CustomFileComboBoxMG.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.gui.customComponent.customComboBox;

import java.io.File;

import javax.swing.JOptionPane;

import edu.yu.einstein.genplay.gui.action.actionWaiting.ActionWaiter;
import edu.yu.einstein.genplay.gui.action.actionWaiting.SwingWorkerActionWaiting;
import edu.yu.einstein.genplay.gui.action.multiGenome.VCFAction.MGAVCFToTBI;
import edu.yu.einstein.genplay.gui.customComponent.customComboBox.customComboBoxEvent.CustomComboBoxListener;
import edu.yu.einstein.genplay.util.Utils;

/**
 * 
 * @author Nicolas Fourel
 * @version 0.1
 */
public class CustomFileComboBoxMG extends CustomFileComboBox implements ActionWaiter {

	/**
	 * Generated default serial version
	 */
	private static final long serialVersionUID = -6704320621396590562L;

	private MGAVCFToTBI action;
	private final Object owner;


	/**
	 * Constructor of {@link CustomFileComboBoxMG}
	 */
	public CustomFileComboBoxMG () {
		super();
		owner = null;
	}


	/**
	 * Constructor of {@link CustomFileComboBoxMG}
	 * @param owner the owner object of the box
	 */
	public CustomFileComboBoxMG (Object owner) {
		super();
		this.owner = owner;
	}


	@Override
	protected File actionPostSelection (File file) {
		File result = file;
		if (file != null) {
			String ext = Utils.getExtension(file);
			if (ext.equals("vcf")) {
				result = null;
				File bgzFile = getFile(file, "gz");
				File tbiFile = getFile(file, "gz.tbi");
				if (bgzFile.exists() && tbiFile.exists()) {
					result = bgzFile;
				} else
					if (showMessage()) {
						action = new MGAVCFToTBI(file);
						action.setLoadingPassBy(true);
						SwingWorkerActionWaiting swAction = new SwingWorkerActionWaiting(this, action);
						swAction.execute();
					}
			}
		}
		return result;
	}


	/**
	 * @param file	a file
	 * @param ext	a extension (without dot)
	 * @return a file adding the extension to the given file
	 */
	private File getFile (File file, String ext) {
		String path = file.getPath() + "." + ext;
		return new File(path);
	}


	/**
	 * Show a message dialog to ask the user whether he wants to compress/index the file or not.
	 * @return true if the user wants to compress/index the VCF, false otherwise.
	 */
	private boolean showMessage () {
		Object[] options = {"Yes", "No"};

		String title = "Do you want GenPlay to compress and index your file?";
		String message = "The selected file is a VCF file (.vcf).\n" +
				"GenPlay Multi Genome works with BGZIP compressed VCF files (.vcf.gz) and their Tabix indexed files (.tbi).\n" +
				"GenPlay can create those two files at the same location as the selected file.";

		int n = JOptionPane.showOptionDialog(null,
				message,
				title,
				JOptionPane.YES_NO_OPTION,
				JOptionPane.QUESTION_MESSAGE,
				null,
				options,
				options[0]);

		if (n == JOptionPane.YES_OPTION) {
			return true;
		}
		return false;
	}


	@Override
	public void doAtTheEnd() {
		addElementToCombo(action.getBgzipFile());
		if (owner != null) {
			lastEvent.setElement(action.getBgzipFile());
			if (owner instanceof CustomComboBoxListener) {
				((CustomComboBoxListener) owner).customComboBoxChanged(lastEvent);
			}
		}
	}

}