Assembly.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.dataStructure.genome;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Locale;

import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.exception.ExceptionManager;

/**
 * This class contains assembly information
 * @author Nicolas Fourel
 */
public class Assembly implements Serializable {

	private static final long serialVersionUID = -1933285290898527392L;	// generated ID
	private static final int  SAVED_FORMAT_VERSION_NUMBER = 0;			// saved format version
	private List<Chromosome>		chromosomeList;
	private String 					name;
	private Date 					date;
	private String 					indexName;
	private SimpleDateFormat 		sdf;
	private long 					genomeLength = 0;


	/**
	 * Method used for serialization
	 * @param out
	 * @throws IOException
	 */
	private void writeObject(ObjectOutputStream out) throws IOException {
		out.writeInt(SAVED_FORMAT_VERSION_NUMBER);
		out.writeObject(chromosomeList);
		out.writeObject(name);
		out.writeObject(date);
		out.writeObject(indexName);
		out.writeObject(sdf);
		out.writeLong(genomeLength);
	}


	/**
	 * Method used for unserialization
	 * @param in
	 * @throws IOException
	 * @throws ClassNotFoundException
	 */
	@SuppressWarnings("unchecked")
	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
		in.readInt();
		chromosomeList = (List<Chromosome>) in.readObject();
		name = (String) in.readObject();
		date = (Date) in.readObject();
		indexName = (String) in.readObject();
		sdf = (SimpleDateFormat) in.readObject();
		genomeLength = in.readLong();
	}


	/**
	 * Constructor of {@link Assembly}
	 * @param name	name of the assembly
	 * @param date	date of build of the assembly
	 */
	public Assembly (String name, String date) {
		chromosomeList = new ArrayList<Chromosome>();
		this.name = name;
		sdf = new SimpleDateFormat("MM yyyy", Locale.US);
		try {
			this.date = sdf.parse(date);
			sdf.applyPattern("yyyy MM");
		} catch (ParseException e) {
			ExceptionManager.getInstance().caughtException(e);
		}
		sdf.applyPattern("yyyy MM ");
		indexName = sdf.format(this.date);
		indexName = indexName.concat(name);
	}


	/**
	 * @return the list of chromosome
	 */
	public List<Chromosome> getChromosomeList() {
		return chromosomeList;
	}


	/**
	 * @param chromosomeList the new chromosome list
	 */
	public void setChromosomeList(List<Chromosome> chromosomeList) {
		this.chromosomeList = chromosomeList;
		computeGenomeSize();
	}


	/**
	 * Compute the size of the genome
	 */
	private synchronized void computeGenomeSize() {
		genomeLength = 0;
		for (Chromosome currenChromosome: chromosomeList) {
			genomeLength += currenChromosome.getLength();
		}
	}


	/**
	 * @return the assembly name for display
	 */
	public String getDisplayName () {
		sdf.applyPattern("MMM yyyy (");
		return sdf.format(this.date).concat(name).concat(")");
	}



	/**
	 * @return the assembly name
	 */
	public String getName() {
		return name;
	}


	/**
	 * @return the assembly date
	 */
	public Date getDate() {
		return date;
	}


	/**
	 * @return the full name of the assembly: name (mm/yyyy)
	 */
	public String getIndexName () {
		return indexName;
	}


	/**
	 * @return the length of the genome in bp
	 */
	public long getGenomeLength() {
		return genomeLength;
	}


	@Override
	public String toString() {
		return getDisplayName();
	}
}