show group annotation menu entries

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a4f0983..23062e3 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -122,6 +122,8 @@ public class GAlignFrame extends JInternalFrame
 
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
+  public JCheckBoxMenuItem showUnconservedMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem htmlMenuItem = new JMenuItem();
 
   JMenuItem overviewMenuItem = new JMenuItem();
@@ -283,6 +285,9 @@ public class GAlignFrame extends JInternalFrame
 
   private JMenuItem justifyRightMenuItem=new JMenuItem();
   
+  protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+  
   public GAlignFrame()
   {
     try
@@ -621,6 +626,15 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
+    showUnconservedMenuItem.setText("Show Unconserved");
+    showUnconservedMenuItem.setState(false);
+    showUnconservedMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showUnconservedMenuItem_actionPerformed(e);
+      }
+    });
     sortPairwiseMenuItem.setText("by Pairwise Identity");
     sortPairwiseMenuItem
             .addActionListener(new java.awt.event.ActionListener()
@@ -979,6 +993,28 @@ public class GAlignFrame extends JInternalFrame
       }
       
     });
+    showGroupConservation.setText("Group Conservation");
+    showGroupConservation.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showGroupConservation_actionPerformed(e);
+      }
+      
+    });
+
+    showGroupConsensus.setText("Group Consensus");
+    showGroupConsensus.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        showGroupConsensus_actionPerformed(e);
+      }
+      
+    });
+
     nucleotideColour.setText("Nucleotide");
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
@@ -1552,9 +1588,9 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
-    // dont add these yet - they cannot be undone!
-    //editMenu.add(justifyLeftMenuItem);
-    //editMenu.add(justifyRightMenuItem);
+    // dont add these yet in the CVS build - they cannot be undone!
+    editMenu.add(justifyLeftMenuItem);
+    editMenu.add(justifyRightMenuItem);
     editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
     viewMenu.add(newView);
@@ -1566,6 +1602,8 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.addSeparator();
     viewMenu.add(followHighlightMenuItem);
     viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(showGroupConservation);
+    viewMenu.add(showGroupConsensus);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
     viewMenu.add(showSeqFeaturesHeight);
@@ -1651,6 +1689,7 @@ public class GAlignFrame extends JInternalFrame
     formatMenu.add(colourTextMenuItem);
     formatMenu.add(renderGapsMenuItem);
     formatMenu.add(centreColumnLabelsMenuItem);
+    formatMenu.add(showUnconservedMenuItem);
     selectMenu.add(findMenuItem);
     selectMenu.addSeparator();
     selectMenu.add(selectAllSequenceMenuItem);
@@ -1660,6 +1699,24 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(deleteGroups);
   }
 
+  protected void showGroupConsensus_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showGroupConservation_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void showSeqFeaturesHeight_actionPerformed(
           ActionEvent actionEvent)
   {