JAL-1705 code tidy/comment only

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c6a042b..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();
@@ -454,7 +458,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     JMenuItem saveAs = new JMenuItem(
-            MessageManager.getString("action.save_as") + "...");
+            MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
     {
       @Override
@@ -491,8 +495,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
-            MessageManager
-            .getString("action.select_all"));
+            MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -703,8 +706,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-            .getString("action.remove_redundancy").concat("..."));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1124,7 +1127,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem printMenuItem = new JMenuItem(
-            MessageManager.getString("action.print") + "...");
+            MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1296,8 +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
@@ -1685,9 +1690,28 @@ 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") + "...");
+            MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
     {
       @Override
@@ -1703,7 +1727,7 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     JMenuItem openFeatureSettings = new JMenuItem(
-            MessageManager.getString("label.feature_settings"));
+            MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
       @Override
@@ -1959,8 +1983,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.ALT_MASK, false);
     al = new ActionListener()
     {
@@ -2051,7 +2075,7 @@ public class GAlignFrame extends JInternalFrame
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
     JMenuItem textColour = new JMenuItem(
-            MessageManager.getString("label.colour_text") + "...");
+            MessageManager.getString("action.set_text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2100,7 +2124,7 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
 
     JMenuItem pageSetup = new JMenuItem(
-            MessageManager.getString("action.page_setup") + "...");
+            MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
     {
       @Override
@@ -2110,7 +2134,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     JMenuItem alignmentProperties = new JMenuItem(
-            MessageManager.getString("label.alignment_props") + "...");
+            MessageManager.getString("label.alignment_props"));
     alignmentProperties.addActionListener(new ActionListener()
     {
       @Override
@@ -2251,6 +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);
@@ -2319,6 +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.
    * 
@@ -2803,6 +2839,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -3057,7 +3094,8 @@ public class GAlignFrame extends JInternalFrame
     return annotationSortOrder;
   }
 
-  protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+  protected void setAnnotationSortOrder(
+          SequenceAnnotationOrder annotationSortOrder)
   {
     this.annotationSortOrder = annotationSortOrder;
   }
@@ -3104,7 +3142,7 @@ public class GAlignFrame extends JInternalFrame
     return this.splitFrame;
   }
 
-  protected void showComplement_actionPerformed(boolean state)
+  protected void showComplement_actionPerformed(boolean complement)
   {
   }
 }