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Microplate library for parsing wet lab data.
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/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

/* -------------------------------- Package -------------------------------- */

package com.github.jessemull.microflex.doubleflex.stat;

/* ----------------------------- Dependencies ------------------------------ */

import java.util.List;

/**
 * This class calculates the harmonic mean of double plate stacks, plates, 
 * wells and well sets.
 *
 * 


 * 
 * From wikipedia: a weight function is a mathematical device used when performing 
 * a sum, integral, or average to give some elements more "weight" or influence on 
 * the result than other elements in the same set. In statistics a weighted function 
 * is often used to correct bias. The weighted statistic class implements a weighted 
 * function by accepting an array of values as weights. The values in each well of 
 * the stack, plate, set or well are multiplied by the values within the double 
 * array prior to the statistical calculation.
 * 
 * 


 * 
 * Weighted statistical operations can be performed on stacks, plates, sets and 
 * wells using standard or aggregated functions. Standard functions calculate the 
 * desired statistic for each well in the stack, plate or set. Aggregated functions 
 * aggregate the values from all the wells in the stack, plate or set and perform 
 * the weighted statistical operation on the aggregated values. Both standard and 
 * aggregated functions can be performed on a subset of data within the stack, 
 * plate, set or well.
 * 
 * 


 * 
 * The methods within the MicroFlex library are meant to be flexible and the
 * descriptive statistic object supports operations using a single stack, plate,
 * set or well as well as collections and arrays of stacks, plates, sets or wells. 
 * 
 * 
 *    
 *    
 *    
 *    
 *    
 *       
 *       
 *       
 *       
 *    
 *    
 *       
 *       
 *       
 *       
 *    
 * Operation Beginning
Index Length of
Subset Input/Output

 *          
 *             
 *                
 *             
 *          Standard  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *             
 *                
 *             
 *          Accepts a single well, set, plate or stack and an array of weights as input
Multiplies the values in each well of a well, set, plate or stack by the values
 *                
 in the weights array then calculates the statistic using the weighted values  
 *       

 *          
 *             
 *                
 *             
 *          Aggregated  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *              
 *                
 *             
 *          Accepts a single well/set/plate/stack or a collection/array of wells/sets/plates/stacks 
 *                
and an array of weights as input
Multiplies the values in each well of a well, set, plate or stack by the values in the 
 *                
weights array, aggregates the data from all the wells in the well/set/plate/stack then 
 *                
calculates the statistic using the aggregated weighted values  
 *       
 * 
 * @author Jesse L. Mull
 * @update Updated Oct 18, 2016
 * @address http://www.jessemull.com
 * @email [email protected]
 */
public class HarmonicMeanDouble extends DescriptiveStatisticDoubleWeights {
    
    /**
     * Calculates the harmonic mean.
     * @param    List    the list
     * @return                   the result
     */
    public double calculate(List list) {
    	
    	if(list.size() == 0) {
            return 0;
        }
    	
    	double sum = 0;

    	for(double value : list) {
    	      sum += 1 / value;
    	}

        return sum / list.size();
    }
    
    /**
     * Calculates the weighted harmonic mean.
     * @param    List        the list
     * @param    double[]        weights for the data set
     * @return                   the result
     */
    public double calculate(List list, double[] weights) {
        
    	if(list.size() == 0) {
            return 0;
        }
    	
    	double sum = 0;

    	for(int i = 0; i < list.size(); i++) {
    	      sum += 1 / (list.get(i) * weights[i]);
    	}

        return sum / list.size();
    }
    
    /**
     * Calculates the harmonic mean of the values between the beginning and 
     * ending indices.
     * @param    List    the list
     * @param    int             beginning index of subset
     * @param    int             length of subset
     * @return                   the result
     */
    public double  calculate(List list, int begin, int length) {
        return calculate(list.subList(begin, begin + length));
    }
    
    /**
     * Calculates the weighted harmonic mean of the values between the beginning and 
     * ending indices.
     * @param    List        the list
     * @param    double[]        weights of the data set
     * @param    int             beginning index of subset
     * @param    int             length of subset
     * @return                   the result
     */
    public double calculate(List list, double[] weights, int begin, int length) {
        return calculate(list.subList(begin, begin + length), weights);
    }
}