X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=71b6b9e90e07627cd8df368c3adb1e2610b9659b;hb=282aa9129a74235dc8d6c22b123d51eb1abd2f55;hp=aac8428dbcb4b8344ff81012657c502ead334211;hpb=62babeb3c6572d8f11e64292febf1e6a382f1fca;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index aac8428..71b6b9e 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,6 +21,8 @@
 package jalview.jbgui;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
@@ -33,7 +35,6 @@ import jalview.util.Platform;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -60,15 +61,18 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+@SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu webService = new JMenu();
+  public JMenu webService = new JMenu();// BH 2019 was protected, but not
+                                        // sufficient for AlignFrame thread run
 
-  protected JMenuItem webServiceNoServices;
+  public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+                                        // sufficient for AlignFrame thread run
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
@@ -76,7 +80,9 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+                                          // sufficient for
+                                          // AlignFrame.printWriter
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -138,7 +144,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenu showTranslation = new JMenu();
 
   protected JMenuItem showReverse = new JMenuItem();
 
@@ -198,6 +204,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
+  protected JMenuItem openFeatureSettings;
+
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
@@ -210,6 +218,10 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+
+      // for Web-page embedding using id=align-frame-div
+      setName("jalview-alignment");
+
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
@@ -223,7 +235,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            outputText_actionPerformed(e);
+            outputText_actionPerformed(e.getActionCommand());
           }
         });
 
@@ -234,7 +246,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!Platform.isAMac())
+    if (Platform.allowMnemonics()) // was "not mac and not JS"
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -258,20 +270,22 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveAs_actionPerformed(e);
+        saveAs_actionPerformed();
       }
     };
 
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -294,7 +308,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -321,7 +337,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -357,7 +375,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -371,7 +391,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -385,7 +407,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -399,8 +423,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -507,7 +531,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -682,7 +708,9 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -696,7 +724,9 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -720,7 +750,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -746,7 +778,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -907,7 +941,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -932,7 +968,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -946,8 +984,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -961,27 +999,31 @@ public class GAlignFrame extends JInternalFrame
 
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
 
     al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        copy_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
 
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -993,7 +1035,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        delete_actionPerformed();
       }
     });
 
@@ -1001,8 +1043,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1017,7 +1059,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1051,7 +1095,7 @@ public class GAlignFrame extends JInternalFrame
     });
     seqLimits.setText(
             MessageManager.getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1201,8 +1245,7 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
-    padGapsMenuitem
-            .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1222,16 +1265,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
     showTranslation
             .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
     {
-      @Override
-      public void actionPerformed(ActionEvent e)
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
       {
-        showTranslation_actionPerformed(e);
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1280,7 +1340,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem openFeatureSettings = new JMenuItem(
+    openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
@@ -1290,6 +1350,10 @@ public class GAlignFrame extends JInternalFrame
         featureSettings_actionPerformed(e);
       }
     });
+
+    /*
+     * add sub-menu of database we can fetch from
+     */
     JMenuItem fetchSequence = new JMenuItem(
             MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
@@ -1297,7 +1361,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fetchSequence_actionPerformed(e);
+        fetchSequence_actionPerformed();
       }
     });
 
@@ -1311,7 +1375,8 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
-    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf = new JMenuItem(
+            MessageManager.getString("label.load_vcf_file"));
     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
     loadVcf.addActionListener(new ActionListener()
     {
@@ -1323,8 +1388,7 @@ public class GAlignFrame extends JInternalFrame
     });
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
-    autoCalculate.setState(
-            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1337,8 +1401,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.sort_alignment_new_tree"));
     sortByTree.setToolTipText("<html>" + MessageManager.getString(
             "label.enable_automatically_sort_alignment_when_open_new_tree"));
-    sortByTree
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+    sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override
@@ -1512,8 +1575,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.ALT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1576,7 +1639,9 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1601,7 +1666,9 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1705,7 +1772,10 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(webService);
+    if (!Platform.isJS())
+    {
+      alignFrameMenuBar.add(webService);
+    }
 
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1723,7 +1793,10 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    fileMenu.add(loadVcf);
+    if (!Platform.isJS())
+    {
+      fileMenu.add(loadVcf);
+    }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 
@@ -1818,17 +1891,26 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    calculateMenu.addSeparator();
-    calculateMenu.add(runGroovy);
+    if (!Platform.isJS())
+    {
+      calculateMenu.addSeparator();
+      calculateMenu.add(runGroovy);
+    }
 
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    exportImageMenu.add(htmlMenuItem);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(htmlMenuItem);
+    }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
-    exportImageMenu.add(createBioJS);
-    exportImageMenu.add(createSVG);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(createBioJS);
+      exportImageMenu.add(createSVG);
+    }
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -2166,7 +2248,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(String formatName)
   {
   }
 
@@ -2332,15 +2414,15 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void copy_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed()
   {
   }
 
-  protected void cut_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed()
   {
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed()
   {
   }
 
@@ -2424,7 +2506,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed()
   {
   }
 
@@ -2442,7 +2524,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }
@@ -2452,7 +2534,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
 
   }