GrayBinaryChromosome.java

package bsearch.representations;

import java.util.LinkedHashMap;

import org.nlogo.util.MersenneTwisterFast;

import bsearch.space.SearchSpace;

/**
 * A Chromosomal representation that uses Gray code for integers
 */
public strictfp class GrayBinaryChromosome extends BinaryChromosome
{
	public GrayBinaryChromosome( SearchSpace searchSpace , MersenneTwisterFast rng )
	{
		super(searchSpace, rng);
	}	
	public GrayBinaryChromosome( SearchSpace searchSpace , LinkedHashMap<String,Object> paramSettings )
	{
		super(searchSpace, paramSettings);
	}	
	public GrayBinaryChromosome( boolean[] bitstring, SearchSpace searchSpace )
	{
		super(bitstring, searchSpace);
	}	
	
	@Override
	public GrayBinaryChromosome clone()
	{
		return new GrayBinaryChromosome(bitstring, searchSpace); 
	}
	
	@Override
	public void binaryEncode(long binval, boolean[] graybits, int offset, int len)
	{
		// efficient shortcut for converting to Gray encoding
		long gray = binval ^ (binval >> 1);
		
		long bitMask = 1;
		for (int i = 0 ; i < len ; i++)
		{
			graybits[offset + i] = ((gray & bitMask) != 0) ;
			bitMask = bitMask << 1;
		}

//		Let B[n:0] be the input array of bits in the 
//        usual binary representation, [0] being LSB
//        Let G[n:0] be the output array of bits in Gray code
//        G[n] = B[n]
//        for i = n-1 downto 0
//            G[i] = B[i+1] XOR B[i]

	}
	
	@Override
	public long binaryDecode(boolean[] graybits, int offset, int len )
	{
		long bitMask = 1L << (len - 1);
		long result = 0;
		boolean previousBit = false;
		if (graybits [offset + len - 1])
		{
			result |= bitMask;
			previousBit = true;
		}
		bitMask = bitMask >> 1;
		for (int i = len - 2; i >= 0; i--)
		{
			if (previousBit ^ graybits[ offset + i ] )
			{
				result = result | bitMask;
				previousBit = true;
			}
			else
			{
				previousBit = false;
			}
			bitMask = bitMask >> 1;
		}
		return result;		
	}
		
	public static class Factory implements ChromosomeFactory
	{
		public Chromosome createChromosome(SearchSpace searchSpace,
				MersenneTwisterFast rng) {
			return new GrayBinaryChromosome(searchSpace, rng);
		}
		public Chromosome createChromosome( SearchSpace searchSpace, LinkedHashMap<String,Object> paramSettings)
		{
			return new GrayBinaryChromosome(searchSpace, paramSettings);
		}
		public String getHTMLHelpText() {
			return "<strong>GrayBinaryChromosome</strong> Similar to StandardBinaryChromosome, " +
					"except that numeric values are encoded to binary strings using a Gray code, " +
					"instead of the standard 'high order' bit ordering. " +
					"Gray codes have generally been found to give better performance for search representations, " +
					"since numeric values that are close together are more likely to be fewer mutations away from each other.";
		}	
	}

}