/***********************************************************************

	This file is part of JavaNPST, a Java library of NonParametric
	Statistical Tests.

	Copyright (C) 2011
	
	J. Derrac (jderrac@decsai.ugr.es)
	S. Garcia (sglopez@ujaen.es)
	F. Herrera (herrera@decsai.ugr.es)

	This program is free software: you can redistribute it and/or modify
	it under the terms of the GNU General Public License as published by
	the Free Software Foundation, either version 3 of the License, or
	(at your option) any later version.

	This program is distributed in the hope that it will be useful,
	but WITHOUT ANY WARRANTY; without even the implied warranty of
	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
	GNU General Public License for more details.

	You should have received a copy of the GNU General Public License
	along with this program.  If not, see http://www.gnu.org/licenses/
  
**********************************************************************/

package javanpst.tests.equality.JTTest;

import javanpst.data.structures.dataTable.DataTable;
import javanpst.distributions.common.continuous.NormalDistribution;
import javanpst.tests.StatisticalTest;

/**
 * The Jonckheere and Terpstra test (JT test)
 * 
 * This test can be applied to test the null hypotheses of equal medians 
 * between populations. Alternative is that the location parameter
 * is in increasing order:
 * 
 * M1 <= M2 <= ... <= Mn
 * 
 * P-values are computed through a normal distribution
 * approximation.
 * 
 * All samples must have the same number of elements.
 * 
 * @author Joaqu�n Derrac Rus (jderrac@decsai.ugr.es)
 * @version 1.0
 */
public class JTTest extends StatisticalTest{

	/**
	 * Data to analyze
	 */
	private DataTable data;
	
	/**
	 * Populations samples
	 */
	private double samples [][];
	
	/**
	 * B statistic
	 */
	private double B;
	
	/**
	 * Z value
	 */
	private double Z;
	
	/**
	 * P-value computed
	 */
	private double pValue;
	
	/**
	 * Default builder
	 */
	public JTTest(){

		setReportFormat();
		clearData();
		
	}//end-method
	
	/**
	 * Clears the data stored in the test
	 */
	public void clearData(){
		
		data=new DataTable();
		
		performed=false;
		dataReady=false;
		
		B=0.0;
		Z=0.0;
		
		samples=null;

		pValue=-1.0;
		
	}//end-method
	
	/**
	 * Builder. Load data to test.
	 * 
	 * @param newData data to test.
	 */
	public JTTest(DataTable newData){
		
		setReportFormat();
		
		data=DataTable.newInstance(newData);
		
		if(data.getColumns()<3){
			System.out.println("Extended median test only can be employed with more than two samples");
			clearData();
			return;
		}
		
		for(int i=0;i0){
				System.out.println("No null values allowed in this test.");
				clearData();
				return;
			}
		}
		
		samples=new double[data.getRows()][data.getColumns()];
		
		for(int i=0;i0){
				System.out.println("No null values allowed in this test.");
				clearData();
				return;
			}
		}
		
		samples=new double[data.getRows()][data.getColumns()];
		
		for(int i=0;isamples[j][first]){
							counter++;
						}
					}
				}
				B+=counter;
			}
		}
		
		//compute standard median and variance of the Z statistic
		
		N=data.getRows()*data.getColumns();
		
		stMean=((N*N)-(data.getColumns()*data.getRows()*data.getRows()))/4.0;
		
		stDev=N*N*((2*N)+3.0)-(data.getColumns()*data.getRows()*data.getRows()*((2*data.getRows())+3.0));
		stDev/=72.0;
		stDev=Math.sqrt(stDev);
		
		Z=(B-stMean)/stDev;

		computePValue();
		
		performed=true;
		
	}//end-method
	
	/**
	 * Compute p-value for hypotheses of equality of medians
	 */
	private void computePValue(){
		
		NormalDistribution normal=new NormalDistribution();

		pValue=1.0-normal.getTipifiedProbability(Z, false);
		
	}//end-method
	
	/**
	 * Get B statistic 
	 * 
	 * @return B statistic 
	 */
	public double getB(){
		
		return B;
		
	}//end-method
	
	/**
	 * Get Z value
	 * 
	 * @return Z value
	 */
	public double getZ(){
		
		return Z;
		
	}//end-method
	
	/**
	 * Get p-value 
	 * 
	 * @return p-value computed
	 */
	public double getPValue(){
		
		return pValue;
		
	}//end-method
	
	/**
	 * Prints the data stored in the test
	 * 
	 * @return Data stored
	 */
	public String printData(){
			
		String text="";
			
		text+="\n"+data;
			
		return text;
			
	}//end-method
		
	/**
	 * Prints a report with the results of the test
	 * 
	 * @return Output report
	 */
	public String printReport(){
			
		String report="";
		
		if(!performed){
			report+="The test has not been performed.\n";
			return report;
		}
			
		report+="\n***************************************\n";
		report+="Jonckheere and Terpstra test (JT test)\n";
		report+="***************************************\n\n";

		report+="B statistic: "+nf6.format(B)+"\n\n";
		
		report+="P-Value computed :"+nf6.format(pValue)+"\n\n";
					
		return report;
			
	}//end-method
		
}//end-class