ChromosomeFactory.java

/**
 * Copyright Copyright 2014 Simon Andrews
 *
 *    This file is part of BamQC.
 *
 *    BamQC is free software; you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation; either version 3 of the License, or
 *    (at your option) any later version.
 *
 *    BamQC is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with BamQC; if not, write to the Free Software
 *    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 */
/*
 * Changelog: 
 * - Piero Dalle Pezze: Optimised data structures (removed unneeded concurrency), optimised algorithm.
 * - Simon Andrews: Class creation.
 */
package uk.ac.babraham.BamQC.DataTypes.Genome;

import java.util.HashMap;

/**
 * 
 * @author Simon Andrews
 * @author Piero Dalle Pezze
 *
 */
public class ChromosomeFactory {

	HashMap<String,Chromosome> chromosomes = new HashMap<String, Chromosome>();
	
	public Chromosome getChromosome (String name) {
		
		if (name.equals("*")) {
			return null;
		}
		if (!chromosomes.containsKey(name)) {
			chromosomes.put(name,new Chromosome(name));
		}
		return chromosomes.get(name);
	}
	
	public Chromosome [] getAllChromosomes () {
		return chromosomes.values().toArray(new Chromosome[0]);
	}
	
	
}