SequenceEncoderFactory.java

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

package bio.pih.genoogle.encoder;

import org.apache.log4j.Logger;

import bio.pih.genoogle.seq.Alphabet;
import bio.pih.genoogle.seq.AminoAcidAlphabet;
import bio.pih.genoogle.seq.DNAAlphabet;
import bio.pih.genoogle.seq.RNAAlphabet;
import bio.pih.genoogle.seq.Reduced_AA_8_Alphabet;

public class SequenceEncoderFactory {

	static Logger logger = Logger.getLogger(SequenceEncoderFactory.class.getCanonicalName());

	private static DNASequenceEncoder[] dnaEncoders = new DNASequenceEncoder[17];
	private static RNASequenceEncoder[] rnaEncoders = new RNASequenceEncoder[17];
	private static AminoAcidsSequenceEncoder[] aaEncoder = new AminoAcidsSequenceEncoder[17];
	private static Reduced_AA_8_SequenceEncoder[] reduced_AA_8 = new Reduced_AA_8_SequenceEncoder[17];
	
	/**
	 * @param subSequenceLength
	 *            length of the subSequences.
	 * @return singleton of the {@link DNASequenceEncoderToInteger}
	 */
	public static SequenceEncoder getEncoder(Alphabet alphabet, int subSequenceLength) {
		if (subSequenceLength < 1 || subSequenceLength > 16) {
			throw new IndexOutOfBoundsException("Invalid sub sequence length '" + subSequenceLength + "'");
		}
			
		if (alphabet == RNAAlphabet.SINGLETON) {
			rnaEncoders[subSequenceLength] = new RNASequenceEncoder(subSequenceLength);
			return rnaEncoders[subSequenceLength];		
		} 
				
		if (alphabet == DNAAlphabet.SINGLETON) {
			dnaEncoders[subSequenceLength] = new DNASequenceEncoder(subSequenceLength);
			return dnaEncoders[subSequenceLength];
		}
		
		if (alphabet == AminoAcidAlphabet.SINGLETON) {
			aaEncoder[subSequenceLength] = new AminoAcidsSequenceEncoder(subSequenceLength);
			return aaEncoder[subSequenceLength];
		}
			
		if (alphabet == Reduced_AA_8_Alphabet.SINGLETON) {
			reduced_AA_8[subSequenceLength] = new Reduced_AA_8_SequenceEncoder(subSequenceLength);
			return reduced_AA_8[subSequenceLength];
		}
		
		return null;
	}	
}