DNAAlphabet.java

/*
 * Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br)
 * Copyright (C) 2008,2009, 2010, 2011, 2012  Felipe Fernandes Albrecht (felipe.albrecht@gmail.com)
 *
 * For further information check the LICENSE file.
 */

package bio.pih.genoogle.seq;

import java.util.Arrays;
import java.util.BitSet;

public class DNAAlphabet implements Alphabet {

	private static final long serialVersionUID = 4036186830403094421L;

	public static Alphabet SINGLETON = new DNAAlphabet();

	private static final int size = 4;

	public static char a = 'a';
	public static char c = 'c';
	public static char g = 'g';
	public static char t = 't';

	
	private static final char[] lLetters = { 'a', 'c', 'g', 't' };
	private static final char[] uLetters = { 'A', 'C', 'G', 'T' };
	private static final char[] lSpecialLetters = { 'r', 'y', 'k', 'm', 's', 'w', 'b', 'd', 'h', 'v', 'n', 'x' };
	private static final char[] uSpecialLetters = { 'R', 'Y', 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N', 'X' };
	private static final char[] allLetters = { 'a', 'c', 'g', 't', 'A', 'C', 'G', 'T', 'r', 'y', 'k', 'm', 's', 'w',
			'b', 'd', 'h', 'v', 'n', 'x', 'R', 'Y', 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N', 'X' };
	
	static {
		Arrays.sort(lLetters);
		Arrays.sort(uLetters);
		Arrays.sort(lSpecialLetters);
		Arrays.sort(uSpecialLetters);
		Arrays.sort(allLetters);
	}
	
	private static final BitSet lLettersBitSet = new BitSet();
	static {
		for (char c : lLetters) {
			lLettersBitSet.set(c);
		}		
	}
	
	private static final BitSet uLettersBitSet = new BitSet();
	static {
		for (char c : uLetters) {
			uLettersBitSet.set(c);
		}		
	}
	
	private static final BitSet lSpecialLettersBitSet = new BitSet();
	static {
		for (char c : lSpecialLetters) {
			lSpecialLettersBitSet.set(c);
		}		
	}

	private static final BitSet uSpecialLettersBitSet = new BitSet();
	static {
		for (char c : uSpecialLetters) {
			uSpecialLettersBitSet.set(c);
		}		
	}
	
	private static final BitSet allLettersBitSet = new BitSet();
	static {
		for (char c : allLetters) {
			allLettersBitSet.set(c);
		}		
	}

	private DNAAlphabet() {
	}

	@Override
	public String getName() {
		return "DNA";
	}

	@Override
	public int getSize() {
		return size;
	}

	@Override
	public boolean isValid(char c) {
		if (allLettersBitSet.get(c)) {
			return true;
		}
		return false;
	}

	@Override
	public char[] getLetters() {
		return lLetters.clone();
	}
	
	@Override
	public String toString() {
		return "DNA Alphabet";
	}
}