/*******************************************************************************
* 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.trackAction.convert;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.border.TitledBorder;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFFile;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFHeaderType.VCFHeaderType;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;
import edu.yu.einstein.genplay.dataStructure.enums.VCFColumnName;
import edu.yu.einstein.genplay.gui.dialog.multiGenomeDialog.trackAction.ExportSettings;
import edu.yu.einstein.genplay.gui.dialog.multiGenomeDialog.trackAction.mainDialog.MultiGenomeTrackActionDialog;
import edu.yu.einstein.genplay.gui.mainFrame.MainFrame;
import edu.yu.einstein.genplay.gui.track.Track;
import edu.yu.einstein.genplay.gui.track.layer.Layer;
/**
* @author Nicolas Fourel
* @version 0.1
*/
public class ConvertSCWDialog extends MultiGenomeTrackActionDialog {
/** Generated serial version ID */
private static final long serialVersionUID = -1321930230220361216L;
private final static String DIALOG_TITLE = "Convert Into Variable Window Track";
private String genomeName;
private JComboBox jcbAlleleTrack01;
private JComboBox jcbAlleleTrack02;
private VCFHeaderType header;
/**
* Constructor of {@link ConvertSCWDialog}
* @param settings the export settings
* @param layer the selected {@link Layer}
*/
public ConvertSCWDialog(ExportSettings settings, Layer<?> layer) {
super(settings, DIALOG_TITLE, layer);
}
@Override
protected String getErrors() {
String error = "";
if ((getFirstAlleleTrack() == null) && (getSecondAlleleTrack() == null)) {
error += "No track has been selected.";
}
if ((jtfDotValue != null) && jtfDotValue.isEnabled() && (getDotValue() == null)) {
if (!error.isEmpty()) {
error += "\n";
}
error += "The defined constant for \".\" in genotype does not seem to be a valid number.";
}
return error;
}
/**
* @return the selected track of the first allele
*/
public Track getFirstAlleleTrack () {
if (jcbAlleleTrack01 != null) {
Object object = jcbAlleleTrack01.getSelectedItem();
if (object instanceof Track) {
return (Track) object;
}
}
return null;
}
/**
* Creates the genome combo box.
* @return the genome combo box
*/
private JComboBox getGenomeComboBox (List<String> genomeList) {
// Creates the combo box
JComboBox jcbGenome = new JComboBox(genomeList.toArray());
jcbGenome.setSelectedIndex(0);
genomeName = jcbGenome.getSelectedItem().toString();
jcbGenome.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
genomeName = ((JComboBox) arg0.getSource()).getSelectedItem().toString();
}
});
return jcbGenome;
}
/**
* @return the selected genome name
*/
public String getGenomeName () {
return genomeName;
}
private JPanel getGenomeSelectionPanel (List<String> genomeList) {
// Create the panel
JPanel panel = new JPanel();
// Create the labels
JLabel genomeLabel = new JLabel("Select a genome to export:");
JLabel alleleTrackLabel01 = null;
JLabel alleleTrackLabel02 = null;
// Create the boxes
JComboBox jcbGenome = getGenomeComboBox(genomeList);
alleleTrackLabel01 = new JLabel("Select the output track for the " + AlleleType.ALLELE01.toString() + " allele:");
alleleTrackLabel02 = new JLabel("Select the output track for the " + AlleleType.ALLELE02.toString() + " allele:");
jcbAlleleTrack01 = getTrackListBox();
jcbAlleleTrack02 = getTrackListBox();
// Create the layout
GridBagLayout layout = new GridBagLayout();
panel.setLayout(layout);
GridBagConstraints gbc = new GridBagConstraints();
gbc.anchor = GridBagConstraints.FIRST_LINE_START;
gbc.insets = new Insets(0, 0, 0, 0);
gbc.weightx = 1;
gbc.weighty = 0;
gbc.gridx = 0;
// Insert the genome label
gbc.gridy = 0;
gbc.insets = new Insets(10, 0, 0, 0);
panel.add(genomeLabel, gbc);
// Insert the genome combo box
gbc.gridy++;
gbc.insets = new Insets(0, 10, 0, 0);
panel.add(jcbGenome, gbc);
if (alleleTrackLabel01 != null) {
// Insert the first allele track label
gbc.gridy++;
gbc.insets = new Insets(10, 0, 0, 0);
panel.add(alleleTrackLabel01, gbc);
// Insert the first allele track combo box
gbc.insets = new Insets(0, 10, 0, 0);
gbc.gridy++;
panel.add(jcbAlleleTrack01, gbc);
}
if (alleleTrackLabel02 != null) {
// Insert the second allele track label
gbc.gridy++;
gbc.insets = new Insets(10, 0, 0, 0);
panel.add(alleleTrackLabel02, gbc);
// Insert the second allele track combo box
gbc.gridy++;
gbc.weighty = 1;
gbc.insets = new Insets(0, 10, 5, 0);
panel.add(jcbAlleleTrack02, gbc);
}
return panel;
}
/**
* @return the header
*/
public VCFHeaderType getHeader() {
return header;
}
private JComboBox getIDComboBox (List<VCFHeaderType> headers) {
JComboBox box = new JComboBox(headers.toArray());
box.setSelectedIndex(0);
header = (VCFHeaderType) box.getSelectedItem();
box.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
header = (VCFHeaderType)((JComboBox) arg0.getSource()).getSelectedItem();
}
});
return box;
}
private JPanel getIDPanel (List<VCFFile> fileList) {
// Create the panel
JPanel panel = new JPanel();
// Create the label
JLabel idLabel = new JLabel("Select the ID field to use as a score value:");
// Create the combo box
JComboBox box = getIDComboBox(retrieveHeaderFields(fileList));
// Create the layout
GridBagLayout layout = new GridBagLayout();
panel.setLayout(layout);
GridBagConstraints gbc = new GridBagConstraints();
gbc.anchor = GridBagConstraints.FIRST_LINE_START;
gbc.insets = new Insets(0, 0, 0, 0);
gbc.weightx = 1;
gbc.weighty = 0;
gbc.gridx = 0;
// Insert the genome label
gbc.gridy = 0;
gbc.insets = new Insets(10, 0, 0, 0);
panel.add(idLabel, gbc);
// Insert the header type combo box
gbc.gridy++;
gbc.weighty = 1;
gbc.insets = new Insets(0, 10, 5, 0);
panel.add(box, gbc);
return panel;
}
/**
* @return the selected track of the second allele
*/
public Track getSecondAlleleTrack () {
if (jcbAlleleTrack02 != null) {
Object object = jcbAlleleTrack02.getSelectedItem();
if (object instanceof Track) {
return (Track) object;
}
}
return null;
}
private JComboBox getTrackListBox () {
Track[] tracks = MainFrame.getInstance().getTrackListPanel().getModel().getTracks();
JComboBox box = new JComboBox();
box.addItem("Do not convert this allele.");
for (Track track: tracks) {
box.addItem(track);
}
return box;
}
@Override
protected void initializeContentPanel() {
// Initialize the content panel
contentPanel = new JPanel();
// Create the field set effect
TitledBorder titledBorder = BorderFactory.createTitledBorder("Conversion settings");
contentPanel.setBorder(titledBorder);
// Create the layout
GridBagLayout layout = new GridBagLayout();
contentPanel.setLayout(layout);
GridBagConstraints gbc = new GridBagConstraints();
gbc.anchor = GridBagConstraints.FIRST_LINE_START;
gbc.insets = new Insets(0, 0, 0, 0);
gbc.weightx = 1;
gbc.weighty = 0;
gbc.gridx = 0;
gbc.gridy = 0;
contentPanel.add(getGenomeSelectionPanel(settings.getGenomeNames()), gbc);
gbc.gridy++;
contentPanel.add(getIDPanel(settings.getFileList()), gbc);
gbc.gridy++;
contentPanel.add(getOptionPanel(), gbc);
}
private List<VCFHeaderType> retrieveHeaderFields (List<VCFFile> fileList) {
List<VCFHeaderType> result = new ArrayList<VCFHeaderType>();
for (VCFFile file: fileList) {
List<VCFHeaderType> numberHeader = file.getHeader().getAllSortedNumberHeader();
for (VCFHeaderType header: numberHeader) {
if (!((header.getColumnCategory() == VCFColumnName.FORMAT) && header.getId().equals("PL"))) {
result.add(header);
}
}
}
return result;
}
}