VariantInfo.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.dialog.multiGenomeDialog.variantInformation;

import java.util.ArrayList;
import java.util.List;

import javax.swing.JPanel;

import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFLine;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFHeader;
import edu.yu.einstein.genplay.util.Utils;

/**
 * @author Nicolas Fourel
 * @version 0.1
 */
public class VariantInfo {

	private PanelInformation 		pane;			// pane containing information
	private final String 			title;			// header of the pane
	private List<String> 			keys;			// key values
	private List<String> 			values;			// values
	private List<String> 			description;	// keys description


	/**
	 * Constructor of {@link VariantInfo}
	 * @param info string containing information about the INFO field of the variant information
	 */
	protected VariantInfo (VCFLine line) {
		title = "Information";

		if (line == null) {
			pane = new PanelInformation(title, null, null, null);
		} else {
			keys = new ArrayList<String>();
			values = new ArrayList<String>();
			description = new ArrayList<String>();

			String[] elements = Utils.split(line.getINFO(), ';');

			for (String element: elements) {
				String[] map = Utils.split(element, '=');
				String key = map[0];
				String value = null;
				if (map.length > 1) {
					value = map[1];
				}
				keys.add(key);
				values.add(value);
			}

			VCFHeader header = null;
			if (line.getGenomeIndexer() instanceof VCFHeader) {
				header = (VCFHeader) line.getGenomeIndexer();
			}
			for (String key: keys) {
				String desc = "-";
				if (header != null) {
					try {
						desc = header.getInfoHeaderFromID(key).getDescription();
					} catch (Exception e) {
						desc = "not defined in the header.";
					}
				}
				description.add(desc);
			}

			pane = new PanelInformation(title, keys, values, description);
		}
	}


	/**
	 * @return the scrollpane containing the information
	 */
	protected JPanel getPane () {
		return pane;
	}

}