MGSAllele.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.multiGenome.data.synchronization;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;

import edu.yu.einstein.genplay.core.comparator.MGOffsetComparator;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.offsetList.IntArrayAsOffsetList;


/**
 * @author Nicolas Fourel
 * @version 0.1
 */
public class MGSAllele implements Serializable {

	/** Default serial version ID */
	private static final long serialVersionUID = -3160689645132714945L;
	private static final int  		SAVED_FORMAT_VERSION_NUMBER = 0;		// saved format version
	private List<List<MGSOffset>> 	offsetList;								// List of offset organized by chromosome


	/**
	 * Constructor of {@link MGSAllele}
	 */
	public MGSAllele () {
		offsetList = new ArrayList<List<MGSOffset>>();
		int chromosomeListSize = ProjectManager.getInstance().getProjectChromosomes().getChromosomeList().size();
		for (int i = 0; i < chromosomeListSize; i++) {
			offsetList.add(new IntArrayAsOffsetList());
		}
	}


	/**
	 * Compacts the list of {@link MGSOffset}
	 */
	public void compact () {
		int projectChromosomeSize = ProjectManager.getInstance().getProjectChromosomes().size();
		for (int i = 0; i < projectChromosomeSize; i++) {
			((IntArrayAsOffsetList)offsetList.get(i)).compact();
		}
	}


	/**
	 * @return the offsetList
	 */
	public List<List<MGSOffset>> getOffsetList() {
		return offsetList;
	}


	/**
	 * Method used for unserialization
	 * @param in
	 * @throws IOException
	 * @throws ClassNotFoundException
	 */
	@SuppressWarnings("unchecked")
	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
		in.readInt();
		offsetList = (List<List<MGSOffset>>) in.readObject();
	}


	/**
	 * @param offsetList the offsetList to set
	 */
	public void setOffsetList(List<List<MGSOffset>> offsetList) {
		this.offsetList = offsetList;
	}


	/**
	 * Show the information of the {@link MGSAllele}
	 */
	public void show () {
		int projectChromosomeSize = ProjectManager.getInstance().getProjectChromosomes().size();
		for (int i = 0; i < projectChromosomeSize; i++) {
			if (offsetList.get(i).size() > 0) {
				int cpt = 0;
				for (MGSOffset offset: offsetList.get(i)) {
					if (cpt < 10) {
						offset.show();
						cpt++;
					}
				}
			}
		}
	}


	/**
	 * Sorts the list of offset for every chromosome.
	 * The sorting is done with the {@link MGOffsetComparator} comparator.
	 */
	public void sort () {
		int chromosomeListSize = ProjectManager.getInstance().getProjectChromosomes().getChromosomeList().size();
		MGOffsetComparator comparator = new MGOffsetComparator();
		for (int i = 0; i < chromosomeListSize; i++) {
			Collections.sort(offsetList.get(i), comparator);
		}
	}


	/**
	 * Method used for serialization
	 * @param out
	 * @throws IOException
	 */
	private void writeObject(ObjectOutputStream out) throws IOException {
		out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
		out.writeObject(offsetList);
	}
}