JAL-4386 - Implementation of substitution matrix and test cases.

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index da35bd4..dd66811 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ package jalview.jbgui;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
+import java.awt.Menu;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -193,6 +194,10 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem gatherViews = new JMenuItem();
 
   protected JMenuItem expandViews = new JMenuItem();
+  
+  protected JCheckBoxMenuItem threeDStructure = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem jPred = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
 
@@ -1799,6 +1804,9 @@ public class GAlignFrame extends JInternalFrame
     JMenu autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
 
+    JMenu selectSS = new JMenu(
+            MessageManager.getString("label.select_secondary_structure_preference"));
+    
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
@@ -1911,6 +1919,8 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConservation);
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
+    selectSS.add(threeDStructure);
+    selectSS.add(jPred);
 
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);