StandardBinaryChromosome.java

package bsearch.representations;

import java.util.LinkedHashMap;

import org.nlogo.util.MersenneTwisterFast;

import bsearch.space.SearchSpace;

/**
 * A Chromosomal representation that uses standard ordering of bits to encode integer (and discretized continuous) values 
 */
public strictfp class StandardBinaryChromosome extends BinaryChromosome
{
	public StandardBinaryChromosome( SearchSpace searchSpace , MersenneTwisterFast rng )
	{
		super(searchSpace, rng);
	}	
	public StandardBinaryChromosome( SearchSpace searchSpace , LinkedHashMap<String,Object> paramSettings )
	{
		super(searchSpace, paramSettings);
	}	
	public StandardBinaryChromosome( boolean[] bitstring, SearchSpace searchSpace )
	{
		super(bitstring, searchSpace);
	}	
	
	@Override
	public StandardBinaryChromosome clone()
	{
		return new StandardBinaryChromosome(bitstring, searchSpace); 
	}
	
	@Override
	public void binaryEncode(long binval, boolean[] bits, int offset, int len)
	{
		long bitMask = 1;
		for (int i = 0 ; i < len ; i++)
		{
			bits[offset + i] = ((binval & bitMask) != 0) ;
			bitMask = bitMask << 1;
		}
	}
	
	@Override
	public long binaryDecode(boolean[] bits, int offset, int len )
	{
		long binval = 0;
		for (int i = len - 1 ; i >= 0 ; i--)
		{
			binval <<= 1;
			if (bits[offset + i])
			{
				binval = binval + 1;
			}
		}
		return binval;
	}
		
	public static class Factory implements ChromosomeFactory
	{
		public Chromosome createChromosome(SearchSpace searchSpace,
				MersenneTwisterFast rng) {
			return new StandardBinaryChromosome(searchSpace, rng);
			
		}
		public Chromosome createChromosome( SearchSpace searchSpace, LinkedHashMap<String,Object> paramSettings)
		{
			return new StandardBinaryChromosome(searchSpace, paramSettings);
		}
		public String getHTMLHelpText() {
			return "<strong>StandardBinaryChromosome</strong> In this encoding, every parameter is converted " +
					"into a string of binary digits, and these sequences are concatenated together into one " +
					"large bit array.  Mutation and crossover then occur on a per-bit basis.";
		}
	}
}