showUnconserved view and group setting

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a4f0983..0249e76 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -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();
@@ -621,6 +623,15 @@ 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()
@@ -1552,9 +1563,9 @@ 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);
@@ -1651,6 +1662,7 @@ 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 +1672,12 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(deleteGroups);
   }
 
+  protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void showSeqFeaturesHeight_actionPerformed(
           ActionEvent actionEvent)
   {