///////////////////////////////////////////////////////////////////////////////
// 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, 2022 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.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.test.IndependenceResult;
import edu.cmu.tetrad.search.test.IndependenceTest;
import edu.cmu.tetrad.search.utils.LogUtilsSearch;
import edu.cmu.tetrad.search.utils.SepsetMap;
import edu.cmu.tetrad.util.ChoiceGenerator;
import edu.cmu.tetrad.util.TetradLogger;

import java.io.PrintStream;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.*;

/**
 * <p>Adjusts FAS (see) for the deterministic case by refusing to removed edges
 * based on conditional independence tests that are judged to be deterministic.
 * That is, if X _||_ Y | Z, but Z determines X or Y, then the edge X---Y is
 * not removed.</p>
 *
 * <p>This class is configured to respect knowledge of forbidden and required
 * edges, including knowledge of temporal tiers.</p>
 *
 * @author peterspirtes
 * @author josephramsey.
 * @see Fas
 * @see Knowledge
 */
public class Fasd implements IFas {

    /**
     * The search graph. It is assumed going in that all of the true adjacencies of x are in this graph for every node
     * x. It is hoped (i.e. true in the large sample limit) that true adjacencies are never removed.
     */
    private Graph graph;

    /**
     * The independence test. This should be appropriate to the types
     */
    private final IndependenceTest test;

    /**
     * Specification of which edges are forbidden or required.
     */
    private Knowledge knowledge = new Knowledge();

    /**
     * The maximum number of variables conditioned on in any conditional independence test. If the depth is -1, it will
     * be taken to be the maximum value, which is 1000. Otherwise, it should be set to a non-negative integer.
     */
    private int depth = 1000;

    /**
     * The number of independence tests.
     */
    private int numIndependenceTests;


    /**
     * The logger, by default the empty logger.
     */
    private final TetradLogger logger = TetradLogger.getInstance();

    /**
     * The sepsets found during the search.
     */
    private SepsetMap sepset = new SepsetMap();

    /**
     * The depth 0 graph, specified initially.
     */
    private Graph externalGraph;

    private final NumberFormat nf = new DecimalFormat("0.00E0");

    /**
     * True iff verbose output should be printed.
     */
    private boolean verbose;

    private PrintStream out = System.out;

    //==========================CONSTRUCTORS=============================//

    /**
     * Constructs a new FastAdjacencySearch.
     *
     * @param graph An initial graph of edges that will be removed.
     * @param test  A test to use as a conditional independence oracle.
     */
    public Fasd(Graph graph, IndependenceTest test) {
        this.graph = graph;
        this.test = test;
    }

    /**
     * Constructs a new FastAdjacencySearch.
     *
     * @param test A test to use as a conditional independence oracle.
     */
    public Fasd(IndependenceTest test) {
        this.graph = new EdgeListGraph(test.getVariables());
        this.test = test;
    }

    /**
     * @throws UnsupportedOperationException This contructor is not implemented.
     */
    public Graph search(List<Node> nodes) {
        throw new UnsupportedOperationException("Constructor not implemented.");
    }

    /**
     * Discovers all adjacencies in data.  The procedure is to remove edges in the graph which connect pairs of
     * variables which are independent conditional on some other set of variables in the graph (the "sepset"). These are
     * removed in tiers.  First, edges which are independent conditional on zero other variables are removed, then edges
     * which are independent conditional on one other variable are removed, then two, then three, and so on, until no
     * more edges can be removed from the graph.  The edges which remain in the graph after this procedure are the
     * adjacencies in the data.
     *
     * @return a graph which indicates which variables are independent conditional on which other variables
     */
    public Graph search() {
        this.logger.log("info", "Starting Fast Adjacency Search.");
        this.graph.removeEdges(this.graph.getEdges());

        this.sepset = new SepsetMap();

        int _depth = this.depth;

        if (_depth == -1) {
            _depth = 1000;
        }

        Map<Node, Set<Node>> adjacencies = new HashMap<>();
        List<Node> nodes = this.graph.getNodes();

        for (Node node : nodes) {
            adjacencies.put(node, new TreeSet<>());
        }

        for (int d = 0; d <= _depth; d++) {
            boolean more;

            if (d == 0) {
                more = searchAtDepth0(nodes, this.test, adjacencies);
            } else {
                more = searchAtDepth(nodes, this.test, adjacencies, d);
            }

            if (!more) {
                break;
            }
        }

        for (int i = 0; i < nodes.size(); i++) {
            for (int j = i + 1; j < nodes.size(); j++) {
                Node x = nodes.get(i);
                Node y = nodes.get(j);

                if (adjacencies.get(x).contains(y)) {
                    this.graph.addUndirectedEdge(x, y);
                }
            }
        }

        this.logger.log("info", "Finishing Fast Adjacency Search.");

        return this.graph;
    }


    /**
     * Sets the maximum number of variables conditoined on in any test.
     *
     * @param depth This maximum.
     */
    public void setDepth(int depth) {
        if (depth < -1) {
            throw new IllegalArgumentException(
                    "Depth must be -1 (unlimited) or >= 0.");
        }

        this.depth = depth;
    }

    /**
     * Sets the knowledge to be used in the search.
     *
     * @param knowledge This knowledge.
     */
    public void setKnowledge(Knowledge knowledge) {
        if (knowledge == null) {
            throw new NullPointerException("Cannot set knowledge to null");
        }
        this.knowledge = knowledge;
    }

    /**
     * Returns the nubmer of conditional independence tests done in the course of search.
     *
     * @return This number.
     */
    public int getNumIndependenceTests() {
        return this.numIndependenceTests;
    }

    /**
     * Returns the map of node pairs to sepsets from the search.
     *
     * @return This map.
     */
    public SepsetMap getSepsets() {
        return this.sepset;
    }

    /**
     * Sets the external graph. Adjacencies not in this external graph will not be judged
     * adjacent in the search result.
     *
     * @param externalGraph This graph.
     */
    public void setExternalGraph(Graph externalGraph) {
        this.externalGraph = externalGraph;
    }

    public boolean isVerbose() {
        return this.verbose;
    }

    /**
     * Sets whether verbose output will be printed.
     *
     * @param verbose True if so.
     */
    public void setVerbose(boolean verbose) {
        this.verbose = verbose;
    }

    /**
     * Returns the elapsed time.
     *
     * @return This time.
     */
    @Override
    public long getElapsedTime() {
        return 0;
    }

    /**
     * Returns the nodes beign searched over.
     *
     * @return This list.
     */
    @Override
    public List<Node> getNodes() {
        return this.test.getVariables();
    }

    /**
     * Returns an empty list. Not used.
     *
     * @param node Whichever node.
     * @return An empty list.
     */
    @Override
    public List<Triple> getAmbiguousTriples(Node node) {
        return new ArrayList<>();
    }

    /**
     * Sets the output to send prints to.
     *
     * @param out This print stream.
     */
    @Override
    public void setOut(PrintStream out) {
        this.out = out;
    }

    private boolean searchAtDepth0(List<Node> nodes, IndependenceTest test, Map<Node, Set<Node>> adjacencies) {
        List<Node> empty = Collections.emptyList();
        for (int i = 0; i < nodes.size(); i++) {
            if (this.verbose) {
                if ((i + 1) % 100 == 0) this.out.println("Node # " + (i + 1));
            }

            Node x = nodes.get(i);

            for (int j = i + 1; j < nodes.size(); j++) {

                Node y = nodes.get(j);

                if (this.externalGraph != null) {
                    Node x2 = this.externalGraph.getNode(x.getName());
                    Node y2 = this.externalGraph.getNode(y.getName());

                    if (!this.externalGraph.isAdjacentTo(x2, y2)) {
                        continue;
                    }
                }


                IndependenceResult result;

                try {
                    this.numIndependenceTests++;
                    result = test.checkIndependence(x, y, empty);
                } catch (Exception e) {
                    e.printStackTrace();
                    result = new IndependenceResult(new IndependenceFact(x, y, empty), false, Double.NaN);
                }

                boolean noEdgeRequired =
                        this.knowledge.noEdgeRequired(x.getName(), y.getName());


                if (result.isIndependent() && noEdgeRequired) {
                    getSepsets().set(x, y, empty);

                    TetradLogger.getInstance().log("independencies", LogUtilsSearch.independenceFact(x, y, empty) + " p = " +
                            this.nf.format(result.getPValue()));

                    if (this.verbose) {
                        this.out.println(LogUtilsSearch.independenceFact(x, y, empty) + " p = " +
                                this.nf.format(result.getPValue()));
                    }

                } else if (!forbiddenEdge(x, y)) {
                    adjacencies.get(x).add(y);
                    adjacencies.get(y).add(x);

                    TetradLogger.getInstance().log("dependencies", LogUtilsSearch.independenceFact(x, y, empty) + " p = " +
                            this.nf.format(result.getPValue()));

                }
            }
        }

        return

                freeDegree(nodes, adjacencies)

                        > 0;
    }

    private int freeDegree(List<Node> nodes, Map<Node, Set<Node>> adjacencies) {
        int max = 0;

        for (Node x : nodes) {
            Set<Node> opposites = adjacencies.get(x);

            for (Node y : opposites) {
                Set<Node> adjx = new HashSet<>(opposites);
                adjx.remove(y);

                if (adjx.size() > max) {
                    max = adjx.size();
                }
            }
        }

        return max;
    }

    private boolean forbiddenEdge(Node x, Node y) {
        String name1 = x.getName();
        String name2 = y.getName();

        if (this.knowledge.isForbidden(name1, name2) &&
                this.knowledge.isForbidden(name2, name1)) {
            this.logger.log("edgeRemoved", "Removed " + Edges.undirectedEdge(x, y) + " because it was " +
                    "forbidden by background knowledge.");

            return true;
        }

        return false;
    }

    private boolean searchAtDepth(List<Node> nodes, IndependenceTest test, Map<Node, Set<Node>> adjacencies, int depth) {
        int count = 0;

        List<IndependenceFact> facts = new ArrayList<>();

        for (Node x : nodes) {
            if (this.verbose) {
                if (++count % 100 == 0) this.out.println("count " + count + " of " + nodes.size());
            }

            List<Node> adjx = new ArrayList<>(adjacencies.get(x));

            EDGE:
            for (Node y : adjx) {
                List<Node> _adjx = new ArrayList<>(adjacencies.get(x));
                _adjx.remove(y);
                List<Node> ppx = possibleParents(x, _adjx, this.knowledge);

                if (ppx.size() >= depth) {
                    ChoiceGenerator cg = new ChoiceGenerator(ppx.size(), depth);
                    int[] choice;

                    while ((choice = cg.next()) != null) {
                        List<Node> condSet = GraphUtils.asList(choice, ppx);

                        IndependenceFact fact = new IndependenceFact(x, y, condSet);
                        if (facts.contains(fact)) continue;
                        facts.add(fact);

                        boolean independent;

                        try {
                            this.numIndependenceTests++;
                            independent = test.checkIndependence(x, y, condSet).isIndependent();

                        } catch (Exception e) {
                            independent = false;
                        }

                        boolean noEdgeRequired =
                                this.knowledge.noEdgeRequired(x.getName(), y.getName());

                        if (independent && noEdgeRequired) {
                            adjacencies.get(x).remove(y);
                            adjacencies.get(y).remove(x);
                            getSepsets().set(x, y, condSet);

                            continue EDGE;
                        }
                    }
                }
            }
        }

        return freeDegree(nodes, adjacencies) > depth;
    }

    private List<Node> possibleParents(Node x, List<Node> adjx,
                                       Knowledge knowledge) {
        List<Node> possibleParents = new LinkedList<>();
        String _x = x.getName();

        for (Node z : adjx) {
            String _z = z.getName();

            if (possibleParentOf(_z, _x, knowledge)) {
                possibleParents.add(z);
            }
        }

        return possibleParents;
    }

    private boolean possibleParentOf(String z, String x, Knowledge knowledge) {
        return !knowledge.isForbidden(z, x) && !knowledge.isRequired(x, z);
    }
}


