/*******************************************************************************
* 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.export;
import java.awt.event.KeyEvent;
import java.io.File;
import java.util.concurrent.CountDownLatch;
import javax.swing.ActionMap;
import javax.swing.JOptionPane;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.operation.ExportEngine;
import edu.yu.einstein.genplay.core.multiGenome.operation.VCF.MGOVCFExportSingleFile;
import edu.yu.einstein.genplay.exception.ExceptionManager;
import edu.yu.einstein.genplay.gui.MGDisplaySettings.MGDisplaySettings;
import edu.yu.einstein.genplay.gui.action.TrackListActionWorker;
import edu.yu.einstein.genplay.gui.dialog.multiGenomeDialog.trackAction.ExportSettings;
/**
* @author Nicolas Fourel
* @version 0.1
*/
public class MGAVCFExport extends TrackListActionWorker<Boolean> {
private static final long serialVersionUID = 6498078428524511709L; // generated ID
private static final String DESCRIPTION =
"Exports the visible variations into a VCF file" + HELP_TOOLTIP_SUFFIX; // tooltip
private static final int MNEMONIC = KeyEvent.VK_M; // mnemonic key
private static String ACTION_NAME = "Export as VCF"; // action name
private static final String HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Export_as_VCF";
/**
* key of the action in the {@link ActionMap}
*/
public static final String ACTION_KEY = "Multi Genome VCF Export";
private final File file;
private final ExportSettings settings;
private boolean success;
/**
* Creates an instance of {@link MGAVCFExport}.
* @param file output file to export
* @param settings the settings for the export
*/
public MGAVCFExport(File file, ExportSettings settings) {
super();
putValue(NAME, ACTION_NAME);
putValue(ACTION_COMMAND_KEY, ACTION_KEY);
putValue(SHORT_DESCRIPTION, DESCRIPTION);
putValue(MNEMONIC_KEY, MNEMONIC);
putValue(HELP_URL_KEY, HELP_URL);
this.file = file;
this.settings = settings;
}
@Override
protected void doAtTheEnd(Boolean actionResult) {
success = actionResult;
if (latch != null) {
latch.countDown();
}
}
/**
* @return true if the action has been correctly finish, false otherwise
*/
public boolean hasBeenDone () {
return success;
}
@Override
protected Boolean processAction() throws Exception {
ProjectManager projectManager = ProjectManager.getInstance();
if (projectManager.isMultiGenomeProject()) {
// Declare the export engine
ExportEngine exportEngine = null;
// Initialize the engine if the export is about only one VCF file
int fileNumber = settings.getFileNumber();
if (fileNumber == 1) {
exportEngine = new MGOVCFExportSingleFile();
} else if (fileNumber > 1) {
JOptionPane.showMessageDialog(getRootPane(), "Cannot export data from more than one VCF.\nMore support coming soon.", "Export error", JOptionPane.INFORMATION_MESSAGE);
} else {
System.err.println("PAMultiGenomeExport.processAction(): Number of file required is not valid: " + fileNumber);
}
// Runs the export process
if ((file != null) && (exportEngine != null)) {
// Notifies the action
notifyActionStart(ACTION_NAME, 1, false);
exportEngine.initializeEngine(settings.getFileMap(), settings.getVariationMap(), settings.getFilterList(), MGDisplaySettings.getInstance().includeReferences(), MGDisplaySettings.getInstance().includeNoCall());
exportEngine.setPath(file.getPath());
try {
exportEngine.compute();
return true;
} catch (Exception e) {
ExceptionManager.getInstance().caughtException(e);
}
}
}
return false;
}
/**
* @param latch the latch to set
*/
public void setLatch(CountDownLatch latch) {
this.latch = latch;
}
}