content: package aliview.aligner;
  
  import java.awt.BorderLayout;
  import java.awt.Component;
  import java.awt.Dimension;
  import java.awt.event.ActionEvent;
  import java.awt.event.ActionListener;
  import java.awt.event.MouseAdapter;
  import java.awt.event.MouseEvent;
  import java.awt.event.WindowAdapter;
  import java.awt.event.WindowEvent;
  import java.util.ArrayList;
  import java.util.Enumeration;
  
  import javax.swing.Box;
  import javax.swing.BoxLayout;
  import javax.swing.ButtonGroup;
  import javax.swing.JButton;
  import javax.swing.JCheckBox;
  import javax.swing.JFrame;
  import javax.swing.JPanel;
  import javax.swing.JScrollPane;
  import javax.swing.JTable;
  import javax.swing.JTextField;
  import javax.swing.ListSelectionModel;
  import javax.swing.border.EmptyBorder;
  import javax.swing.event.ListSelectionEvent;
  import javax.swing.event.ListSelectionListener;
  import javax.swing.table.DefaultTableModel;
  import javax.swing.table.TableColumn;
  import javax.swing.text.StyledEditorKit.BoldAction;
  
  import org.apache.log4j.Logger;
  
  import aliview.AliViewWindow;
  import aliview.externalcommands.CommandItem;
  import aliview.old.MyScrollPane;
  import aliview.settings.Settings;
  
  public class AlignerALLItemsFrame extends JFrame {
  	private static final Logger logger = Logger.getLogger(AlignerALLItemsFrame.class);
  	JPanel mainPanel;
  
  	public AlignerALLItemsFrame(final AliViewWindow aliViewWin){
  
  		getContentPane().add(new AlignerALLItemsPanel(this), BorderLayout.CENTER);
  
  		// Arrange Frame
  		this.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
  		this.addWindowListener(new WindowAdapter() {		
  			public void windowClosing(WindowEvent e){
  				// Dont save here - only close
  				dispose();
  			}
  		});
  
  		this.setTitle("Alignment program settings");
  		this.setPreferredSize(new Dimension(650,600));
  		this.pack();
  		this.centerLocationToThisComponent(aliViewWin);
  		this.setVisible(true);
  	}
  
  	public void centerLocationToThisComponent(Component parent){
  		// align to middle of parent window
  		if(parent != null){
  			int newX = parent.getX() + parent.getWidth()/2 - this.getWidth()/2;
  			int newY = parent.getY() + parent.getHeight()/2 - this.getHeight()/2;
  
  			if(newX > parent.getX() && newX > parent.getY()){
  				this.setLocation(newX, newY);
  			}
  		}
  	}
  }