///////////////////////////////////////////////////////////////////////////////
// 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.CovarianceMatrix;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DataUtils;
import edu.cmu.tetrad.data.ICovarianceMatrix;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradMatrix;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;

/**
 * Tests independence using a bootstrapped Fisher Z method.
 */
public class IndTestFisherZBootstrap implements IndependenceTest {

    /**
     * The variables of the correlation matrix, in order. (Unmodifiable list.)
     */
    private final List<Node> variables;

    /**
     * The significance level of the independence tests.
     */
    private double alpha = 0.05;

    private DataSet dataSet;
    private int numBootstrapSamples;
    private IndependenceTest[] tests;
    private boolean verbose = false;

    public IndTestFisherZBootstrap(DataSet dataSet, double alpha, int numBootstrapSamples, int bootstrapSampleSize) {
        if (!(dataSet.isContinuous())) {
            throw new IllegalArgumentException("Data set must be continuous.");
        }

        if (!(alpha >= 0 && alpha <= 1)) {
            throw new IllegalArgumentException("Alpha mut be in [0, 1]");
        }

        ICovarianceMatrix covMatrix = new CovarianceMatrix(dataSet);
        this.dataSet = dataSet;

        this.variables = Collections.unmodifiableList(covMatrix.getVariables());
        setAlpha(alpha);

        this.numBootstrapSamples = numBootstrapSamples;
        TetradMatrix[] bootstrapSamples = new TetradMatrix[numBootstrapSamples];
        this.tests = new IndependenceTest[numBootstrapSamples];

        for (int i = 0; i < numBootstrapSamples; i++) {
            TetradMatrix fullData = dataSet.getDoubleData();
            bootstrapSamples[i] = DataUtils.getBootstrapSample(fullData, bootstrapSampleSize);
            tests[i] = new IndTestFisherZ(bootstrapSamples[i], dataSet.getVariables(), alpha);

        }

    }

    public IndependenceTest indTestSubset(List<Node> vars) {
        return null;
    }

    public boolean isIndependent(Node x, Node y, List<Node> z) {
        int[] independentGuys = new int[numBootstrapSamples];

        for (int i = 0; i < numBootstrapSamples; i++) {
            boolean independent = tests[i].isIndependent(x, y, z);
            independentGuys[i] = independent ? 1 : 0;
        }

        int sum = 0;
        for (int i = 0; i < numBootstrapSamples; i++) sum += independentGuys[i];
        boolean independent = sum > numBootstrapSamples / 2;

        if (verbose) {
            if (independent) {
                TetradLogger.getInstance().log("independencies",
                        SearchLogUtils.independenceFactMsg(x, y, z, getPValue()));
            } else {
                TetradLogger.getInstance().log("dependencies",
                        SearchLogUtils.dependenceFactMsg(x, y, z, getPValue()));
            }
        }

        return independent;
    }

    public boolean isIndependent(Node x, Node y, Node... z) {
        List<Node> zList = Arrays.asList(z);
        return isIndependent(x, y, zList);
    }

    public boolean isDependent(Node x, Node y, List<Node> z) {
        return !isIndependent(x, y, z);
    }

    public boolean isDependent(Node x, Node y, Node... z) {
        List<Node> zList = Arrays.asList(z);
        return isDependent(x, y, zList);
    }

    public double getPValue() {
        return 0;
    }

    /**
     * @return the list of variables over which this independence checker is capable of determinine independence
     * relations-- that is, all the variables in the given graph or the given data set.
     */
    public List<Node> getVariables() {
        return this.variables;
    }

    /**
     * @return the variable with the given name.
     */
    public Node getVariable(String name) {
        for (int i = 0; i < getVariables().size(); i++) {
            Node variable = getVariables().get(i);
            if (variable.getName().equals(name)) {
                return variable;
            }
        }

        return null;
    }

    /**
     * @return the list of variable varNames.
     */
    public List<String> getVariableNames() {
        List<Node> variables = getVariables();
        List<String> variableNames = new ArrayList<>();
        for (Node variable1 : variables) {
            variableNames.add(variable1.getName());
        }
        return variableNames;
    }

    public boolean determines(List<Node> z, Node x1) {
        return false;
    }

    public double getAlpha() {
        return alpha;
    }

    public void setAlpha(double alpha) {
        this.alpha = alpha;
    }

    public String toString() {
        return "Fisher's Z Bootstrap";
    }


    public DataSet getData() {
        return dataSet;
    }

    @Override
    public ICovarianceMatrix getCov() {
        return null;
    }

    @Override
    public List<DataSet> getDataSets() {
        return null;
    }

    @Override
    public int getSampleSize() {
        return 0;
    }

    @Override
    public List<TetradMatrix> getCovMatrices() {
        return null;
    }

    @Override
    public double getScore() {
        return -(getPValue() - getAlpha());
    }

    public boolean isVerbose() {
        return verbose;
    }

    public void setVerbose(boolean verbose) {
        this.verbose = verbose;
    }
}