X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1cbe15c5dc274a5b6a56e0e49f50c2448d7311c2;hb=cb8ec179c020265666678572815ab056a024da22;hp=bddc504c96cf3f6474717430677d19267d551144;hpb=935e15fa16def9e538c8befaf061441b52f269ed;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bddc504..1cbe15c 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -110,7 +110,7 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenu jMenu2 = new JMenu();
-  JMenuItem padGapsMenuitem = new JMenuItem();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
@@ -124,6 +124,7 @@ public class GAlignFrame
 
 
   JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
 
@@ -977,6 +978,15 @@ public class GAlignFrame
         associatedData_actionPerformed(e);
       }
     });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState(true);
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -1051,11 +1061,11 @@ public class GAlignFrame
     colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
-    colourMenu.add(annotationColour);
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1063,6 +1073,7 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
     webService.add(webServiceNoServices);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
@@ -1373,11 +1384,6 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
-  {
-
-  }
-
   public void featureSettings_actionPerformed(ActionEvent e)
   {
 
@@ -1407,4 +1413,9 @@ public class GAlignFrame
   {
 
   }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
 }