GenomeSelectionPanel.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.genomeSelectionPanel;

import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;

import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.utils.FormattedMultiGenomeName;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;


/**
 * Panel for the selection of a genome as a reference in a multi-genome project
 * @author Julien Lajugie
 * @author Nicolas Fourel
 */
public class GenomeSelectionPanel extends JPanel {

	private static final long 	serialVersionUID = -2863825210102188370L;	// generated ID
	private 					JComboBox 	jcbGenome; 									// combo box to choose the genome
	private						JComboBox	jcbAllele;									// combo box to choose the allele type
	private static int 						defaultGenome = 1;	// default selected genome
	private static int 						defaultAllele = 0;	// default selected allele


	/**
	 * Creates an instance of a {@link GenomeSelectionPanel}
	 */
	public GenomeSelectionPanel() {
		super();

		//Layout
		GridBagLayout layout = new GridBagLayout();
		setLayout(layout);
		GridBagConstraints gbc = new GridBagConstraints();
		gbc.anchor = GridBagConstraints.FIRST_LINE_START;
		gbc.weightx = 1;
		gbc.weighty = 0;

		// Insert the genome label
		gbc.gridx = 0;
		gbc.gridy = 0;
		gbc.insets = new Insets(4, 10, 5, 10);
		add(getDescriptionLabel(), gbc);

		// Insert the genome label
		gbc.gridy = 1;
		gbc.insets = new Insets(7, 10, 0, 10);
		add(new JLabel("Select a genome:"), gbc);

		// Insert the genome combo box
		gbc.gridy = 2;
		gbc.insets = new Insets(2, 10, 0, 10);
		add(getGenomeComboBox(), gbc);

		// Insert the allele type label
		gbc.gridy = 3;
		gbc.insets = new Insets(7, 10, 0, 10);
		add(new JLabel("Select an allele:"), gbc);

		// Insert the allele type combo box
		gbc.gridy = 4;
		gbc.insets = new Insets(2, 10, 4, 10);
		add(getAlleleTypeComboBox(), gbc);

		setBorder(BorderFactory.createTitledBorder("Genome Selection"));
	}


	/**
	 * @return the selected allele type
	 */
	public AlleleType getAlleleType () {
		if (jcbAllele.isEnabled()) {
			return (AlleleType)jcbAllele.getSelectedItem();
		}
		return AlleleType.BOTH;
	}


	/**
	 * Create the allele type combo box.
	 * @return the allele type combo box
	 */
	private JComboBox getAlleleTypeComboBox () {
		// Creates the combo box
		Object[] alleles = new Object[]{AlleleType.ALLELE01, AlleleType.ALLELE02};
		jcbAllele = new JComboBox(alleles);
		jcbAllele.setSelectedIndex(defaultAllele);

		// Tool tip text
		jcbAllele.setToolTipText("Select an allele to synchronize with");

		updateAlleleTypeComboBox(jcbGenome.getSelectedItem().toString());

		return jcbAllele;
	}


	/**
	 * Creates the label about the description of this panel.
	 * @return the description label
	 */
	private JLabel getDescriptionLabel () {
		JLabel label = new JLabel();
		String text = "<html>";
		text += "<i>";
		text += "Please select the genome used";
		text += "<br>";
		text += "for the alignement.";
		text += "</i>";
		text += "</html>";
		label.setText(text);
		return label;
	}


	/**
	 * Creates the genome combo box.
	 * @return the genome combo box
	 */
	private JComboBox getGenomeComboBox () {
		// Creates the combo box
		jcbGenome = new JComboBox(ProjectManager.getInstance().getMultiGenomeProject().getFormattedGenomeArray());
		jcbGenome.setSelectedIndex(defaultGenome);

		// Tool tip text
		jcbGenome.setToolTipText("Select a genome");

		jcbGenome.addActionListener(new ActionListener() {
			@Override
			public void actionPerformed(ActionEvent arg0) {
				String genome = ((JComboBox) arg0.getSource()).getSelectedItem().toString();
				updateAlleleTypeComboBox(genome);
			}
		});

		return jcbGenome;
	}


	/**
	 * @return the selected score calculation method
	 */
	public int getGenomeIndex() {
		return jcbGenome.getSelectedIndex();
	}


	/**
	 * @return the full name of the selected genome
	 */
	public String getGenomeName () {
		return (String)jcbGenome.getSelectedItem();
	}


	/**
	 * Saves the default selected items
	 */
	public void saveDefault() {
		defaultGenome = getGenomeIndex();
		defaultAllele = jcbAllele.getSelectedIndex();
	}


	/**
	 * Update the allele type combo box state.
	 * If the reference genome is selected, the allele type box should not be enabled.
	 * @param genomeName a genome name
	 */
	private void updateAlleleTypeComboBox (String genomeName) {
		if (genomeName.equals(ProjectManager.getInstance().getAssembly().getDisplayName()) || genomeName.equals(FormattedMultiGenomeName.META_GENOME_NAME)) {
			jcbAllele.setEnabled(false);
		} else {
			jcbAllele.setEnabled(true);
		}
	}
}