Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8d18064..205b9c6 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -173,6 +173,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem showTranslation = new JMenuItem();
 
+  protected JMenuItem showReverse = new JMenuItem();
+
+  protected JMenuItem showReverseComplement = new JMenuItem();
+
   protected JMenu showProducts = new JMenu();
 
   protected JMenuItem rnahelicesColour = new JMenuItem();
@@ -1295,8 +1299,10 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
-    showAutoFirst.setSelected(Cache.getDefault(
-            Preferences.SHOW_AUTOCALC_ABOVE, false));
+    final boolean autoFirst = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
+    showAutoFirst.setSelected(autoFirst);
+    setShowAutoCalculatedAbove(autoFirst);
     showAutoFirst.addActionListener(new ActionListener()
     {
       @Override
@@ -1684,6 +1690,25 @@ public class GAlignFrame extends JInternalFrame
         showTranslation_actionPerformed(e);
       }
     });
+    showReverse.setText(MessageManager.getString("label.reverse"));
+    showReverse.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(false);
+      }
+    });
+    showReverseComplement.setText(MessageManager
+            .getString("label.reverse_complement"));
+    showReverseComplement.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(true);
+      }
+    });
 
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
@@ -2250,6 +2275,8 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(showReverse);
+    calculateMenu.add(showReverseComplement);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);
@@ -2318,6 +2345,16 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
+   * Generate the reverse sequence (or reverse complement if the flag is true)
+   * and add it to the alignment
+   * 
+   * @param complement
+   */
+  protected void showReverse_actionPerformed(boolean complement)
+  {
+  }
+
+  /**
    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
    * 
@@ -3105,7 +3142,7 @@ public class GAlignFrame extends JInternalFrame
     return this.splitFrame;
   }
 
-  protected void showComplement_actionPerformed(boolean state)
+  protected void showComplement_actionPerformed(boolean complement)
   {
   }
 }