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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.calc;


public class CorrelationCalculator {
    public static final String[] TYPE_LONG_NAME = { "Bravais-Pearson (linear correlation)", "Spearman (correlation of ranks)" };
    public static final String[] TYPE_NAME = { "Bravais-Pearson", "Spearman" };
    public static final String[] TYPE_CODE = { "bravais-pearson", "spearman" };
    public static final int TYPE_NONE = -1;
    public static final int TYPE_BRAVAIS_PEARSON = 0;
    public static final int TYPE_SPEARMAN = 1;

    private int mValueCount;

    private int[][] mValueCountMatrix;

    /**
     * Calculates the correlation coefficient between two columns of data.
     * Use the TYPE_BRAVAIS_PEARSON for normal distributed data and the
     * more robust TYPE_SPEARMAN if the data is not normal distributed.
     * If type==TYPE_BRAVAIS_PEARSON and one of a row's values is Double.NaN,
     * then the row is skipped.
     * If less than two valid rows are found or if both columns have a
     * different number of values, than Double.NaN is returned.
     * @param column1
     * @param column2
     * @param correlationType
     * @return
     */
    public double calculateCorrelation(INumericalDataColumn column1,
                                              INumericalDataColumn column2,
                                              int correlationType) {
        int valueCount = column1.getValueCount();
        if (valueCount != column2.getValueCount())
            return Double.NaN;

        double r = Double.NaN;

        if (correlationType == TYPE_BRAVAIS_PEARSON) {
            // http://de.wikibooks.org/wiki/Mathematik:_Statistik:_Korrelationsanalyse
            mValueCount = 0;
            double xMean = 0;
            double yMean = 0;
            for (int i=0; i 0 && array[position1-1] == value)
            position1--;
        int position2 = position;
        while (position2 < array.length-1 && array[position2+1] == value)
            position2++;
        return ((double)(position1+position2))/2 + 1;
        }
    }