.println("orientUnshieldedTriples 6");
  
                      if (colliderAllowed(x, y, z, knowledge)) {
                          graph.setEndpoint(x, y, Endpoint.ARROW);
                          graph.setEndpoint(z, y, Endpoint.ARROW);
  
                          TetradLogger.getInstance().log("colliderOrientations", SearchLogUtils.colliderOrientedMsg(x, y, z));
                      }
  
                      colliderTriples.add(new Triple(x, y, z));
                  } else if (type == SearchGraphUtils.CpcTripleType.AMBIGUOUS) {
  //                    System.out.println("orientUnshieldedTriples 7");
  
                      Triple triple = new Triple(x, y, z);
                      ambiguousTriples.add(triple);
                      graph.addAmbiguousTriple(triple.getX(), triple.getY(), triple.getZ());
                  } else {
  //                    System.out.println("orientUnshieldedTriples 8");
  
                      noncolliderTriples.add(new Triple(x, y, z));
                  }
              }
          }
  
          TetradLogger.getInstance().log("info", "Finishing Collider Orientation.");
      }
  
      private boolean colliderAllowed(Node x, Node y, Node z, IKnowledge knowledge) {
          return isArrowpointAllowed1(x, y, knowledge) &&
                  isArrowpointAllowed1(z, y, knowledge);
      }
  
      private static boolean isArrowpointAllowed1(Node from, Node to,
                                                  IKnowledge knowledge) {
          return knowledge == null || !knowledge.isRequired(to.toString(), from.toString()) &&
                  !knowledge.isForbidden(from.toString(), to.toString());
      }
  }
  
  
  