SimpleChromosomeWindow.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.chromosomeWindow;

import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.Serializable;
import java.text.NumberFormat;
import java.text.ParseException;

import edu.yu.einstein.genplay.exception.exceptions.ChromosomeWindowException;


/**
 * A simple implementation of the {@link ChromosomeWindow} interface.
 * {@link SimpleChromosomeWindow} objects are immutable.
 * @author Julien Lajugie
 */
public final class SimpleChromosomeWindow extends AbstractChromosomeWindow implements ChromosomeWindow, Serializable, Comparable<ChromosomeWindow> {

	/**  Generated serial ID */
	private static final long serialVersionUID = -6548181911063983578L;

	/**  Version number of the class */
	private static final transient int CLASS_VERSION_NUMBER = 0;

	/** Start position of the window */
	private final int start;

	/** Stop position of the window */
	private final int stop;


	/**
	 * Creates an instance of {@link SimpleChromosomeWindow}.
	 * @param start a window start
	 * @param stop a window stop
	 */
	public SimpleChromosomeWindow(int start, int stop) {
		this.start = start;
		this.stop = stop;
	}


	/**
	 * Creates an instance of {@link SimpleChromosomeWindow} from a String.
	 * @param windowStr String following the format "startpos-stoppos" (example: "100-500")
	 * @throws ChromosomeWindowException
	 */
	public SimpleChromosomeWindow(String windowStr) throws ChromosomeWindowException {
		String startStr = windowStr.substring(0, windowStr.lastIndexOf("-"));
		String stopStr = windowStr.substring(windowStr.lastIndexOf("-") + 1);
		try {
			start = (NumberFormat.getInstance().parse(startStr.trim())).intValue();
		} catch (ParseException e) {
			throw new ChromosomeWindowException("Invalid start position.");
		}
		try {
			stop = (NumberFormat.getInstance().parse(stopStr.trim())).intValue();
		} catch (ParseException e) {
			throw new ChromosomeWindowException("Invalid stop position.");
		}
		if (start > stop) {
			throw new ChromosomeWindowException("Invalid window, the start position must be greatter than the stop position");
		}
	}


	/**
	 * Creates an instance of {@link SimpleChromosomeWindow} from a String representing the start position and a string representing the stop position.
	 * @param startStr string representing the start position
	 * @param stopStr string representing the stop position
	 * @throws ChromosomeWindowException
	 */
	public SimpleChromosomeWindow(String startStr, String stopStr) throws ChromosomeWindowException {
		this(startStr + "-" + stopStr);
	}


	/**
	 * @return the start
	 */
	@Override
	public int getStart() {
		return start;
	}


	/**
	 * @return the stop
	 */
	@Override
	public int getStop() {
		return stop;
	}


	/**
	 * Method used for deserialization
	 * @param in
	 * @throws IOException
	 * @throws ClassNotFoundException
	 */
	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
		// read the version number of the object
		in.readInt();
		// read the final fields
		in.defaultReadObject();
	}


	/**
	 * Method used for serialization
	 * @param out
	 * @throws IOException
	 */
	private void writeObject(java.io.ObjectOutputStream out) throws IOException {
		// write the format version number of the object
		out.writeInt(CLASS_VERSION_NUMBER);
		// write the final fields
		out.defaultWriteObject();
	}
}