GenomeListLoader.java

/*******************************************************************************
 * GenPlay, Einstein Genome Analyzer
 * Copyright (C) 2009, 2014 Albert Einstein College of Medicine
 * 
 * This program 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.
 * 
 * This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 * Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
 *          Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
 *          Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
 * 
 * Website: <http://genplay.einstein.yu.edu>
 ******************************************************************************/
package edu.yu.einstein.genplay.core.IO.genomeListLoader;

import java.util.ArrayList;
import java.util.List;

import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;

import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.chromosome.SimpleChromosome;
import edu.yu.einstein.genplay.dataStructure.genome.Assembly;
import edu.yu.einstein.genplay.dataStructure.genome.Clade;
import edu.yu.einstein.genplay.dataStructure.genome.Genome;

/**
 * This class picks up genome information from xml files.
 * @author Nicolas Fourel
 */
public class GenomeListLoader extends DefaultHandler {

	private Clade 					clade;			// The clade
	private Genome 					genome;			// The genome
	private Assembly 				assembly;		// The assembly
	private final List<Chromosome> 		chromosomeList;	// The chromosome list


	/**
	 * Constructor of {@link GenomeListLoader}
	 */
	protected GenomeListLoader() {
		super();
		chromosomeList = new ArrayList<Chromosome>();
	}


	/**
	 * This method associates clade information to make a full clade object.
	 */
	protected void computeClade () {
		assembly.setChromosomeList(chromosomeList);
		genome.getAssemblyList().put(assembly.getIndexName(), assembly);
		clade.getGenomeList().put(genome.getName(), genome);
	}


	/**
	 * @return the clade
	 */
	protected Clade getClade() {
		return clade;
	}


	@Override
	public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException {
		if (qName.equalsIgnoreCase("assembly")) {
			clade = new Clade(attributes.getValue("clade"));
			genome = new Genome(attributes.getValue("genome"));
			assembly = new Assembly(attributes.getValue("name"), attributes.getValue("date"));
		} else if (qName.equalsIgnoreCase("chromosome")) {
			chromosomeList.add(new SimpleChromosome(attributes.getValue("name"), Integer.parseInt(attributes.getValue("length").trim())));
		}
	}
}