MGAVCFStatistics.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.event.KeyEvent;

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

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFStatistics.VCFFileMixStatistic;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFStatistics.VCFFileStatistics;
import edu.yu.einstein.genplay.core.multiGenome.operation.VCF.MGOVCFStatisticsSingleFile;
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.statistics.MGStatisticsDialog;
import edu.yu.einstein.genplay.gui.dialog.multiGenomeDialog.trackAction.ExportSettings;
import edu.yu.einstein.genplay.gui.track.layer.variantLayer.MultiGenomeDrawer;
import edu.yu.einstein.genplay.gui.track.layer.variantLayer.VariantLayer;


/**
 * @author Nicolas Fourel
 */
public class MGAVCFStatistics extends TrackListActionWorker<VCFFileStatistics> {

	private static final long serialVersionUID = 6498078428524511709L;	// generated ID
	private static final String 	DESCRIPTION =
			"Generates statistics for a track" + HELP_TOOLTIP_SUFFIX;			// tooltip
	private static final int 		MNEMONIC = KeyEvent.VK_M; 					// mnemonic key
	private static		 String 	ACTION_NAME = "Generate track statistics";	// action name
	private static final String		HELP_URL = "http://genplay.einstein.yu.edu/wiki/index.php/Documentation#Generate_track_statistics";


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

	private MGOVCFStatisticsSingleFile operation;


	/**
	 * Creates an instance of {@link MGAVCFStatistics}.
	 */
	public MGAVCFStatistics() {
		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);
	}


	@Override
	protected void doAtTheEnd(VCFFileStatistics actionResult) {
		if (actionResult != null) {
			actionResult.processStatistics();
			VariantLayer selectedLayer = (VariantLayer) getValue("Layer");
			selectedLayer.getGenomeDrawer().setStatistics(actionResult);
			MGStatisticsDialog dialog = new MGStatisticsDialog(actionResult);
			dialog.show(getRootPane());
		} else {
			System.out.println("No statistic generated");
		}
	}


	@Override
	protected VCFFileStatistics processAction() {
		ProjectManager projectManager = ProjectManager.getInstance();
		VCFFileStatistics result = null;
		if (projectManager.isMultiGenomeProject()) {
			// Get layer information
			VariantLayer selectedLayer = (VariantLayer) getValue("Layer");
			MultiGenomeDrawer genomeDrawer = selectedLayer.getGenomeDrawer();
			if (genomeDrawer.getStatistics() == null) {
				// Create the export settings
				ExportSettings settings = new ExportSettings(selectedLayer);
				// Create the operation
				operation = new MGOVCFStatisticsSingleFile();
				operation.initializeEngine(settings.getFileMap(), settings.getVariationMap(), settings.getFilterList(), MGDisplaySettings.getInstance().includeReferences(), MGDisplaySettings.getInstance().includeNoCall());
				if (operation.isSingleExport()) {
					// Notifies the action
					notifyActionStart(ACTION_NAME, 1, false);
					// Run the operation
					try {
						operation.compute();
					} catch (Exception e) {
						ExceptionManager.getInstance().caughtException(e);
					}
					// Return the result
					result = new VCFFileMixStatistic(operation.getNativeStatistics(), operation.getNewStatistics());
				} else {
					JOptionPane.showMessageDialog(getRootPane(), "Statistics can be generated with data from only one file.", "Statistics report error", JOptionPane.INFORMATION_MESSAGE);
				}
			} else {
				result = genomeDrawer.getStatistics();
			}
		}
		return result;
	}
}