*/
package jalview.jbgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
+import jalview.schemes.ColourSchemeProperty;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
-
+
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
colours.add(nucleotideColour);
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
+ colours.add(tcoffeeColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
nucleotideColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
case ColourSchemeProperty.PURINEPYRIMIDINE:
purinePyrimidineColour.setSelected(true);
nucleotideColour_actionPerformed(e);
}
});
+
+ tcoffeeColour.setText("T-Coffee scores");
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener( new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ } );
+
+
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.setText("Load Associated Tree");
LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
LoadtreeMenuItem_actionPerformed(e);
}
});
+
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
// colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
+
+ }
+
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event) {
+
+ }
+
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
+
}
+
protected void jpred_actionPerformed(ActionEvent e)
{