MGAVCFToTBI.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.action.multiGenome.VCFAction;

import java.awt.Toolkit;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.io.File;

import javax.swing.ActionMap;
import javax.swing.JOptionPane;
import javax.swing.KeyStroke;

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.operation.convert.MGOBGZIPCompression;
import edu.yu.einstein.genplay.core.multiGenome.operation.convert.MGOTBIIndex;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.gui.action.TrackListAction;
import edu.yu.einstein.genplay.util.Utils;


/**
 * Updates the tracks after important changes as:
 * - validating the multi genome properties dialog
 * - changing chromosome
 * 
 * The updates consist in managing in the following order:
 * - the SNP (if required)
 * - the filters (if required)
 * - the track display
 * 
 * @author Nicolas Fourel
 * @author Julien Lajugie
 * @version 0.1
 */
public final class MGAVCFToTBI extends TrackListAction {

	private static final 	long serialVersionUID = -6475180772964541278L; 			// generated ID
	private static final 	String ACTION_NAME = "VCF Convertion & Indexation";		// action name
	private static final 	String DESCRIPTION = "Convert and index a VCF file"; 	// tooltip
	private static final 	int 	MNEMONIC = KeyEvent.VK_P; 						// mnemonic key

	/**
	 * action accelerator {@link KeyStroke}
	 */
	public static final KeyStroke 	ACCELERATOR = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());


	/**
	 * key of the action in the {@link ActionMap}
	 */
	public static final String ACTION_KEY = "PAMultiGenomeVCFToTBI";

	private final File vcfFile;		// the vcf file
	private File bgzipFile;			// the gz file
	private File tbiFile;			// the tbi file
	private boolean loadingPassBy;


	/**
	 * Creates an instance of {@link MGAVCFToTBI}
	 * @param file the vcf file to compress and to index
	 */
	public MGAVCFToTBI(File file) {
		super();
		putValue(NAME, ACTION_NAME);
		putValue(ACTION_COMMAND_KEY, ACTION_KEY);
		putValue(SHORT_DESCRIPTION, DESCRIPTION);
		putValue(MNEMONIC_KEY, MNEMONIC);
		vcfFile = file;
		bgzipFile = null;
		tbiFile = null;
		loadingPassBy = false;
	}


	@Override
	public void trackListActionPerformed(ActionEvent arg0) {
		if (ProjectManager.getInstance().isMultiGenomeProject() || loadingPassBy) {		// if it is a multi genome project
			// Compress the VCF
			try {
				compression();
			} catch (Exception e) {
				ExceptionManager.getInstance().caughtException(e);
			}

			// Index the VCF
			try {
				indexation();
			} catch (Exception e) {
				ExceptionManager.getInstance().caughtException(e);
			}

			// Many data has been loaded, removed, garbage collecting free some memory
			Utils.garbageCollect();
		}
	}


	/**
	 * Compress the VCF with BGZIP
	 * @throws Exception
	 */
	private void compression () throws Exception {

		MGOBGZIPCompression operation = new MGOBGZIPCompression(vcfFile);
		boolean success = false;
		try {
			success = operation.compute();
		} catch (Exception e) {
			ExceptionManager.getInstance().caughtException(e);
		}

		if (!success) {
			JOptionPane.showMessageDialog(null, "The VCF extension has not been found.\nThe file to compress must be a VCF file.\nThe file will not be compressed.", "Compression error.", JOptionPane.INFORMATION_MESSAGE);
		}


		bgzipFile = operation.getBgzFile();
	}


	/**
	 * @return the bgzipFile
	 */
	public File getBgzipFile() {
		return bgzipFile;
	}


	/**
	 * @return the tbiFile
	 */
	public File getTbiFile() {
		return tbiFile;
	}


	/**
	 * @return the vcfFile
	 */
	public File getVcfFile() {
		return vcfFile;
	}


	/**
	 * Index the compressed VCF with Tabix
	 * @throws Exception
	 */
	private void indexation () throws Exception {
		if (bgzipFile != null) {
			MGOTBIIndex operation = new MGOTBIIndex(bgzipFile);
			boolean success = false;
			try {
				success = operation.compute();
			} catch (Exception e) {
				ExceptionManager.getInstance().caughtException(e);
			}

			if (!success) {
				JOptionPane.showMessageDialog(null, "The BGZIP extension has not been found.\nThe file will not be indexed.", "Indexing error.", JOptionPane.INFORMATION_MESSAGE);
			}

			tbiFile = operation.getTbiFile();
		}
	}


	/**
	 * @param loadingPassBy the loadingPassBy to set
	 */
	public void setLoadingPassBy(boolean loadingPassBy) {
		this.loadingPassBy = loadingPassBy;
	}
}