/*
* 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 Mon Nov 26 16:20:15 EST 2012
*/
package org.broad.igv.plugin.mongocollab;
import com.mongodb.DBCollection;
import org.apache.log4j.Logger;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.color.ColorChooserPanel;
import org.broad.igv.ui.util.MessageUtils;
import htsjdk.tribble.Feature;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
/**
* Dialog for inserting a feature annotation
* into collaborative database
*/
public class FeatureAnnotDialog extends JDialog {
private static Logger log = Logger.getLogger(MongoCollabPlugin.class);
private DBCollection collection;
private DBFeature dbFeat;
FeatureAnnotDialog(Frame owner, DBCollection collection, Feature feature) {
super(owner);
initComponents();
if(collection == null) throw new IllegalArgumentException("DBCollection must not be null");
this.collection = collection;
if(feature instanceof DBFeature){
this.dbFeat = (DBFeature) feature;
}else{
this.dbFeat = DBFeature.create(feature);
}
initComponentData(this.dbFeat);
}
private void initComponentData(DBFeature feature) {
setTitle("Add/Save Feature in " + this.collection.getFullName());
chrField.setText(feature.getChr());
startField.setText("" + (feature.getStart() + 1));
stopField.setText("" + feature.getEnd());
nameField.setText(feature.getName());
descField.setText("" + feature.getDescription());
colorField.setSelectedColor(feature.getColor());
if(this.dbFeat.get_id() == null){
delButton.setVisible(false);
}
validate();
}
private void cancelButtonActionPerformed(ActionEvent e) {
setVisible(false);
}
private DBFeature createDBObjectFromFields(){
int start, end;
try{
//Change from 1-based (user entered) to 0-based
start = Integer.parseInt(startField.getText()) - 1;
end = Integer.parseInt(stopField.getText());
}catch(NumberFormatException e){
MessageUtils.showErrorMessage(e.getMessage(), e);
return null;
}
if(start >= end){
String msg = String.format("Start (%s) must be less than End (%s), but it's greater or equal", start, end);
MessageUtils.showMessage(msg);
return null;
}
this.dbFeat.setChr(chrField.getText());
this.dbFeat.setStart(start);
this.dbFeat.setEnd(end);
this.dbFeat.setColor(colorField.getSelectedColor());
this.dbFeat.setDescription(descField.getText());
this.dbFeat.setName(nameField.getText());
return this.dbFeat;
}
/**
* Save information to MongoDB
*
* @param e
*/
private void okButtonActionPerformed(ActionEvent e) {
DBFeature featDBObject = createDBObjectFromFields();
String errorMessage = MongoCollabPlugin.saveFeature(collection, featDBObject);
if (errorMessage != null) {
MessageUtils.showErrorMessage(errorMessage, new IOException(errorMessage));
} else {
setVisible(false);
refreshTrack();
}
}
private void refreshTrack(){
//Find the track showing results, clear it to force a refresh
for (FeatureTrack ft : IGV.getInstance().getFeatureTracks()) {
//TODO This is a somewhat fragile way of identifying the corresponding track
if(ft.getId() != null && ft.getId().equals(this.collection.getFullName())){
ft.clearPackedFeatures();
}
}
IGV.getInstance().revalidateTrackPanels();
}
private void delButtonActionPerformed(ActionEvent e) {
MongoCollabPlugin.removeFeature(collection, this.dbFeat);
setVisible(false);
refreshTrack();
}
private void createUIComponents() {
// TODO: add custom component creation code here
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
dialogPane = new JPanel();
contentPanel = new JPanel();
panel4 = new JPanel();
label7 = new JLabel();
chrField = new JTextField();
panel5 = new JPanel();
label8 = new JLabel();
startField = new JTextField();
panel6 = new JPanel();
label9 = new JLabel();
stopField = new JTextField();
panel7 = new JPanel();
color = new JLabel();
colorField = new ColorChooserPanel();
panel9 = new JPanel();
name = new JLabel();
nameField = new JTextField();
panel8 = new JPanel();
label11 = new JLabel();
descField = new JTextField();
buttonBar = new JPanel();
okButton = new JButton();
cancelButton = new JButton();
delButton = new JButton();
//======== this ========
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== dialogPane ========
{
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setPreferredSize(new Dimension(600, 150));
dialogPane.setLayout(new BorderLayout());
//======== contentPanel ========
{
contentPanel.setLayout(new BoxLayout(contentPanel, BoxLayout.X_AXIS));
//======== panel4 ========
{
panel4.setMaximumSize(new Dimension(46, 1000));
panel4.setLayout(new BoxLayout(panel4, BoxLayout.Y_AXIS));
//---- label7 ----
label7.setText("Chr");
label7.setHorizontalAlignment(SwingConstants.LEFT);
label7.setVerticalAlignment(SwingConstants.TOP);
label7.setLabelFor(chrField);
panel4.add(label7);
panel4.add(chrField);
}
contentPanel.add(panel4);
//======== panel5 ========
{
panel5.setMaximumSize(new Dimension(100, 1000));
panel5.setMinimumSize(new Dimension(80, 32));
panel5.setPreferredSize(new Dimension(80, 32));
panel5.setLayout(new BoxLayout(panel5, BoxLayout.Y_AXIS));
//---- label8 ----
label8.setText("Start");
label8.setHorizontalAlignment(SwingConstants.LEFT);
label8.setMaximumSize(new Dimension(100, 16));
panel5.add(label8);
panel5.add(startField);
}
contentPanel.add(panel5);
//======== panel6 ========
{
panel6.setMaximumSize(new Dimension(100, 1000));
panel6.setMinimumSize(new Dimension(80, 32));
panel6.setPreferredSize(new Dimension(80, 32));
panel6.setLayout(new BoxLayout(panel6, BoxLayout.Y_AXIS));
//---- label9 ----
label9.setText("End");
label9.setHorizontalAlignment(SwingConstants.LEFT);
label9.setMaximumSize(new Dimension(100, 16));
panel6.add(label9);
panel6.add(stopField);
}
contentPanel.add(panel6);
//======== panel7 ========
{
panel7.setMaximumSize(new Dimension(80, 1000));
panel7.setMinimumSize(new Dimension(60, 44));
panel7.setPreferredSize(new Dimension(60, 44));
panel7.setToolTipText("Click to edit");
panel7.setLayout(new BoxLayout(panel7, BoxLayout.Y_AXIS));
//---- color ----
color.setText("Color");
color.setHorizontalAlignment(SwingConstants.LEFT);
color.setMaximumSize(new Dimension(100, 16));
panel7.add(color);
//---- colorField ----
colorField.setSelectedColor(DBFeature.DEFAULT_COLOR);
panel7.add(colorField);
}
contentPanel.add(panel7);
//======== panel9 ========
{
panel9.setMaximumSize(new Dimension(200, 1000));
panel9.setMinimumSize(new Dimension(100, 44));
panel9.setPreferredSize(new Dimension(100, 44));
panel9.setLayout(new BoxLayout(panel9, BoxLayout.Y_AXIS));
//---- name ----
name.setText("Name");
name.setHorizontalAlignment(SwingConstants.LEFT);
name.setMaximumSize(new Dimension(100, 16));
panel9.add(name);
panel9.add(nameField);
}
contentPanel.add(panel9);
//======== panel8 ========
{
panel8.setMaximumSize(new Dimension(500, 1000));
panel8.setMinimumSize(new Dimension(100, 32));
panel8.setPreferredSize(new Dimension(100, 32));
panel8.setLayout(new BoxLayout(panel8, BoxLayout.Y_AXIS));
//---- label11 ----
label11.setText("Description");
label11.setHorizontalAlignment(SwingConstants.LEFT);
label11.setMaximumSize(new Dimension(100, 16));
label11.setLabelFor(descField);
label11.setAlignmentX(1.0F);
panel8.add(label11);
//---- descField ----
descField.setPreferredSize(new Dimension(100, 28));
descField.setMinimumSize(new Dimension(100, 28));
panel8.add(descField);
}
contentPanel.add(panel8);
}
dialogPane.add(contentPanel, BorderLayout.NORTH);
//======== buttonBar ========
{
buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
buttonBar.setLayout(new GridBagLayout());
((GridBagLayout)buttonBar.getLayout()).columnWidths = new int[] {0, 85, 85, 0};
((GridBagLayout)buttonBar.getLayout()).columnWeights = new double[] {1.0, 0.0, 0.0, 0.0};
//---- okButton ----
okButton.setText("Save");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
okButtonActionPerformed(e);
}
});
buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 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.BOTH,
new Insets(0, 0, 0, 5), 0, 0));
//---- delButton ----
delButton.setText("Delete");
delButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
delButtonActionPerformed(e);
}
});
buttonBar.add(delButton, new GridBagConstraints(3, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0), 0, 0));
}
dialogPane.add(buttonBar, BorderLayout.SOUTH);
}
contentPane.add(dialogPane, BorderLayout.CENTER);
setSize(700, 160);
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 JPanel panel4;
private JLabel label7;
private JTextField chrField;
private JPanel panel5;
private JLabel label8;
private JTextField startField;
private JPanel panel6;
private JLabel label9;
private JTextField stopField;
private JPanel panel7;
private JLabel color;
private ColorChooserPanel colorField;
private JPanel panel9;
private JLabel name;
private JTextField nameField;
private JPanel panel8;
private JLabel label11;
private JTextField descField;
private JPanel buttonBar;
private JButton okButton;
private JButton cancelButton;
private JButton delButton;
// JFormDesigner - End of variables declaration //GEN-END:variables
}