/** Genotype.java
 *J Scott Cameron 
 *This class contains a bit-vector with the "genes"
 *and a rating to be determined by the fitness
 *function of the Genetic Algorithm.
 *  
 *Note: All the contructors take a Random as a parameter
 *because when creating a whole slew of Genetypes very quickly
 *if each Genotype creates its own Random object then there are a lot
 *of identical Random objects since they're all initialized using the
 *current time in milliseconds. It takes less than a millisecond to create
 *a Genotype so the Random objects are initialized with the same time.
 *This is very bad if you want a population of unique Genotypes.
 *By including a Random object in the constructor the Genetic Algorithm
 *sends all the Genotypes a reference to the same Random object. This way
 *each objects gets the object at a different point in its progression.
 */
import java.io.*;
import java.util.*;

public class Genotype
{
    private boolean bits[];
    private int rating;
    private int length;
    private Random random;
    
    public Genotype()
    {
        random = new Random();
    }
    
    /* creates a Random genetoype */
    public Genotype(int length, Random r)
    {
        random = r;
        this.length = length;
        bits = new boolean[length];
        for(int i=0;i<length;i++)
        {
            bits[i] =random.nextBoolean();
        }
    }
    
    /* copy constructor */
    public Genotype(Genotype g,Random r)
    {
        random = r;
        bits = new boolean[g.length];
        rating = g.rating;
        length = g.length;
        for(int i=0;i<length;i++)
        {
            bits[i] = g.bits[i];
        }
        
    }
    
        /* Crossover Constructor
         */
    public Genotype(Genotype g1,Genotype g2,Random r)
    {
        random = r;
        bits = new boolean[g1.length];
        rating = 0;
        length = g1.length;
        
        /* find a random point to cross Genotypes */
        int crosspoint = Math.abs(random.nextInt())%length;
        
        /*copy bits before crossover point from first Genotype
         * to new Genotype*/
        for(int i = 0;i<crosspoint;i++)
        {
            bits[i]=g1.bits[i];
        }
        /*copy bits after crossover point from second Genotype
         * to new Genotype*/
        for(int i = crosspoint;i<length;i++)
        {
            bits[i]=g2.bits[i];
        }
        
    }
    
    /* mutates Genotype*/
    public void mutate(double rate)
    {
        /* iterates through all the bits, flipping the bit
         * if a random double between 0 and 1 is less
         * than the mutation rate */
        for(int i=0;i<length;i++)
        { 
            if(Math.abs(random.nextDouble()) < rate)
            {
                bits[i] = !bits[i];
            }
        }
    }
    
    /* return the bit array*/
    public boolean[] getBitSet()
    {
        return bits;
    }
    
    /* returns the rating of the genotype */
    public int getRating()
    {
        return rating;
    }
    
    /* returns the length of the bit array */
    public int getLength()
    {
        return length;
    }
    
        
    /* sets the rating of the genotype */
    public void setRating(int rating)
    {
        this.rating = rating;
    }
    
    /* returns a String of "1"'s and "0"'s to represent
     * the bit array */
    public String toString()
    {
        StringWriter sw = new StringWriter();
        
        for(int i=0;i<length;i++)
        {
            if(bits[i])
            {
                sw.write("1");
            }
            else
            {
                sw.write("0");
            }
        }
        return sw.toString();
    }
}