GeneralPanel.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.MGProperties;

import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.util.List;
import java.util.Map;

import javax.swing.JLabel;
import javax.swing.JPanel;

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFFile;
import edu.yu.einstein.genplay.core.multiGenome.utils.FormattedMultiGenomeName;
import edu.yu.einstein.genplay.gui.dialog.multiGenomeDialog.vcfLoader.VCFData;

/**
 * @author Nicolas Fourel
 * @version 0.1
 */
class GeneralPanel extends JPanel {

	/** Generated serial version ID */
	private static final long serialVersionUID = 538823729476349982L;


	/**
	 * Constructor of {@link GeneralPanel}
	 */
	protected GeneralPanel () {
		// Layout settings
		GridBagLayout layout = new GridBagLayout();
		setLayout(layout);
		GridBagConstraints gbc = new GridBagConstraints();
		gbc.anchor = GridBagConstraints.FIRST_LINE_START;
		gbc.weightx = 1;
		gbc.weighty = 0;

		// Global information header
		gbc.gridx = 0;
		gbc.gridy = 0;
		gbc.insets = PropertiesDialog.FIRST_TITLE_INSET;
		add(Utils.getTitleLabel("Global project information"), gbc);

		// Global information
		gbc.gridy = 1;
		gbc.insets = PropertiesDialog.PANEL_INSET;
		add(getGlobalInformationPanel(), gbc);

		// VCF mapping information header
		gbc.gridy = 2;
		gbc.insets = PropertiesDialog.TITLE_INSET;
		add(Utils.getTitleLabel("VCF files mapping information"), gbc);

		// VCF mapping information
		gbc.gridy = 3;
		gbc.weighty = 1;
		gbc.insets = PropertiesDialog.PANEL_INSET;
		add(getVCFMappingPanel(), gbc);
	}


	/**
	 * Creates the panel that contains all global information about the project
	 * @return the panel
	 */
	private JPanel getGlobalInformationPanel () {
		// The main panel
		JPanel panel = new JPanel();

		// Key labels
		JLabel jlKeyProjectName = new JLabel("Project name: ");
		JLabel jlKeyAssembly = new JLabel("Assembly: ");

		// Value labels
		JLabel jlValProjectName = new JLabel(ProjectManager.getInstance().getProjectName());
		JLabel jlValAssembly = new JLabel(ProjectManager.getInstance().getAssembly().getDisplayName());

		// Layout settings
		GridBagLayout layout = new GridBagLayout();
		panel.setLayout(layout);
		GridBagConstraints gbc = new GridBagConstraints();
		Insets keyInset = new Insets(0, 0, 0, 0);
		Insets valueInset = new Insets(0, 10, 0, 0);
		gbc.anchor = GridBagConstraints.FIRST_LINE_START;

		// jlKeyProjectName
		gbc.gridx = 0;
		gbc.gridy = 0;
		gbc.insets = keyInset;
		panel.add(jlKeyProjectName, gbc);

		// jlValProjectName
		gbc.gridx = 1;
		gbc.gridy = 0;
		gbc.insets = valueInset;
		panel.add(jlValProjectName, gbc);

		// jlKeyAssembly
		gbc.gridx = 0;
		gbc.gridy = 1;
		gbc.insets = keyInset;
		panel.add(jlKeyAssembly, gbc);

		// jlValAssembly
		gbc.gridx = 1;
		gbc.gridy = 1;
		gbc.insets = valueInset;
		panel.add(jlValAssembly, gbc);

		return panel;
	}


	/**
	 * Creates the panel that contains information about VCF files and how user decided to load them
	 * @return the panel
	 */
	private JPanel getVCFMappingPanel () {
		// Association between full genome names and their readers
		Map<String, List<VCFFile>> map = ProjectManager.getInstance().getMultiGenomeProject().getGenomeFileAssociation();

		// Column names
		String[] columnNames = {VCFData.GROUP_NAME,
				VCFData.NICKNAME,
				VCFData.RAW_NAME,
				VCFData.FILE_NAME};

		// Counts the number of row
		int rowNumber = 0;
		for (List<VCFFile> readers: map.values()) {
			rowNumber += readers.size();
		}

		// Initializes data
		Object[][] data = new Object[rowNumber][columnNames.length];

		// Fills data
		int rowIndex = 0;
		for (String fullGenomeName: map.keySet()) {
			for (VCFFile reader: map.get(fullGenomeName)) {
				data[rowIndex][0] = FormattedMultiGenomeName.getGroupName(fullGenomeName);
				data[rowIndex][1] = FormattedMultiGenomeName.getUsualName(fullGenomeName);
				data[rowIndex][2] = FormattedMultiGenomeName.getRawName(fullGenomeName);
				data[rowIndex][3] = reader.getFile().getName();
				rowIndex++;
			}
		}

		return Utils.getTablePanel(columnNames, data);
	}

}