JAL-1065 - Visualize T-Coffee quality scores for an alignment

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6253e36..c7249de 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -17,13 +17,35 @@
  */
 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
 {
@@ -113,6 +135,9 @@ public class GAlignFrame extends JInternalFrame
 
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+ 
+  
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -176,6 +201,8 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem epsFile = new JMenuItem();
 
   JMenuItem LoadtreeMenuItem = new JMenuItem();
+  
+  JMenuItem loadScoresMenuItem = new JMenuItem();
 
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
@@ -417,6 +444,7 @@ public class GAlignFrame extends JInternalFrame
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
+    colours.add(tcoffeeColour);
 
     setColourSelected(jalview.bin.Cache
             .getDefault("DEFAULT_COLOUR", "None"));
@@ -486,6 +514,10 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour.setSelected(true);
 
         break;
+        
+      case ColourSchemeProperty.TCOFFEE:
+       tcoffeeColour.setSelected(true);
+       break;
 
       case ColourSchemeProperty.USER_DEFINED:
         userDefinedColour.setSelected(true);
@@ -1090,6 +1122,18 @@ public class GAlignFrame extends JInternalFrame
         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()
@@ -1202,7 +1246,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     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)
@@ -1210,6 +1254,17 @@ public class GAlignFrame extends JInternalFrame
         LoadtreeMenuItem_actionPerformed(e);
       }
     });
+    
+    loadScoresMenuItem.setActionCommand("Load T-Coffee scores");
+    loadScoresMenuItem.setText("Load T-Coffee scores");
+    loadScoresMenuItem.addActionListener(new ActionListener() {
+               
+               @Override
+               public void actionPerformed(ActionEvent e) {
+                       loadScores_actionPerformed(e);
+               }
+       });
+    
     scaleAbove.setVisible(false);
     scaleAbove.setText("Scale Above");
     scaleAbove.addActionListener(new java.awt.event.ActionListener()
@@ -1696,6 +1751,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
     fileMenu.add(associatedData);
+    fileMenu.add(loadScoresMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -1760,6 +1816,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
+    colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -2224,7 +2281,32 @@ public class GAlignFrame extends JInternalFrame
 
   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)
   {