///////////////////////////////////////////////////////////////////////////////
// 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.study.gene.tetrad.gene.history;

import edu.cmu.tetrad.util.TetradSerializable;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.SortedSet;

/**
 * <p>Stores a "shapshot" of the indexedConnectivity of a lag graph, using
 * indices rather than Strings to refer to factors. Since lag graphs are
 * dynamic, they can't do this directly, as the indices might change from one
 * time to the next. However, for certain uses of lag graphs, the graph itself
 * may be assumed to be static, so this optimization is useful.
 *
 * @author josephramsey
 */
public class IndexedConnectivity implements TetradSerializable {
    static final long serialVersionUID = 23L;

    /**
     * The factors in the graph, in the order that they are used.
     *
     * @serial
     */
    private final List<String> factors;

    /**
     * The graph that this "snapshot" of indexedConnectivity was taken from.
     *
     * @serial
     */
    private final IndexedParent[][] parents;

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

    /**
     * Constructs an indexed connectivity for the getModel state of the given lag
     * graph, including all edges.
     */
    public IndexedConnectivity(LagGraph lagGraph) {
        this(lagGraph, false);
    }

    /**
     * Constructs an indexed connectivity for the getModel state of the given lag
     * graph.
     *
     * @param excludeSelfOneBack excludes from the connectivity any edge from a
     *                           gene one time step back to the same gene in the
     *                           getModel time step.
     */
    public IndexedConnectivity(LagGraph lagGraph, boolean excludeSelfOneBack) {
        if (lagGraph == null) {
            throw new NullPointerException("Lag graph must not be null.");
        }

        // Construct factor and parent lists in fixed order.
        this.factors = new ArrayList<>(lagGraph.getFactors());
        this.parents = new IndexedParent[this.factors.size()][];

        for (int i = 0; i < this.factors.size(); i++) {
            String factor = this.factors.get(i);
            SortedSet<LaggedFactor> factorParents = lagGraph.getParents(factor);
            List<IndexedParent> list = new ArrayList<>();

            for (LaggedFactor factorParent1 : factorParents) {
                int index = this.factors.indexOf(factorParent1.getFactor());
                int lag = factorParent1.getLag();

                if (excludeSelfOneBack && index == i && lag == 1) {
                    continue;
                }

                IndexedParent parent = new IndexedParent(index, lag);
                list.add(parent);
            }

            IndexedParent[] _parents = new IndexedParent[list.size()];

            for (int i2 = 0; i2 < list.size(); i2++) {
                _parents[i2] = list.get(i2);
            }

            this.parents[i] = _parents;
        }
    }

    /**
     * Generates a simple exemplar of this class to test serialization.
     */
    public static IndexedConnectivity serializableInstance() {
        return new IndexedConnectivity(BasicLagGraph.serializableInstance());
    }

    //===============================PUBLIC METHODS======================//

    /**
     * Returns the number of factors.
     */
    public int getNumFactors() {
        return this.factors.size();
    }

    /**
     * Returns the (string name of) the factor at the given index.
     */
    public String getFactor(int factor) {
        return this.factors.get(factor);
    }

    /**
     * Returns the index of the given String factor.
     */
    public int getIndex(String factor) {
        return this.factors.indexOf(factor);
    }

    /**
     * Returns the index of the given parent for the given factor.
     */
    public int getIndex(String factor, LaggedFactor parent) {
        int factorIndex = this.factors.indexOf(factor);
        int parentIndex = this.factors.indexOf(parent.getFactor());
        IndexedParent indexedParent =
                new IndexedParent(parentIndex, parent.getLag());
        return getIndex(factorIndex, indexedParent);
    }

    /**
     * Returns the index of the parent of the given factor that is equal to the
     * given IndexedParent, or -1 if the given IndexedParent is not equal to any
     * parent.
     */
    public int getIndex(int factor, IndexedParent parent) {
        for (int i = 0; i < this.parents[factor].length; i++) {
            if (parent.equals(this.parents[factor][i])) {
                return i;
            }
        }
        return -1;
    }

    /**
     * Returns the number of parents of the given factor. Each parent is a
     * factor at a given lag.
     */
    public int getNumParents(int factor) {
        return this.parents[factor].length;
    }

    /**
     * Returns the given parent as an IndexedParent.
     */
    public IndexedParent getParent(int factor, int parent) {
        return this.parents[factor][parent];
    }

    /**
     * Returns a string representation of the graph, indicating for each factor
     * which lagged factors map into it.
     *
     * @return this string.
     */
    public String toString() {

        StringBuilder buf = new StringBuilder();

        buf.append("\nIndexed connectivity:\n");

        for (int i = 0; i < getNumFactors(); i++) {
            String factor = getFactor(i);

            buf.append("\n");
            buf.append(factor);
            buf.append("\t<-- ");

            for (int j = 0; j < getNumParents(i); j++) {
                IndexedParent parent = getParent(i, j);
                buf.append("\t");
                buf.append(getFactor(parent.getIndex()));
                buf.append(":");
                buf.append(parent.getLag());
            }
        }

        buf.append("\n");

        return buf.toString();
    }

    /**
     * Adds semantic checks to the default deserialization method. This method
     * must have the standard signature for a readObject method, and the body of
     * the method must begin with "s.defaultReadObject();". Other than that, any
     * semantic checks can be specified and do not need to stay the same from
     * version to version. A readObject method of this form may be added to any
     * class, even if Tetrad sessions were previously saved out using a version
     * of the class that didn't include it. (That's what the
     * "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for help.
     */
    private void readObject(ObjectInputStream s)
            throws IOException, ClassNotFoundException {
        s.defaultReadObject();

        if (this.factors == null) {
            throw new NullPointerException();
        }

        if (this.parents == null) {
            throw new IllegalStateException();
        }

    }
}






