/*******************************************************************************
* 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.project;
import java.awt.Toolkit;
import java.awt.event.KeyEvent;
import java.io.File;
import java.security.InvalidParameterException;
import javax.swing.ActionMap;
import javax.swing.JOptionPane;
import javax.swing.KeyStroke;
import edu.yu.einstein.genplay.core.IO.fileSorter.ExternalSortAdapter;
import edu.yu.einstein.genplay.gui.action.TrackListActionWorker;
import edu.yu.einstein.genplay.gui.dialog.exceptionDialog.WarningReportDialog;
import edu.yu.einstein.genplay.util.FileChooser;
import edu.yu.einstein.genplay.util.Utils;
/**
* Sorts the specified genomic file by chromosome, start and then stop position
* @author Julien Lajugie
*/
public class PASortFile extends TrackListActionWorker<Boolean> {
private static final long serialVersionUID = -1635888549644450204L; // generated serial ID
private static final String DESCRIPTION = "Sort the specified file by chromosome, start and stop position"; // tooltip
private static final int MNEMONIC = KeyEvent.VK_R; // mnemonic key
private static final String ACTION_NAME = "Sort File"; // action name
/**
* action accelerator {@link KeyStroke}
*/
public static final KeyStroke ACCELERATOR = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
/**
* key of the action in the {@link ActionMap}
*/
public static final String ACTION_KEY = PASortFile.class.getName();
/**
* Creates an instance of {@link PASortFile}
*/
public PASortFile() {
super();
putValue(NAME, ACTION_NAME);
putValue(ACTION_COMMAND_KEY, ACTION_KEY);
putValue(SHORT_DESCRIPTION, DESCRIPTION);
putValue(MNEMONIC_KEY, MNEMONIC);
putValue(ACCELERATOR_KEY, ACCELERATOR);
}
@Override
protected void doAtTheEnd(Boolean actionResult) {
if ((actionResult != null) && (actionResult)) {
JOptionPane.showMessageDialog(getRootPane(), "File Sorted Successfully");
}
}
@Override
protected Boolean processAction() throws Exception {
File selectedFile = FileChooser.chooseFile(getRootPane(), FileChooser.OPEN_FILE_MODE, "Select File to Sort", Utils.getSortableFileFilters(), false);
if (selectedFile != null) {
if (!Utils.cancelBecauseFileExist(getRootPane(), ExternalSortAdapter.generateOutputFile(selectedFile))) {
notifyActionStart("Sorting File", 1, false);
try {
ExternalSortAdapter.externalSortGenomicFile(selectedFile);
return true;
} catch (InvalidParameterException e) {
WarningReportDialog.getInstance().addMessage(e.getMessage());
WarningReportDialog.getInstance().showDialog(getRootPane());
}
}
}
return false;
}
}