com.github.jessemull.microflex.bigintegerflex.stat.QuartileDeviationBigInteger Maven / Gradle / Ivy

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Microplate library for parsing wet lab data.
There is a newer version: 1.0.4
/**
 * 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.bigintegerflex.stat;

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

import java.math.BigDecimal;
import java.math.MathContext;
import java.util.Collections;
import java.util.List;

/**
 * This class calculates the quartile deviation of BigInteger plate stacks, plates, 
 * wells and well sets.
 *
 * 


 * 
 * 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 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 as input
Calculates the statistic for each well in a well, set, plate or stack  
 *       

 *          
 *             
 *                
 *             
 *          Aggregated  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *          +/-  
 *       
 *          
 *             
 *                
 *             
 *              
 *                
 *             
 *          Accepts a single well/set/plate/stack or a collection/array of wells/sets/plates/stacks as input
Aggregates the data from all the wells in a well/set/plate/stack and calculates the statistic using the aggregated data  
 *       
 * 
 * @author Jesse L. Mull
 * @update Updated Oct 18, 2016
 * @address http://www.jessemull.com
 * @email [email protected]
 */
public class QuartileDeviationBigInteger extends DescriptiveStatisticBigIntegerContext {
    
    /**
     * Calculates the quartile deviation.
     * @param    List    the list
     * @param    MathContext         the math context
     * @return                       the result
     */
    public BigDecimal calculate(List list, MathContext mc) {
        
    	Collections.sort(list);
        
        if(list.size() < 2) {
            return BigDecimal.ZERO;
        }
        
        int index = list.size() / 2;
        
        List listQ1 = list.subList(0, index);
        int lowQ1 = (int) Math.floor((listQ1.size() - 1.0) / 2.0);
        int highQ1 = (int) Math.ceil((listQ1.size() - 1.0) / 2.0);
        BigDecimal q1 = (listQ1.get(lowQ1).add(listQ1.get(highQ1))).divide(new BigDecimal(2), mc);
        
        if(list.size() % 2 != 0) {
        	index++;
        }
        
        List listQ3 = list.subList(index, list.size());
        int lowQ3 = (int) Math.floor((listQ3.size() - 1.0) / 2.0);
        int highQ3 = (int) Math.ceil((listQ3.size() - 1.0) / 2.0);
        BigDecimal q3 = (listQ3.get(lowQ3).add(listQ3.get(highQ3))).divide(new BigDecimal(2), mc);

        return q3.subtract(q1).divide(new BigDecimal(2), mc);
    }
    
    /**
     * Calculates the quartile deviation of the values between the beginning and 
     * ending indices.
     * @param    List    the list
     * @param    int                 beginning index of subset
     * @param    int                 length of subset
     * @param    MathContext         the math context
     * @return                       the result
     */
    public BigDecimal  calculate(List list, int begin, int length, MathContext mc) {
        return calculate(list.subList(begin, begin + length), mc);
    }

}