content: /*
   * 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
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   * (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.classification;
  
  import com.actelion.research.util.Formatter;
  
  import java.io.Serializable;
  import java.util.List;
  
  /**
   * PrecisionAndRecall
   * @author Modest von Korff
   * @version 1.0
   * Jun 18, 2015 MvK Start implementation
   */
  public class PrecisionAndRecall implements Serializable {
  
  	public static final String ATTR_TP = "TP";
  	public static final String ATTR_TN = "TN";
  	public static final String ATTR_FP = "FP";
  	public static final String ATTR_FN = "FN";
  
  
  	public int truePositive=0;
  	public int trueNegative=0;
  	public int falsePositive=0;
  	public int falseNegative=0;
  	
  	/**
  	 * @param truePositive
  	 * @param trueNegative
  	 * @param falsePositive
  	 * @param falseNegative
  	 */
  	public PrecisionAndRecall(int truePositive, int trueNegative,
  			int falsePositive, int falseNegative) {
  		super();
  		this.truePositive = truePositive;
  		this.trueNegative = trueNegative;
  		this.falsePositive = falsePositive;
  		this.falseNegative = falseNegative;
  	}
  	/**
  	 * 
  	 */
  	public PrecisionAndRecall() {
  	}
  
  	public void add(PrecisionAndRecall p){
  		this.truePositive+=p.truePositive;
  		this.trueNegative+=p.trueNegative;
  		this.falsePositive+=p.falsePositive;
  		this.falseNegative+=p.falseNegative;
  	}
  
  	public void parse2PrecisionAndRecall(String sVal){
  
  		if(PrecisionAndRecall.ATTR_TP.equals(sVal)) {
  			truePositive++;
  		} else if(PrecisionAndRecall.ATTR_TN.equals(sVal)) {
  			trueNegative++;
  		} else if(PrecisionAndRecall.ATTR_FP.equals(sVal)) {
  			falsePositive++;
  		} else if(PrecisionAndRecall.ATTR_FN.equals(sVal)) {
  			falseNegative++;
  		} else {
  			throw new RuntimeException("Parsing error for '" + sVal + "'.");
  		}
  	}
  
  
  
  	/**
  	 * @return the truePositive
  	 */
  	public int getTruePositive() {
  		return truePositive;
  	}
  
  	/**
  	 * @param truePositive the truePositive to set
  	 */
  	public void setTruePositive(int truePositive) {
  		this.truePositive = truePositive;
  	}
  
  	/**
  	 * @return the trueNegative
  	 */
  	public int getTrueNegative() {
  		return trueNegative;
  	}
  
  	/**
  	 * @param trueNegative the trueNegative to set
  	 */
  	public void setTrueNegative(int trueNegative) {
  		this.trueNegative = trueNegative;
  	}
  
  	/**
  	 * @return the falsePositive
  	 */
  	public int getFalsePositive() {
  		return falsePositive;
  	}
  
  	/**
  	 * @param falsePositive the falsePositive to set
  	 */
  	public void setFalsePositive(int falsePositive) {
  		this.falsePositive = falsePositive;
  	}
  
  	/**
  	 * @return the falseNegative
  	 */
  	public int getFalseNegative() {
  		return falseNegative;
  	}
  
  	/**
  	 * @param falseNegative the falseNegative to set
  	 */
  	public void setFalseNegative(int falseNegative) {
  		this.falseNegative = falseNegative;
  	}
  
  	public int getSum(){
  		return trueNegative+truePositive+falsePositive+falseNegative;
  	}
  
  	public double calculatePrecision(){
  		
  		int tp_fp = truePositive+falsePositive;
  		
  		if(tp_fp==0){
  			return 0;
  		}
  		
  		return truePositive/(double)(truePositive+falsePositive);
  		
  	}
  	
  	public double calculateRecall(){
  				
  		int tp_fn = truePositive+falseNegative;
  		
  		if(tp_fn==0){
  			return 0;
  		}
  		
  		return truePositive/(double)(truePositive+falseNegative);
  		
  	}
  	public double calculateAccuracy(){
  
  		double acc = (truePositive+trueNegative)/(double)getSum();
  
  		return acc;
  
  	}
  	
  	/**
  	 * F1 score
  	 * @return
  	 */
  	public double calculateHarmonicMean(){
  		
  		double p = calculatePrecision();
  		
  		double r = calculateRecall();
  		
  		if((p+r)==0){
  			return 0;
  		}
  		
  		double f1 = 2.0 * (p*r/(p+r));
  		
  		return f1;
  		
  	}
  
  	public double calculateCohensKappa(){
  
  		double all = getSum();
  
  		double pYes = ((truePositive+falseNegative)/all) * ((truePositive+falsePositive)/all);
  
  		double pNo = ((falsePositive+trueNegative)/all) * ((falseNegative+trueNegative)/all);
  
  		double pe = pYes+pNo;
  
  		double po = calculateAccuracy();
  
  		double k = (po-pe)/(1.0-pe);
  
  		return k;
  	}
  
  	
  	/* (non-Javadoc)
  	 * @see java.lang.Object#toString()
  	 */
  	@Override
  	public String toString() {
  		
  		StringBuilder sb = new StringBuilder();
  		
  		sb.append("Accuracy " + Formatter.format3(calculateAccuracy()));
  		sb.append(", precision " + Formatter.format3(calculatePrecision()));
  		sb.append(", recall " + Formatter.format3(calculateRecall()));
  		sb.append(", F1 "+ Formatter.format3(calculateHarmonicMean()));
  		sb.append(", Cohens' kappa " + Formatter.format3(calculateCohensKappa()));
  		sb.append("\n");
  		sb.append("True positive " + truePositive);
  		sb.append("\n");
  		sb.append("True negative " + trueNegative);
  		sb.append("\n");
  		sb.append("False positive " + falsePositive);
  		sb.append("\n");
  		sb.append("False negative " + falseNegative);
  		
  		return sb.toString();
  	}
  
  
  	public static double getHarmonicMean(List<PrecisionAndRecall> li){
  
  		double sum=0;
  		for (PrecisionAndRecall precisionAndRecall : li) {
  
  			sum += precisionAndRecall.calculateHarmonicMean();
  		}
  
  		return sum / li.size();
  	}
  
  	public static void main(String[] args) {
  
  		PrecisionAndRecall pr = new PrecisionAndRecall();
  
  		pr.truePositive=20;
  		pr.trueNegative=15;
  		pr.falseNegative=5;
  		pr.falsePositive=10;
  
  		System.out.println("Cohen's kappa: " + pr.calculateCohensKappa());
  
  	}
  
  	
  }
  