Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4a7c3f0..6e8b420 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
 {
@@ -120,6 +142,9 @@ public class GAlignFrame extends JInternalFrame
   // protected JRadioButtonMenuItem covariationColour = new
   // JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+ 
+  
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -181,6 +206,8 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem epsFile = new JMenuItem();
 
   JMenuItem LoadtreeMenuItem = new JMenuItem();
+  
+  JMenuItem loadScoresMenuItem = new JMenuItem();
 
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
@@ -216,7 +243,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu showProducts = new JMenu();
 
-  public JMenuItem featureSettings = new JMenuItem();
+  public JMenuItem openFeatureSettings = new JMenuItem();
 
   JMenuItem fetchSequence = new JMenuItem();
 
@@ -314,6 +341,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   private JMenuItem grpsFromSelection = new JMenuItem();
@@ -426,6 +455,7 @@ public class GAlignFrame extends JInternalFrame
     colours.add(nucleotideColour);
     colours.add(purinePyrimidineColour);
     // colours.add(covariationColour);
+    colours.add(tcoffeeColour);
 
     setColourSelected(jalview.bin.Cache
             .getDefault("DEFAULT_COLOUR", "None"));
@@ -495,6 +525,10 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour.setSelected(true);
 
         break;
+        
+      case ColourSchemeProperty.TCOFFEE:
+       tcoffeeColour.setSelected(true);
+       break;
 
       case ColourSchemeProperty.PURINEPYRIMIDINE:
         purinePyrimidineColour.setSelected(true);
@@ -1113,6 +1147,16 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
+    normaliseSequenceLogo.setText("Normalise Consensus Logo");
+    normaliseSequenceLogo.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        normaliseSequenceLogo_actionPerformed(e);
+      }
+
+    });
     applyAutoAnnotationSettings.setText("Apply to all groups");
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
@@ -1134,6 +1178,18 @@ 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()
@@ -1246,7 +1302,7 @@ 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)
@@ -1254,6 +1310,17 @@ 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()
@@ -1408,8 +1475,8 @@ public class GAlignFrame extends JInternalFrame
      * public void actionPerformed(ActionEvent e) {
      * showProducts_actionPerformed(e); } });
      */
-    featureSettings.setText("Feature Settings...");
-    featureSettings.addActionListener(new ActionListener()
+    openFeatureSettings.setText("Feature Settings...");
+    openFeatureSettings.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -1750,6 +1817,7 @@ 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);
@@ -1783,6 +1851,7 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(applyAutoAnnotationSettings);
     autoAnnMenu.add(showConsensusHistogram);
     autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.add(normaliseSequenceLogo);
     autoAnnMenu.addSeparator();
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
@@ -1791,7 +1860,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(showSeqFeatures);
     // viewMenu.add(showSeqFeaturesHeight);
 
-    viewMenu.add(featureSettings);
+    viewMenu.add(openFeatureSettings);
     tooltipSettingsMenu.add(showDbRefsMenuitem);
     tooltipSettingsMenu.add(showNpFeatsMenuitem);
     viewMenu.add(tooltipSettingsMenu);
@@ -1816,6 +1885,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
     // colourMenu.add(covariationColour);
+    colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -1894,6 +1964,12 @@ public class GAlignFrame extends JInternalFrame
     //selectMenu.add(listenToViewSelections);
   }
 
+  protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void listenToViewSelections_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
@@ -2289,7 +2365,32 @@ 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)
   {