package com.biolab.node.nexTest.Jama;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;

/**
 * A utility class that provides some simple statistical functions.
 */
public abstract class Statistics {

    /**
     * Returns the mean of an array of numbers.
     *
     * @param values  the values (<code>null</code> permitted, returns
     *                <code>Double.NaN</code>).
     *
     * @return The mean.
     */
    public static double calculateMean(Number[] values) {
        double result = Double.NaN;
        if (values != null && values.length > 0) {
            double sum = 0.0;
            int counter = 0;
            for (; counter < values.length; counter++) {
                sum = sum + values[counter].doubleValue();
            }
            result = (sum / counter);
        }
        return result;
    }

    /**
    * Returns the mean of an array of numbers.
    *
    * @param values  the values

    * @return The mean.
       zhangweian   2006/03/08
    */
   public static double calculateMean(double[] values) {
       double result = Double.NaN;
       if (values != null && values.length > 0) {
           double sum = 0.0;
           int counter = 0;
           for (; counter < values.length; counter++) {
               sum = sum + values[counter];
           }
           result = (sum / counter);
       }
       return result;
   }

    /**
     * Returns the mean of a collection of <code>Number</code> objects.
     *
     * @param values  the values (<code>null</code> permitted, returns
     *                <code>Double.NaN</code>).
     *
     * @return The mean.
     */
    public static double calculateMean(Collection values) {

        double result = Double.NaN;
        int count = 0;
        double total = 0.0;
        Iterator iterator = values.iterator();
        while (iterator.hasNext()) {
            Object object = iterator.next();
            if (object != null && object instanceof Number) {
                Number number = (Number) object;
                total = total + number.doubleValue();
                count = count + 1;
            }
        }
        if (count > 0) {
            result = total / count;
        }
        return result;

    }

    /**
     * Calculates the median for a list of values (<code>Number</code> objects).
     * The list of values will be sorted first.
     *
     * @param values  the values.
     *
     * @return The median.
     */
    public static double calculateMedian(List values) {
        return calculateMedian(values, true);
    }

    /**
     * Calculates the median for a list of values (<code>Number</code> objects)
     * that are assumed to be in ascending order.
     *
     * @param values  the values.
     * @param copyAndSort  a flag that controls whether the list of values is
     *                     copied and sorted.
     *
     * @return The median.
     */
    public static double calculateMedian(List values, boolean copyAndSort) {

        double result = Double.NaN;
        if (values != null) {
            if (copyAndSort) {
                int itemCount = values.size();
                List copy = new ArrayList(itemCount);
                for (int i = 0; i < itemCount; i++) {
                    copy.add(i, values.get(i));
                }
                Collections.sort(copy);
                values = copy;
            }
            int count = values.size();
            if (count > 0) {
                if (count % 2 == 1) {
                    if (count > 1) {
                        Number value = (Number) values.get((count - 1) / 2);
                        result = value.doubleValue();
                    }
                    else {
                        Number value = (Number) values.get(0);
                        result = value.doubleValue();
                    }
                }
                else {
                    Number value1 = (Number) values.get(count / 2 - 1);
                    Number value2 = (Number) values.get(count / 2);
                    result = (value1.doubleValue() + value2.doubleValue())
                             / 2.0;
                }
            }
        }
        return result;
    }

    /**
     * Calculates the median for a sublist within a list of values
     * (<code>Number</code> objects).
     *
     * @param values  the values (in any order).
     * @param start  the start index.
     * @param end  the end index.
     *
     * @return The median.
     */
    public static double calculateMedian(List values, int start, int end) {
        return calculateMedian(values, start, end, true);
    }

    /**
     * Calculates the median for a sublist within a list of values
     * (<code>Number</code> objects).  The entire list will be sorted if the
     * <code>ascending</code< argument is <code>false</code>.
     *
     * @param values  the values.
     * @param start  the start index.
     * @param end  the end index.
     * @param copyAndSort  a flag that that controls whether the list of values
     *                     is copied and sorted.
     *
     * @return The median.
     */
    public static double calculateMedian(List values, int start, int end,
                                         boolean copyAndSort) {

        double result = Double.NaN;
        if (copyAndSort) {
            List working = new ArrayList(end - start + 1);
            for (int i = start; i <= end; i++) {
                working.add(values.get(i));
            }
            Collections.sort(working);
            result = calculateMedian(working, false);
        }
        else {
            int count = end - start + 1;
            if (count > 0) {
                if (count % 2 == 1) {
                    if (count > 1) {
                        Number value
                            = (Number) values.get(start + (count - 1) / 2);
                        result = value.doubleValue();
                    }
                    else {
                        Number value = (Number) values.get(start);
                        result = value.doubleValue();
                    }
                }
                else {
                    Number value1 = (Number) values.get(start + count / 2 - 1);
                    Number value2 = (Number) values.get(start + count / 2);
                    result
                        = (value1.doubleValue() + value2.doubleValue()) / 2.0;
                }
            }
        }
        return result;

    }

    /**
     * Returns the standard deviation of a set of numbers.
     *
     * @param data  the data.
     *
     * @return The standard deviation of a set of numbers.
     */
    public static double getStdDev(Number[] data) {
        double avg = calculateMean(data);
        double sum = 0.0;

        for (int counter = 0; counter < data.length; counter++) {
            double diff = data[counter].doubleValue() - avg;
            sum = sum + diff * diff;
        }
        return Math.sqrt(sum / (data.length - 1));
    }


    /**
     * Returns the standard deviation of a set of numbers.
     *
     * @param data  the data.
     *
     * @return The standard deviation of a set of numbers.
         zhangweian  2006/03/08

     */
    public static double getStdDev(double[] data) {
        double avg = calculateMean(data);
        double sum = 0.0;