X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=b523763b3ff023681b0a53c04faa5879752ede66;hb=4ea6a00274e0a209a7dbec074f04a21ec1a80b28;hp=6e8b420d39d4a4dd831ceeb60d3c5a087877bd09;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6e8b420..b523763 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -143,8 +143,7 @@ public class GAlignFrame extends JInternalFrame
   // JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
- 
-  
+
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
 
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
@@ -206,8 +205,6 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem epsFile = new JMenuItem();
 
   JMenuItem LoadtreeMenuItem = new JMenuItem();
-  
-  JMenuItem loadScoresMenuItem = new JMenuItem();
 
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
@@ -525,10 +522,10 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour.setSelected(true);
 
         break;
-        
+
       case ColourSchemeProperty.TCOFFEE:
-    	tcoffeeColour.setSelected(true);
-    	break;
+        tcoffeeColour.setSelected(true);
+        break;
 
       case ColourSchemeProperty.PURINEPYRIMIDINE:
         purinePyrimidineColour.setSelected(true);
@@ -1178,18 +1175,19 @@ 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);
-		}
-	} );
-    
-    
+    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()
@@ -1302,7 +1300,7 @@ 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)
@@ -1310,17 +1308,7 @@ 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()
@@ -1529,9 +1517,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     sortByTree.setText("Sort Alignment With New Tree");
-    sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
-    sortByTree.setState(jalview.bin.Cache.getDefault(
-            "SORT_BY_TREE", false));
+    sortByTree
+            .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
+    sortByTree
+            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1541,8 +1530,9 @@ public class GAlignFrame extends JInternalFrame
     });
 
     listenToViewSelections.setText("Listen for selections");
-    listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
-    listenToViewSelections.setState(false); 
+    listenToViewSelections
+            .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
+    listenToViewSelections.setState(false);
     listenToViewSelections.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1817,7 +1807,6 @@ 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);
@@ -1959,21 +1948,22 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(invertColSel);
     selectMenu.add(deleteGroups);
     selectMenu.add(grpsFromSelection);
-    // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
-    //selectMenu.addSeparator();
-    //selectMenu.add(listenToViewSelections);
+    // TODO - determine if the listenToViewSelections button is needed : see bug
+    // JAL-574
+    // selectMenu.addSeparator();
+    // 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
-    
+
   }
 
   protected void showAllhidden_actionPerformed(ActionEvent e)
@@ -2367,30 +2357,32 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
-  
+
   /**
-   * Template method to handle the 'load T-Coffee scores' menu event. 
+   * 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
+   * 
+   * @param event
+   *          The raised event
    */
-  protected void loadScores_actionPerformed(ActionEvent event) {
-	   
+  protected void loadScores_actionPerformed(ActionEvent event)
+  {
+
   }
-  
 
   /**
-   * Template method to handle the 'Color T-Coffee scores' menu 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
+   * 
+   * @param event
+   *          The raised event
    */
-  protected void tcoffeeColorScheme_actionPerformed(ActionEvent event) {
-	  
+  protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+  {
+
   }
-  
 
   protected void jpred_actionPerformed(ActionEvent e)
   {