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



	This file is part of KEEL-software, the Data Mining tool for regression, 

	classification, clustering, pattern mining and so on.



	Copyright (C) 2004-2010

	

	F. Herrera (herrera@decsai.ugr.es)

    L. Sánchez (luciano@uniovi.es)

    J. Alcalá-Fdez (jalcala@decsai.ugr.es)

    S. García (sglopez@ujaen.es)

    A. Fernández (alberto.fernandez@ujaen.es)

    J. Luengo (julianlm@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 keel.Algorithms.Subgroup_Discovery.MESDIF.MESDIF;



import org.core.*;



/**

 * <p> Defines the structure and manage the contents of a canonical rule.

     * This implementation uses only integer values to store the gens.

     *

 * @author Created by Pedro González (University of Jaen) 18/02/2004

 * @author Modified by Pedro González (University of Jaen) 4/08/2007

 * @author Modified by Cristóbal J. Carmona (University of Jaen) 30/06/2010

 * @version 2.0

 * @since JDK1.5

 * </p>

 */

public class CromCAN {

    



    private int num_genes;      // Number of genes

    private int chromosome [];   // Individual content - integer representation

      

    /**

     * <p>

     * Creates new instance of chromosome, no initialization

     * </p>

     * @param length          Length of the chromosome

     */

    public CromCAN(int length) {

      num_genes = length;

      chromosome = new int [length];

    }



    /**

     * <p>

     * Random initialization of an existing chromosome

     * </p>

     * @param Variables     contents the characteristics of the variables

     */

    public void initCromRnd (TableVar Variables) {

        for (int i=0; i<num_genes; i++) 

            chromosome[i] = Randomize.Randint (0, Variables.getNLabelVar(i));

    }







    /**

     * <p>

     * Biased Random initialization of an existing chromosome

     * The random inicializacion is biased by generating

     *    chromosomes with a maximum number or participating variables

     *    and for an indicated % of the population (the rest is random)

     * </p>

     * @param Variables 		contents the type of the variable, and the number of labels.

     * @param porcVar           percentage of variables to appear in the biased initialization

     */

    public void initCromBsd (TableVar Variables , float porcVar) {

        int num_var;



        /* Array of integers to show if each chromosome is initialized */

        int  crom_inic[]= new int[num_genes];

        for (int i=0; i<num_genes; i++)

           crom_inic[i] = 0;



        /* First, obtain the number of variables to appear in the chromosome */

        int numInterv = Randomize.Randint (1, Math.round(porcVar*num_genes));



        /* Initialize numInterv variables to take part in the individual */

        int var=0;

        while (var<numInterv) {

            num_var = Randomize.Randint (0, num_genes-1);

            /* If not initialized, initialize and increase the count */

            if (crom_inic[num_var]==0) {

                chromosome[num_var] = Randomize.Randint (0, Variables.getNLabelVar(num_var));

                crom_inic[num_var]=1;

                var++;

            }

        }



        /* Initialize the rest of variables to "not-intervene" */

        for (int i=0; i<num_genes; i++)  {

            if (crom_inic[i]!=0) {

                chromosome[i] = Variables.getNLabelVar(i);

            }

        }



    }





    /**

     * <p>

     * Retuns the value of the gene indicated

     * </p>

     * @param pos          Position of the variable in the chromosome

     * @return                  Value of the variable

     */

    public int getCromElem (int pos) {

      return chromosome[pos];

    }

    

    /**

     * <p>

     * Sets the value of the indicated gene of the chromosome

     * </p>

     * @param pos          Position of the variable in the chromosome

     * @param value             Value of the variable

     */

    public void setCromElem (int pos, int value ) {

      chromosome[pos] = value;

    }





    /**

     * <p>

     * Retuns the length of the chromosome

     * </p>

     * @return                  Length of the chromosome

     */

    public int getCromLength () {

      return num_genes;

    }







    /**

     * <p>

     * Prints the chromosome genes

     * </p>

     * @param nFile         File to write the chromosome

     */

    public void print(String nFile) {

        String contents;

        contents = "Chromosome: ";

        for(int i=0; i<num_genes; i++)

            contents+= chromosome[i] + " ";

        contents+= "\n";

        if (nFile=="") 

            System.out.print (contents);

        else 

           Files.addToFile(nFile, contents);

    }

    

}