added preferences for usage stats, questionnaire check and version check.

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 49ab7c1..04955e3 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -285,6 +285,10 @@ public class GAlignFrame extends JInternalFrame
 
   private JMenuItem justifyRightMenuItem=new JMenuItem();
   
+  protected JCheckBoxMenuItem showGroupConsensus=new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem showGroupConservation=new JCheckBoxMenuItem();
+
+  private JMenuItem grpsFromSelection = new JMenuItem();
   public GAlignFrame()
   {
     try
@@ -540,6 +544,15 @@ public class GAlignFrame extends JInternalFrame
                 invertSequenceMenuItem_actionPerformed(e);
               }
             });
+    grpsFromSelection.setText("Make Groups for selection");
+    grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        makeGrpsFromSelection_actionPerformed(e);
+      }      
+    });
+
     remove2LeftMenuItem.setText("Remove Left");
     remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
@@ -990,6 +1003,28 @@ 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()
     {
@@ -1577,6 +1612,8 @@ 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);
@@ -1670,6 +1707,25 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
     selectMenu.add(deleteGroups);
+    selectMenu.add(grpsFromSelection);
+  }
+
+  protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  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)