/*
* 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 Fri Nov 30 11:55:45 EST 2012
*/
package org.broad.igv.util.blat;
import org.broad.igv.DirectoryManager;
import org.broad.igv.feature.PSLRecord;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.util.FileDialogUtils;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.util.LongRunningTask;
import java.awt.*;
import java.awt.event.*;
import java.io.File;
import java.io.IOException;
import javax.swing.*;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
/**
* @author Jim Robinson
*/
public class BlatQueryWindow extends JFrame {
BlatTableModel model;
public BlatQueryWindow(Component parent, String querySequence, java.util.List<PSLRecord> records) {
if(parent != null) this.setLocationRelativeTo(parent);
model = new BlatTableModel(records);
initComponents();
addSelectionListener();
querySeqTextPane.setContentType("text/html");
StringBuffer headerBuffer = new StringBuffer("<html>");
headerBuffer.append(" BLAT result for query sequence: <br> ");
headerBuffer.append(querySequence);
headerBuffer.append("<br><br> <i>Click on a row to go to alignment");
querySeqTextPane.setText(headerBuffer.toString());
}
private void addSelectionListener() {
blatTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
ListSelectionModel rowSM = blatTable.getSelectionModel();
rowSM.addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
//Ignore extra messages.
if (e.getValueIsAdjusting()) return;
ListSelectionModel lsm = (ListSelectionModel) e.getSource();
if (!lsm.isSelectionEmpty()) {
int selectedRow = lsm.getMinSelectionIndex();
final String chr = model.getChr(selectedRow);
int start = model.getStart(selectedRow);
int end = model.getEnd(selectedRow);
// Expand region slightly for context
int w = (end - start) / 4;
final int estart = Math.max(0, start - w);
final int eend = end + w;
LongRunningTask.submit(new Runnable() {
@Override
public void run() {
IGV.getInstance().goToLocus(chr + ":" + estart + "-" + eend);
}
});
}
}
});
}
private void closeItemActionPerformed(ActionEvent e) {
setVisible(false);
dispose();
}
private void saveItemActionPerformed(ActionEvent e) {
File f = FileDialogUtils.chooseFile("Save BLAT results", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE);
if (f != null) {
try {
model.save(f);
} catch (IOException e1) {
MessageUtils.showErrorMessage("Error saving blat results ", e1);
}
}
}
private void initComponents() {
// JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents
// Generated using JFormDesigner non-commercial license
menuBar = new JMenuBar();
menu1 = new JMenu();
saveItem = new JMenuItem();
closeItem = new JMenuItem();
contentPanel = new JPanel();
scrollPane1 = new JScrollPane();
blatTable = new JTable(model);
headerPanel = new JPanel();
panel1 = new JPanel();
scrollPane2 = new JScrollPane();
querySeqTextPane = new JTextPane();
//======== this ========
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());
//======== menuBar ========
{
//======== menu1 ========
{
menu1.setText("File");
//---- saveItem ----
saveItem.setText("Save...");
saveItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
saveItemActionPerformed(e);
}
});
menu1.add(saveItem);
//---- closeItem ----
closeItem.setText("Close");
closeItem.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
closeItemActionPerformed(e);
}
});
menu1.add(closeItem);
}
menuBar.add(menu1);
}
setJMenuBar(menuBar);
//======== contentPanel ========
{
contentPanel.setLayout(new BorderLayout(0, 5));
//======== scrollPane1 ========
{
scrollPane1.setViewportView(blatTable);
}
contentPanel.add(scrollPane1, BorderLayout.CENTER);
//======== headerPanel ========
{
headerPanel.setLayout(new BorderLayout());
//======== panel1 ========
{
panel1.setLayout(new FlowLayout(FlowLayout.LEFT));
}
headerPanel.add(panel1, BorderLayout.NORTH);
//======== scrollPane2 ========
{
scrollPane2.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
scrollPane2.setViewportView(querySeqTextPane);
}
headerPanel.add(scrollPane2, BorderLayout.CENTER);
}
contentPanel.add(headerPanel, BorderLayout.NORTH);
}
contentPane.add(contentPanel, BorderLayout.CENTER);
setSize(870, 570);
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 JMenuBar menuBar;
private JMenu menu1;
private JMenuItem saveItem;
private JMenuItem closeItem;
private JPanel contentPanel;
private JScrollPane scrollPane1;
private JTable blatTable;
private JPanel headerPanel;
private JPanel panel1;
private JScrollPane scrollPane2;
private JTextPane querySeqTextPane;
// JFormDesigner - End of variables declaration //GEN-END:variables
}