Merge branch 'develop' into merged_2_11_2_0_to_2_12

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 25db31a..0fa4379 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -64,8 +65,6 @@ import jalview.io.FileFormats;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-
-
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
@@ -214,7 +213,6 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
-
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   protected JMenuItem openFeatureSettings;
@@ -235,7 +233,6 @@ public class GAlignFrame extends JInternalFrame
       // for Web-page embedding using id=align-frame-div
       setName(Platform.getAppID("alignment"));
 
-
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
@@ -276,6 +273,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
+
   
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
@@ -287,11 +285,13 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed();
       }
     };
+
   
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
   
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
@@ -304,6 +304,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
   
     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
@@ -314,9 +315,7 @@ public class GAlignFrame extends JInternalFrame
     JMenu calculateMenu = new JMenu(
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
-
     initHMMERMenu();
-
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
@@ -330,6 +329,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
   
     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.deselect_all"));
@@ -343,6 +343,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
   
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
@@ -357,6 +358,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
   
     JMenuItem grpsFromSelection = new JMenuItem(
             MessageManager.getString("action.make_groups_selection"));
@@ -393,6 +395,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
   
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
@@ -407,6 +410,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
   
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
@@ -421,6 +425,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
   
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
@@ -437,6 +442,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
   
     JMenuItem justifyLeftMenuItem = new JMenuItem(
             MessageManager.getString("action.left_justify_alignment"));
@@ -529,6 +535,7 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
+
     JMenuItem sortEValueMenuItem = new JMenuItem(
             MessageManager.getString("action.by_evalue"));
     sortEValueMenuItem.addActionListener(new ActionListener()
@@ -598,6 +605,7 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
+
   
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -605,11 +613,9 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-
     outputTextboxMenu
             .setText(MessageManager.getString("label.out_to_textbox"));
 
-
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem
             .setText(MessageManager.getString("label.show_annotations"));
@@ -677,7 +683,6 @@ public class GAlignFrame extends JInternalFrame
     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
             MessageManager.getString("label.sort_annotations_by_label"));
 
-
     sortAnnBySequence.setSelected(
             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
@@ -718,6 +723,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
+
   
     JMenuItem htmlMenuItem = new JMenuItem(
             MessageManager.getString("label.html"));
@@ -729,6 +735,7 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
+
   
     JMenuItem createBioJS = new JMenuItem(
             MessageManager.getString("label.biojs_html_export"));
@@ -740,6 +747,7 @@ public class GAlignFrame extends JInternalFrame
         bioJSMenuItem_actionPerformed(e);
       }
     });
+
   
     JMenuItem overviewMenuItem = new JMenuItem(
             MessageManager.getString("label.overview_window"));
@@ -751,6 +759,7 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
+
   
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
@@ -765,6 +774,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
   
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
@@ -779,6 +789,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
   
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
@@ -789,6 +800,7 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
+
   
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
@@ -803,6 +815,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
   
     renderGapsMenuItem
             .setText(MessageManager.getString("action.show_gaps"));
@@ -815,6 +828,7 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
+
   
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
@@ -834,7 +848,6 @@ public class GAlignFrame extends JInternalFrame
 
     showSeqFeatures.setText(
             MessageManager.getString("label.show_sequence_features"));
-
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -853,36 +866,42 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showDbRefs_actionPerformed(e);
       }
+
   
     });
     showNpFeatsMenuitem.setText(
             MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showNpFeats_actionPerformed(e);
       }
+
   
     });
     showGroupConservation
             .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConservation_actionPerformed(e);
       }
+
   
     });
 
@@ -890,48 +909,56 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConsensus_actionPerformed(e);
       }
+
   
     });
     showConsensusHistogram.setText(
             MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showConsensusHistogram_actionPerformed(e);
       }
+
   
     });
     showSequenceLogo
             .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showSequenceLogo_actionPerformed(e);
       }
+
   
     });
     normaliseSequenceLogo
             .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         normaliseSequenceLogo_actionPerformed(e);
       }
+
   
     });
     applyAutoAnnotationSettings
@@ -946,6 +973,7 @@ public class GAlignFrame extends JInternalFrame
         applyAutoAnnotationSettings_actionPerformed(e);
       }
     });
+
   
     ButtonGroup buttonGroup = new ButtonGroup();
     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
@@ -977,6 +1005,7 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
+
   
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
@@ -991,6 +1020,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
   
     JMenuItem annotationColumn = new JMenuItem(
             MessageManager.getString("action.select_by_annotation"));
@@ -1002,6 +1032,7 @@ public class GAlignFrame extends JInternalFrame
         annotationColumn_actionPerformed(e);
       }
     });
+
   
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
@@ -1016,6 +1047,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
   
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
@@ -1032,6 +1064,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
   
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
@@ -1046,6 +1079,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
+
   
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
@@ -1059,6 +1093,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
+
   
     JMenuItem delete = new JMenuItem(
             MessageManager.getString("action.delete"));
@@ -1070,6 +1105,7 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed();
       }
     });
+
   
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
@@ -1094,6 +1130,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
   
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
@@ -1115,6 +1152,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
   
     JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
@@ -1127,6 +1165,7 @@ public class GAlignFrame extends JInternalFrame
     });
     createPNG.setActionCommand(
             MessageManager.getString("label.save_png_image"));
+
     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
     {
@@ -1138,7 +1177,7 @@ 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
@@ -1156,6 +1195,7 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
+
   
     JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
@@ -1166,6 +1206,7 @@ public class GAlignFrame extends JInternalFrame
         createSVG(null);
       }
     });
+
   
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
@@ -1179,6 +1220,7 @@ public class GAlignFrame extends JInternalFrame
         loadTreeMenuItem_actionPerformed(e);
       }
     });
+
   
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
@@ -1230,14 +1272,17 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
+
   
       @Override
       public void actionPerformed(ActionEvent e)
       {
         followHighlight_actionPerformed();
       }
+
   
     });
+
   
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
@@ -1283,16 +1328,19 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortByAnnotScore);
     sort.addMenuListener(new javax.swing.event.MenuListener()
     {
+
   
       @Override
       public void menuCanceled(MenuEvent e)
       {
       }
+
   
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
+
   
       @Override
       public void menuSelected(MenuEvent e)
@@ -1306,8 +1354,7 @@ 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
@@ -1373,6 +1420,7 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(true);
       }
     });
+
   
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
@@ -1386,9 +1434,11 @@ public class GAlignFrame extends JInternalFrame
     });
     extractScores.setVisible(true);
     // JBPNote: TODO: make gui for regex based score extraction
+
   
     // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
+
   
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
     runGroovy.setToolTipText(
@@ -1426,6 +1476,7 @@ public class GAlignFrame extends JInternalFrame
         fetchSequence_actionPerformed();
       }
     });
+
   
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
@@ -1457,8 +1508,7 @@ 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
@@ -1471,8 +1521,7 @@ 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
@@ -1496,6 +1545,7 @@ public class GAlignFrame extends JInternalFrame
         listenToViewSelections_actionPerformed(e);
       }
     });
+
   
     JMenu addSequenceMenu = new JMenu(
             MessageManager.getString("label.add_sequences"));
@@ -1642,6 +1692,7 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
+
   
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
@@ -1658,6 +1709,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
   
     showComplementMenuItem.setVisible(false);
     showComplementMenuItem.addActionListener(new ActionListener()
@@ -1668,6 +1720,7 @@ public class GAlignFrame extends JInternalFrame
         showComplement_actionPerformed(showComplementMenuItem.getState());
       }
     });
+
   
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
@@ -1689,6 +1742,7 @@ public class GAlignFrame extends JInternalFrame
           tabbedPane_mousePressed(e);
         }
       }
+
   
       @Override
       public void mouseReleased(MouseEvent e)
@@ -1707,6 +1761,7 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
+
   
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
@@ -1720,6 +1775,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, save, al);
+
   
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
@@ -1731,6 +1787,7 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
+
   
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
@@ -1745,10 +1802,12 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, newView, al);
+
   
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
+
   
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
@@ -1763,6 +1822,7 @@ public class GAlignFrame extends JInternalFrame
         idRightAlign_actionPerformed(e);
       }
     });
+
   
     gatherViews.setEnabled(false);
     gatherViews.setText(MessageManager.getString("action.gather_views"));
@@ -1776,6 +1836,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
   
     expandViews.setEnabled(false);
     expandViews.setText(MessageManager.getString("action.expand_views"));
@@ -1789,6 +1850,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
   
     JMenuItem pageSetup = new JMenuItem(
             MessageManager.getString("action.page_setup"));
@@ -1839,6 +1901,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
+
   
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
@@ -1856,6 +1919,7 @@ public class GAlignFrame extends JInternalFrame
     {
       alignFrameMenuBar.add(hmmerMenu);
     }
+
   
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1879,6 +1943,7 @@ public class GAlignFrame extends JInternalFrame
     }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+
   
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
@@ -1901,6 +1966,7 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
+
     editMenu.addSeparator();
     editMenu.add(filterByEValue);
     editMenu.add(filterByScore);
@@ -1932,6 +1998,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
+
   
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
@@ -1981,6 +2048,7 @@ public class GAlignFrame extends JInternalFrame
       calculateMenu.addSeparator();
       calculateMenu.add(runGroovy);
     }
+
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
@@ -2001,6 +2069,7 @@ public class GAlignFrame extends JInternalFrame
     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+
   
     formatMenu.add(font);
     formatMenu.addSeparator();
@@ -2625,7 +2694,6 @@ public class GAlignFrame extends JInternalFrame
   protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
   {
   }
-
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -2720,7 +2788,6 @@ public class GAlignFrame extends JInternalFrame
   protected void hmmAlign_actionPerformed(boolean withDefaults)
   {
   }
-
   public void createPNG(java.io.File f)
   {
   }
@@ -2784,7 +2851,6 @@ public class GAlignFrame extends JInternalFrame
   protected void filterByScore_actionPerformed()
   {
   }
-
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
   }
@@ -3042,5 +3108,4 @@ public class GAlignFrame extends JInternalFrame
   {
   }
   
-
 }