///////////////////////////////////////////////////////////////////////////////
// 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());
    }
}