/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* Created by JFormDesigner on Wed May 16 16:09:07 EDT 2012
*/
package org.broad.igv.track;
import com.google.common.base.Predicate;
import org.apache.log4j.Logger;
import org.broad.igv.cli_plugin.ui.TrackArgument;
import org.broad.igv.data.CombinedDataSource;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.PanelName;
import org.broad.igv.util.StringUtils;
import org.broad.igv.util.collections.CollUtils;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
/**
* @author jacob
*/
public class CombinedDataSourceDialog extends JDialog {
private static Logger log = Logger.getLogger(CombinedDataSourceDialog.class);
public CombinedDataSourceDialog(Frame owner) {
super(owner, "Combine tracks");
initComponents();
ArrayList<CombinedDataSource.Operation> dialogOperations = new ArrayList<CombinedDataSource.Operation>(
Arrays.asList(CombinedDataSource.Operation.values()));
operation.setModel(new DefaultComboBoxModel(dialogOperations.toArray()));
List<DataTrack> visibleTracks = CollUtils.filter(IGV.getInstance().getDataTracks(), new Predicate<DataTrack>() {
@Override
public boolean apply(DataTrack input) {
return input.isVisible();
}
});
trackABox.setModel(new DefaultComboBoxModel(visibleTracks.toArray()));
trackBBox.setModel(new DefaultComboBoxModel(visibleTracks.toArray()));
//Show 1st and 2nd track by default
if(visibleTracks.size() >= 2) trackBBox.setSelectedIndex(1);
operation.setRenderer(new OperationComboBoxRenderer());
trackABox.setRenderer(new TrackArgument.TrackComboBoxRenderer());
trackBBox.setRenderer(new TrackArgument.TrackComboBoxRenderer());
setOutputTrackName();
operation.addItemListener(new SetOutputTrackNameListener());
}
public CombinedDataSourceDialog(Frame owner, Iterator<Track> tracks) {
this(owner);
trackABox.setSelectedItem(tracks.next());
trackBBox.setSelectedItem(tracks.next());
}
private void cancelButtonActionPerformed(ActionEvent e) {
this.setVisible(false);
}
private void okButtonActionPerformed(ActionEvent e) {
DataTrack track0 = (DataTrack) trackABox.getSelectedItem();
DataTrack track1 = (DataTrack) trackBBox.getSelectedItem();
CombinedDataSource.Operation op = (CombinedDataSource.Operation) operation.getSelectedItem();
String text = resultName.getText();
CombinedDataSource source = new CombinedDataSource(track0, track1, op);
DataSourceTrack newTrack = new DataSourceTrack(null, track0.getId() + track1.getId() + text, text, source);
TrackMenuUtils.changeRenderer(Arrays.<Track>asList(newTrack), track0.getRenderer().getClass());
newTrack.setDataRange(track0.getDataRange());
newTrack.setColorScale(track0.getColorScale());
IGV.getInstance().addTracks(Arrays.<Track>asList(newTrack), PanelName.DATA_PANEL);
this.setVisible(false);
IGV.getInstance().repaint();
}
private void helpButtonActionPerformed(ActionEvent e) {
String defInfo = "Error retrieving help. See the IGV User Guide.";
InputStream is = this.getClass().getResourceAsStream("/resources/bedtools_help.txt");
String info = "";
String line;
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
try {
while ((line = reader.readLine()) != null) {
info += line + "\n";
}
} catch (IOException exc) {
log.error(exc);
info = defInfo;
}
JTextArea textArea = new JTextArea(info);
textArea.setLineWrap(true);
textArea.setWrapStyleWord(true);
JScrollPane scrollPane = new JScrollPane(textArea);
JOptionPane pane = new JOptionPane(scrollPane, JOptionPane.PLAIN_MESSAGE);
JDialog dialog = pane.createDialog(null, "Help");
dialog.setAlwaysOnTop(true);
dialog.setResizable(true);
dialog.setSize(400, 400);
dialog.setVisible(true);
//JOptionPane.showMessageDialog(this, scrollPane, "Help", JOptionPane.PLAIN_MESSAGE);
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
label2 = new JLabel();
trackABox = new JComboBox();
label4 = new JLabel();
operation = new JComboBox();
label3 = new JLabel();
trackBBox = new JComboBox();
label1 = new JLabel();
scrollPane1 = new JScrollPane();
resultName = new JTextArea();
buttonBar = new JPanel();
okButton = new JButton();
helpButton = new JButton();
cancelButton = new JButton();
//======== this ========
setAlwaysOnTop(true);
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(null);
//---- label2 ----
label2.setText("Track A:");
label2.setLabelFor(trackABox);
contentPanel.add(label2);
label2.setBounds(new Rectangle(new Point(5, 20), label2.getPreferredSize()));
contentPanel.add(trackABox);
trackABox.setBounds(70, 15, 205, trackABox.getPreferredSize().height);
//---- label4 ----
label4.setText("Operation:");
contentPanel.add(label4);
label4.setBounds(new Rectangle(new Point(5, 65), label4.getPreferredSize()));
contentPanel.add(operation);
operation.setBounds(70, 60, 150, operation.getPreferredSize().height);
//---- label3 ----
label3.setText("Track B:");
label3.setLabelFor(trackBBox);
contentPanel.add(label3);
label3.setBounds(5, 110, 52, 16);
contentPanel.add(trackBBox);
trackBBox.setBounds(70, 105, 205, trackBBox.getPreferredSize().height);
//---- label1 ----
label1.setText("Result Track Name");
contentPanel.add(label1);
label1.setBounds(50, 150, 128, label1.getPreferredSize().height);
//======== scrollPane1 ========
{
//---- resultName ----
resultName.setLineWrap(true);
scrollPane1.setViewportView(resultName);
}
contentPanel.add(scrollPane1);
scrollPane1.setBounds(10, 170, 270, 65);
{ // compute preferred size
Dimension preferredSize = new Dimension();
for(int i = 0; i < contentPanel.getComponentCount(); i++) {
Rectangle bounds = contentPanel.getComponent(i).getBounds();
preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width);
preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height);
}
Insets insets = contentPanel.getInsets();
preferredSize.width += insets.right;
preferredSize.height += insets.bottom;
contentPanel.setMinimumSize(preferredSize);
contentPanel.setPreferredSize(preferredSize);
}
}
dialogPane.add(contentPanel, BorderLayout.CENTER);
//======== buttonBar ========
{
buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
buttonBar.setLayout(new GridBagLayout());
((GridBagLayout)buttonBar.getLayout()).columnWidths = new int[] {0, 80, 80};
((GridBagLayout)buttonBar.getLayout()).columnWeights = new double[] {1.0, 0.0, 0.0};
//---- okButton ----
okButton.setText(" OK ");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
okButtonActionPerformed(e);
}
});
buttonBar.add(okButton, new GridBagConstraints(0, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.VERTICAL,
new Insets(0, 0, 0, 0), 0, 0));
//---- helpButton ----
helpButton.setText("Help");
helpButton.setVisible(false);
helpButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
helpButtonActionPerformed(e);
}
});
buttonBar.add(helpButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.VERTICAL,
new Insets(0, 0, 0, 0), 0, 0));
//---- cancelButton ----
cancelButton.setText("Cancel");
cancelButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
cancelButtonActionPerformed(e);
}
});
buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.VERTICAL,
new Insets(0, 0, 0, 0), 0, 0));
}
dialogPane.add(buttonBar, BorderLayout.SOUTH);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
pack();
setLocationRelativeTo(getOwner());
// JFormDesigner - End of component initialization //GEN-END:initComponents
}
// JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables
// Generated using JFormDesigner non-commercial license
private JPanel dialogPane;
private JPanel contentPanel;
private JLabel label2;
private JComboBox trackABox;
private JLabel label4;
private JComboBox operation;
private JLabel label3;
private JComboBox trackBBox;
private JLabel label1;
private JScrollPane scrollPane1;
private JTextArea resultName;
private JPanel buttonBar;
private JButton okButton;
private JButton helpButton;
private JButton cancelButton;
// JFormDesigner - End of variables declaration //GEN-END:variables
private class OperationComboBoxRenderer extends DefaultListCellRenderer {
@Override
public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
CombinedDataSource.Operation op = (CombinedDataSource.Operation) value;
String toShow = StringUtils.capWords(op.name());
return super.getListCellRendererComponent(list, toShow, index, isSelected, cellHasFocus);
}
}
private class SetOutputTrackNameListener implements ItemListener {
@Override
public void itemStateChanged(ItemEvent e) {
setOutputTrackName();
}
}
private void setOutputTrackName() {
String name = "Sum";
CombinedDataSource.Operation op = (CombinedDataSource.Operation) operation.getSelectedItem();
switch (op){
case ADD:
break;
case SUBTRACT:
name = "Difference";
break;
}
resultName.setText(name);
// String name = ((Track) trackABox.getSelectedItem()).getName();
// name += " " + operation.getSelectedItem() + " ";
// name += ((Track) trackBBox.getSelectedItem()).getName();
}
}