From c2d20237e2d13f1209025f1620c182fa3e4e81cf Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 26 Apr 2007 17:16:07 +0000
Subject: [PATCH] added/tested sort by scores menu and added basic
 extractScores function.

---
 src/jalview/gui/AlignFrame.java    |   69 +-
 src/jalview/jbgui/GAlignFrame.java | 3708 ++++++++++++++++++------------------
 2 files changed, 1943 insertions(+), 1834 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index edd8cec..8ba8628 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -28,6 +28,7 @@ import java.awt.dnd.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
+import javax.swing.event.MenuEvent;
 
 import jalview.analysis.*;
 import jalview.commands.*;
@@ -2818,7 +2819,6 @@ public class AlignFrame
 
     alignPanel.paintAlignment(true);
   }
-
   /**
    * DOCUMENT ME!
    *
@@ -3036,6 +3036,60 @@ public class AlignFrame
       }
     });
   }
+  /**
+   * Add a new sort by annotation score menu item
+   * @param sort the menu to add the option to
+   * @param scoreLabel the label used to retrieve scores for each sequence on the alignment
+   */
+  public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel)
+  {
+    final JMenuItem item = new JMenuItem(scoreLabel);
+    sort.add(item);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
+        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+        addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
+        alignPanel.paintAlignment(true);
+      }
+    });
+  }
+  /**
+   * last hash for alignment's annotation array - used to minimise cost of rebuild.
+   */
+  protected int _annotationScoreVectorHash;
+  /**
+   * search the alignment and rebuild the sort by annotation score submenu
+   * the last alignment annotation vector hash is stored to minimize
+   * cost of rebuilding in subsequence calls.
+   *
+   */
+  public void buildSortByAnnotationScoresMenu()
+  {
+    if (viewport.alignment.getAlignmentAnnotation().hashCode()!=_annotationScoreVectorHash)
+    {
+      sortByAnnotScore.removeAll();
+      // almost certainly a quicker way to do this - but we keep it simple
+      Hashtable scoreSorts=new Hashtable();
+      AlignmentAnnotation aann[] = viewport.alignment.getAlignmentAnnotation();
+      for (int i=0;i<aann.length; i++)
+      {
+        if (aann[i].hasScore() && aann[i].sequenceRef!=null)
+        {
+          scoreSorts.put(aann[i].label, aann[i].label);
+        }
+      }
+      Enumeration labels = scoreSorts.keys();
+      while (labels.hasMoreElements())
+      {
+        addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels.nextElement());
+      }
+      sortByAnnotScore.setVisible(scoreSorts.size()>0);
+      scoreSorts.clear();
+    }
+  }
 
   /**
    * Maintain the Order by->Displayed Tree menu.
@@ -3647,6 +3701,19 @@ public void drop(DropTargetDropEvent evt)
   {
     return viewport;
   }
+
+
+  /**
+   * Open the dialog for regex description parsing.
+   */
+  protected void extractScores_actionPerformed(ActionEvent e)
+  {
+    ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
+    if (pp.getScoresFromDescription("col", "score column ", "\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)")>0)
+    {
+      buildSortByAnnotationScoresMenu();
+    }
+  }
 }
 
 class PrintThread
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bf45112..6b7c1c7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,1833 +1,1875 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
-
-public class GAlignFrame
-    extends JInternalFrame
-{
-  protected JMenuBar alignFrameMenuBar = new JMenuBar();
-  protected JMenu fileMenu = new JMenu();
-  protected JMenuItem closeMenuItem = new JMenuItem();
-  protected JMenu editMenu = new JMenu();
-  protected JMenu viewMenu = new JMenu();
-  protected JMenu colourMenu = new JMenu();
-  protected JMenu calculateMenu = new JMenu();
-  protected JMenu webService = new JMenu();
-  protected JMenuItem webServiceNoServices;
-  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
-  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
-  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
-  protected JMenuItem remove2RightMenuItem = new JMenuItem();
-  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
-  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
-  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
-  protected JMenuItem sortIDMenuItem = new JMenuItem();
-  protected JMenuItem sortGroupMenuItem = new JMenuItem();
-  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
-  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
-  protected JMenuItem PCAMenuItem = new JMenuItem();
-  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
-  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-  BorderLayout borderLayout1 = new BorderLayout();
-  public JLabel statusBar = new JLabel();
-  protected JMenuItem saveAs = new JMenuItem();
-  protected JMenu outputTextboxMenu = new JMenu();
-  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-  JMenuItem njTreeBlosumMenuItem = new JMenuItem();
-  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-  JMenuItem htmlMenuItem = new JMenuItem();
-  JMenuItem overviewMenuItem = new JMenuItem();
-  protected JMenuItem undoMenuItem = new JMenuItem();
-  protected JMenuItem redoMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-  JMenuItem printMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-  JMenuItem findMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-  JMenuItem deleteGroups = new JMenuItem();
-  JMenuItem delete = new JMenuItem();
-  JMenuItem copy = new JMenuItem();
-  JMenuItem cut = new JMenuItem();
-  JMenu pasteMenu = new JMenu();
-  JMenuItem pasteNew = new JMenuItem();
-  JMenuItem pasteThis = new JMenuItem();
-  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
-  JMenuItem createPNG = new JMenuItem();
-  protected JMenuItem font = new JMenuItem();
-  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
-  JMenuItem epsFile = new JMenuItem();
-  JMenuItem LoadtreeMenuItem = new JMenuItem();
-  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-  protected JMenuItem modifyPID = new JMenuItem();
-  protected JMenuItem modifyConservation = new JMenuItem();
-  protected JMenu sortByTreeMenu = new JMenu();
-  protected JMenu sort = new JMenu();
-  JMenu calculate = new JMenu();
-  JMenu jMenu2 = new JMenu();
-  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
-  protected ButtonGroup colours = new ButtonGroup();
-  JMenuItem vamsasStore = new JMenuItem();
-  protected JMenuItem showTranslation = new JMenuItem();
-  public JMenuItem featureSettings = new JMenuItem();
-  JMenuItem fetchSequence = new JMenuItem();
-  JMenuItem annotationColour = new JMenuItem();
-  JMenuItem associatedData = new JMenuItem();
-  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
-  JMenu addSequenceMenu = new JMenu();
-  JMenuItem addFromFile = new JMenuItem();
-  JMenuItem addFromText = new JMenuItem();
-  JMenuItem addFromURL = new JMenuItem();
-  JMenuItem exportAnnotations = new JMenuItem();
-  JMenuItem exportFeatures = new JMenuItem();
-  protected JPanel statusPanel = new JPanel();
-  GridLayout gridLayout1 = new GridLayout();
-  JMenu jMenu3 = new JMenu();
-  JMenuItem showAllSeqs = new JMenuItem();
-  JMenuItem showAllColumns = new JMenuItem();
-  JMenu hideMenu = new JMenu();
-  JMenuItem hideSelSequences = new JMenuItem();
-  JMenuItem hideSelColumns = new JMenuItem();
-  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
-  JMenuItem invertColSel = new JMenuItem();
-  protected JTabbedPane tabbedPane = new JTabbedPane();
-  JMenuItem save = new JMenuItem();
-  protected JMenuItem reload = new JMenuItem();
-  JMenuItem newView = new JMenuItem();
-  JMenuItem textColour = new JMenuItem();
-  JMenu formatMenu = new JMenu();
-  JMenu selectMenu = new JMenu();
-  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
-  protected JMenuItem gatherViews = new JMenuItem();
-  protected JMenuItem expandViews = new JMenuItem();
-  JMenuItem pageSetup = new JMenuItem();
-  JMenuItem alignmentProperties = new JMenuItem();
-  public GAlignFrame()
-  {
-    try
-    {
-      jbInit();
-      setJMenuBar(alignFrameMenuBar);
-
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
-      {
-        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
-                                       WRITEABLE_FORMATS[i]);
-
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            outputText_actionPerformed(e);
-          }
-        });
-
-        outputTextboxMenu.add(item);
-      }
-    }
-    catch (Exception e)
-    {
-    }
-
-    if (!System.getProperty("os.name").startsWith("Mac"))
-    {
-      closeMenuItem.setMnemonic('C');
-      outputTextboxMenu.setMnemonic('T');
-      undoMenuItem.setMnemonic('Z');
-      redoMenuItem.setMnemonic('0');
-      copy.setMnemonic('C');
-      cut.setMnemonic('U');
-      pasteMenu.setMnemonic('P');
-      reload.setMnemonic('R');
-    }
-
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
-    {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
-      {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-            userColours.
-            nextElement().toString());
-        radioItem.setName("USER_DEFINED");
-        radioItem.addMouseListener(new MouseAdapter()
-        {
-          public void mousePressed(MouseEvent evt)
-          {
-            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
-            {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
-                  Desktop.desktop,
-                  "Remove from default list?",
-                  "Remove user defined colour",
-                  JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
-                jalview.gui.UserDefinedColours.removeColourFromDefaults(
-                    radioItem.getText());
-                colourMenu.remove(radioItem);
-              }
-              else
-              {
-                radioItem.addActionListener(new ActionListener()
-                {
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    userDefinedColour_actionPerformed(evt);
-                  }
-                });
-              }
-            }
-          }
-        });
-        radioItem.addActionListener(new ActionListener()
-        {
-          public void actionPerformed(ActionEvent evt)
-          {
-            userDefinedColour_actionPerformed(evt);
-          }
-        });
-        colourMenu.insert(radioItem, 15);
-        colours.add(radioItem);
-      }
-    }
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(nucleotideColour);
-
-    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
-  }
-
-  public void setColourSelected(String defaultColour)
-  {
-
-    if (defaultColour != null)
-    {
-      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
-
-      switch (index)
-      {
-        case ColourSchemeProperty.NONE:
-          noColourmenuItem.setSelected(true);
-          break;
-        case ColourSchemeProperty.CLUSTAL:
-          clustalColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.BLOSUM:
-          BLOSUM62Colour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.PID:
-          PIDColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.ZAPPO:
-          zappoColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.TAYLOR:
-          taylorColour.setSelected(true);
-          break;
-
-        case ColourSchemeProperty.HYDROPHOBIC:
-          hydrophobicityColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.HELIX:
-          helixColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.STRAND:
-          strandColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.TURN:
-          turnColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.BURIED:
-          buriedColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.NUCLEOTIDE:
-          nucleotideColour.setSelected(true);
-
-          break;
-
-        case ColourSchemeProperty.USER_DEFINED:
-          userDefinedColour.setSelected(true);
-
-          break;
-      }
-    }
-
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    fileMenu.setText("File");
-    saveAs.setText("Save As...");
-    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
-    saveAs.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        saveAs_actionPerformed(e);
-      }
-    });
-    closeMenuItem.setText("Close");
-    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        closeMenuItem_actionPerformed(false);
-      }
-    });
-    editMenu.setText("Edit");
-    viewMenu.setText("View");
-    colourMenu.setText("Colour");
-    calculateMenu.setText("Calculate");
-    webService.setText("Web Service");
-    selectAllSequenceMenuItem.setText("Select All");
-    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_A,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    deselectAllSequenceMenuItem.setText("Deselect All");
-    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                               getKeyStroke(
-        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    invertSequenceMenuItem.setText("Invert Sequence Selection");
-    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        invertSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    remove2LeftMenuItem.setText("Remove Left");
-    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_L,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2LeftMenuItem_actionPerformed(e);
-      }
-    });
-    remove2RightMenuItem.setText("Remove Right");
-    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_R,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2RightMenuItem_actionPerformed(e);
-      }
-    });
-    removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                              getKeyStroke(java.awt.event.
-        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
-                                                 ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeGappedColumnMenuItem_actionPerformed(e);
-      }
-    });
-    removeAllGapsMenuItem.setText("Remove All Gaps");
-    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_E,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeAllGapsMenuItem_actionPerformed(e);
-      }
-    });
-    viewBoxesMenuItem.setText("Boxes");
-    viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        viewBoxesMenuItem_actionPerformed(e);
-      }
-    });
-    viewTextMenuItem.setText("Text");
-    viewTextMenuItem.setState(true);
-    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        viewTextMenuItem_actionPerformed(e);
-      }
-    });
-    sortPairwiseMenuItem.setText("by Pairwise Identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortPairwiseMenuItem_actionPerformed(e);
-      }
-    });
-    sortIDMenuItem.setText("by ID");
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortIDMenuItem_actionPerformed(e);
-      }
-    });
-    sortGroupMenuItem.setText("by Group");
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortGroupMenuItem_actionPerformed(e);
-      }
-    });
-    removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_D,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.
-                                               ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeRedundancyMenuItem_actionPerformed(e);
-      }
-    });
-    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
-      }
-    });
-    PCAMenuItem.setText("Principal Component Analysis");
-    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
-    averageDistanceTreeMenuItem.setText(
-        "Average Distance Using % Identity");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
-    this.getContentPane().setLayout(borderLayout1);
-    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setBackground(Color.white);
-    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
-    statusBar.setText("Status bar");
-    outputTextboxMenu.setText("Output to Textbox");
-    clustalColour.setText("Clustalx");
-
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setText("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setText("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setText("Helix Propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setText("Strand Propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setText("Turn Propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setText("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setText("User Defined...");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour.setText("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour.setText("BLOSUM62 Score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    avDistanceTreeBlosumMenuItem.setText(
-        "Average Distance Using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
-        ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
-        "SHOW_ANNOTATIONS", true));
-    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotationPanelMenuItem_actionPerformed(e);
-      }
-    });
-    colourTextMenuItem.setText("Colour Text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        colourTextMenuItem_actionPerformed(e);
-      }
-    });
-    htmlMenuItem.setText("HTML");
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        htmlMenuItem_actionPerformed(e);
-      }
-    });
-    overviewMenuItem.setText("Overview Window");
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        overviewMenuItem_actionPerformed(e);
-      }
-    });
-    undoMenuItem.setEnabled(false);
-    undoMenuItem.setText("Undo");
-    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_Z,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        undoMenuItem_actionPerformed(e);
-      }
-    });
-    redoMenuItem.setEnabled(false);
-    redoMenuItem.setText("Redo");
-    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        redoMenuItem_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.setText("By Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed(e);
-      }
-    });
-    noColourmenuItem.setText("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
-    wrapMenuItem.setText("Wrap");
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        wrapMenuItem_actionPerformed(e);
-      }
-    });
-    printMenuItem.setText("Print ...");
-    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        printMenuItem_actionPerformed(e);
-      }
-    });
-    renderGapsMenuItem.setText("Show Gaps");
-    renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        renderGapsMenuItem_actionPerformed(e);
-      }
-    });
-    findMenuItem.setText("Find...");
-    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_F,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        findMenuItem_actionPerformed(e);
-      }
-    });
-    abovePIDThreshold.setText("Above Identity Threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDThreshold_actionPerformed(e);
-      }
-    });
-    showSeqFeatures.setText("Show Sequence Features");
-    showSeqFeatures.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        showSeqFeatures_actionPerformed(actionEvent);
-      }
-    });
-    nucleotideColour.setText("Nucleotide");
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideColour_actionPerformed(e);
-      }
-    });
-    deleteGroups.setText("Undefine groups");
-    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    deleteGroups.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteGroups_actionPerformed(e);
-      }
-    });
-    copy.setText("Copy");
-    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_C,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-
-    copy.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copy_actionPerformed(e);
-      }
-    });
-    cut.setText("Cut");
-    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_X,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    cut.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cut_actionPerformed(e);
-      }
-    });
-    delete.setText("Delete");
-    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_BACK_SPACE, 0, false));
-    delete.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        delete_actionPerformed(e);
-      }
-    });
-    pasteMenu.setText("Paste");
-    pasteNew.setText("To New Alignment");
-    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
-    pasteNew.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pasteNew_actionPerformed(e);
-      }
-    });
-    pasteThis.setText("Add To This Alignment");
-    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    pasteThis.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pasteThis_actionPerformed(e);
-      }
-    });
-    applyToAllGroups.setText("Apply Colour To All Groups");
-    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        applyToAllGroups_actionPerformed(e);
-      }
-    });
-    createPNG.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        createPNG(null);
-      }
-    });
-    createPNG.setActionCommand("Save As PNG Image");
-    createPNG.setText("PNG");
-    font.setText("Font...");
-    font.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        font_actionPerformed(e);
-      }
-    });
-
-    seqLimits.setText("Show Sequence Limits");
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
-    seqLimits.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        seqLimit_actionPerformed(e);
-      }
-    });
-    epsFile.setText("EPS");
-    epsFile.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        createEPS(null);
-      }
-    });
-    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Associated Tree");
-    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        LoadtreeMenuItem_actionPerformed(e);
-      }
-    });
-    scaleAbove.setVisible(false);
-    scaleAbove.setText("Scale Above");
-    scaleAbove.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        scaleAbove_actionPerformed(e);
-      }
-    });
-    scaleLeft.setVisible(false);
-    scaleLeft.setSelected(true);
-    scaleLeft.setText("Scale Left");
-    scaleLeft.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        scaleLeft_actionPerformed(e);
-      }
-    });
-    scaleRight.setVisible(false);
-    scaleRight.setSelected(true);
-    scaleRight.setText("Scale Right");
-    scaleRight.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        scaleRight_actionPerformed(e);
-      }
-    });
-    modifyPID.setText("Modify Identity Threshold...");
-    modifyPID.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed(e);
-      }
-    });
-    modifyConservation.setText("Modify Conservation Threshold...");
-    modifyConservation.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed(e);
-      }
-    });
-    sortByTreeMenu.setText("By Tree Order");
-    sort.setText("Sort");
-    sort.addMenuListener(new MenuListener()
-    {
-      public void menuSelected(MenuEvent e)
-      {
-        buildTreeMenu();
-      }
-
-      public void menuDeselected(MenuEvent e)
-      {
-      }
-
-      public void menuCanceled(MenuEvent e)
-      {
-      }
-    });
-    calculate.setText("Calculate Tree");
-
-    jMenu2.setText("Export Image");
-    padGapsMenuitem.setText("Pad Gaps");
-    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
-    padGapsMenuitem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        padGapsMenuitem_actionPerformed(e);
-      }
-    });
-    vamsasStore.setVisible(false);
-    vamsasStore.setText("VAMSAS store");
-    vamsasStore.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        vamsasStore_actionPerformed(e);
-      }
-    });
-    showTranslation.setText("Translate cDNA");
-    showTranslation.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showTranslation_actionPerformed(e);
-      }
-    });
-
-    featureSettings.setText("Feature Settings...");
-    featureSettings.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        featureSettings_actionPerformed(e);
-      }
-    });
-    fetchSequence.setText("Fetch Sequence(s)...");
-    fetchSequence.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fetchSequence_actionPerformed(e);
-      }
-    });
-
-    annotationColour.setText("By Annotation...");
-    annotationColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotationColour_actionPerformed(e);
-      }
-    });
-    associatedData.setText("Load Features / Annotations");
-    associatedData.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        associatedData_actionPerformed(e);
-      }
-    });
-    autoCalculate.setText("Autocalculate Consensus");
-    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
-    autoCalculate.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        autoCalculate_actionPerformed(e);
-      }
-    });
-    addSequenceMenu.setText("Add Sequences");
-    addFromFile.setText("From File");
-    addFromFile.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addFromFile_actionPerformed(e);
-      }
-    });
-    addFromText.setText("From Textbox");
-    addFromText.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addFromText_actionPerformed(e);
-      }
-    });
-    addFromURL.setText("From URL");
-    addFromURL.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        addFromURL_actionPerformed(e);
-      }
-    });
-    exportFeatures.setText("Export Features...");
-    exportFeatures.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        exportFeatures_actionPerformed(e);
-      }
-    });
-    exportAnnotations.setText("Export Annotations...");
-    exportAnnotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        exportAnnotations_actionPerformed(e);
-      }
-    });
-    statusPanel.setLayout(gridLayout1);
-    jMenu3.setText("Show");
-    showAllSeqs.setText("All Sequences");
-    showAllSeqs.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showAllSeqs_actionPerformed(e);
-      }
-    });
-    showAllColumns.setText("All Columns");
-    showAllColumns.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        showAllColumns_actionPerformed(e);
-      }
-    });
-    hideMenu.setText("Hide");
-    hideSelSequences.setText("Selected Sequences");
-    hideSelSequences.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hideSelSequences_actionPerformed(e);
-      }
-    });
-    hideSelColumns.setText("Selected Columns");
-    hideSelColumns.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hideSelColumns_actionPerformed(e);
-      }
-    });
-    hiddenMarkers.setText("Show Hidden Markers");
-    hiddenMarkers.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hiddenMarkers_actionPerformed(e);
-      }
-    });
-    invertColSel.setText("Invert Column Selection");
-    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-        | java.awt.event.KeyEvent.ALT_MASK,
-        false));
-    invertColSel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        invertColSel_actionPerformed(e);
-      }
-    });
-    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        JTabbedPane pane = (JTabbedPane) evt.getSource();
-        int sel = pane.getSelectedIndex();
-        tabSelectionChanged(sel);
-      }
-    });
-    tabbedPane.addMouseListener(new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent e)
-      {
-        tabbedPane_mousePressed(e);
-      }
-    });
-    tabbedPane.addFocusListener(new FocusAdapter()
-    {
-      public void focusGained(FocusEvent e)
-      {
-        tabbedPane_focusGained(e);
-      }
-    });
-    save.setText("Save");
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    save.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        save_actionPerformed(e);
-      }
-    });
-    reload.setEnabled(false);
-    reload.setText("Reload");
-    reload.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        reload_actionPerformed(e);
-      }
-    });
-    newView.setText("New View");
-    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    newView.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        newView_actionPerformed(e);
-      }
-    });
-    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
-                              +
-        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
-    textColour.setText("Text Colour");
-    textColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        textColour_actionPerformed(e);
-      }
-    });
-    formatMenu.setText("Format");
-    selectMenu.setText("Select");
-    idRightAlign.setText("Right Align Sequence Id");
-    idRightAlign.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        idRightAlign_actionPerformed(e);
-      }
-    });
-    gatherViews.setEnabled(false);
-    gatherViews.setText("Gather Views");
-    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_G, 0, false));
-    gatherViews.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        gatherViews_actionPerformed(e);
-      }
-    });
-    expandViews.setEnabled(false);
-    expandViews.setText("Expand Views");
-    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_X, 0, false));
-    expandViews.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        expandViews_actionPerformed(e);
-      }
-    });
-    pageSetup.setText("Page Setup ...");
-    pageSetup.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pageSetup_actionPerformed(e);
-      }
-    });
-    alignmentProperties.setText("Alignment Properties...");
-    alignmentProperties.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        alignmentProperties();
-      }
-    });
-
-    alignFrameMenuBar.add(fileMenu);
-    alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(selectMenu);
-    alignFrameMenuBar.add(viewMenu);
-    alignFrameMenuBar.add(formatMenu);
-    alignFrameMenuBar.add(colourMenu);
-    alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(webService);
-    fileMenu.add(fetchSequence);
-    fileMenu.add(addSequenceMenu);
-    fileMenu.add(reload);
-    fileMenu.addSeparator();
-    fileMenu.add(vamsasStore);
-    fileMenu.add(save);
-    fileMenu.add(saveAs);
-    fileMenu.add(outputTextboxMenu);
-    fileMenu.add(pageSetup);
-    fileMenu.add(printMenuItem);
-    fileMenu.addSeparator();
-    fileMenu.add(jMenu2);
-    fileMenu.add(exportFeatures);
-    fileMenu.add(exportAnnotations);
-    fileMenu.add(LoadtreeMenuItem);
-    fileMenu.add(associatedData);
-    fileMenu.addSeparator();
-    fileMenu.add(closeMenuItem);
-    editMenu.add(undoMenuItem);
-    editMenu.add(redoMenuItem);
-    editMenu.add(cut);
-    editMenu.add(copy);
-    editMenu.add(pasteMenu);
-    editMenu.add(delete);
-    editMenu.addSeparator();
-    editMenu.add(remove2LeftMenuItem);
-    editMenu.add(remove2RightMenuItem);
-    editMenu.add(removeGappedColumnMenuItem);
-    editMenu.add(removeAllGapsMenuItem);
-    editMenu.add(removeRedundancyMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(padGapsMenuitem);
-    viewMenu.add(newView);
-    viewMenu.add(expandViews);
-    viewMenu.add(gatherViews);
-    viewMenu.addSeparator();
-    viewMenu.add(jMenu3);
-    viewMenu.add(hideMenu);
-    viewMenu.addSeparator();
-    viewMenu.add(annotationPanelMenuItem);
-    viewMenu.addSeparator();
-    viewMenu.add(showSeqFeatures);
-    viewMenu.add(featureSettings);
-    viewMenu.addSeparator();
-    viewMenu.add(alignmentProperties);
-    viewMenu.addSeparator();
-    viewMenu.add(overviewMenuItem);
-    colourMenu.add(applyToAllGroups);
-    colourMenu.add(textColour);
-    colourMenu.addSeparator();
-    colourMenu.add(noColourmenuItem);
-    colourMenu.add(clustalColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydrophobicityColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(nucleotideColour);
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(conservationMenuItem);
-    colourMenu.add(modifyConservation);
-    colourMenu.add(abovePIDThreshold);
-    colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
-    calculateMenu.add(sort);
-    calculateMenu.add(calculate);
-    calculateMenu.addSeparator();
-    calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
-    calculateMenu.addSeparator();
-    calculateMenu.add(showTranslation);
-    calculateMenu.add(autoCalculate);
-    webServiceNoServices = new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);
-    pasteMenu.add(pasteNew);
-    pasteMenu.add(pasteThis);
-    sort.add(sortIDMenuItem);
-    sort.add(sortGroupMenuItem);
-    sort.add(sortPairwiseMenuItem);
-    sort.add(sortByTreeMenu);
-    calculate.add(averageDistanceTreeMenuItem);
-    calculate.add(neighbourTreeMenuItem);
-    calculate.add(avDistanceTreeBlosumMenuItem);
-    calculate.add(njTreeBlosumMenuItem);
-    jMenu2.add(htmlMenuItem);
-    jMenu2.add(epsFile);
-    jMenu2.add(createPNG);
-    addSequenceMenu.add(addFromFile);
-    addSequenceMenu.add(addFromText);
-    addSequenceMenu.add(addFromURL);
-    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
-    statusPanel.add(statusBar, null);
-    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    jMenu3.add(showAllColumns);
-    jMenu3.add(showAllSeqs);
-    hideMenu.add(hideSelColumns);
-    hideMenu.add(hideSelSequences);
-    formatMenu.add(font);
-    formatMenu.addSeparator();
-    formatMenu.add(wrapMenuItem);
-    formatMenu.add(scaleAbove);
-    formatMenu.add(scaleLeft);
-    formatMenu.add(scaleRight);
-    formatMenu.add(seqLimits);
-    formatMenu.add(idRightAlign);
-    formatMenu.add(hiddenMarkers);
-    formatMenu.add(viewBoxesMenuItem);
-    formatMenu.add(viewTextMenuItem);
-    formatMenu.add(colourTextMenuItem);
-    formatMenu.add(renderGapsMenuItem);
-    selectMenu.add(findMenuItem);
-    selectMenu.addSeparator();
-    selectMenu.add(selectAllSequenceMenuItem);
-    selectMenu.add(deselectAllSequenceMenuItem);
-    selectMenu.add(invertSequenceMenuItem);
-    selectMenu.add(invertColSel);
-    selectMenu.add(deleteGroups);
-  }
-
-  protected void outputText_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void addFromFile_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void addFromText_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void addFromURL_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void exportFeatures_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void exportAnnotations_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void closeMenuItem_actionPerformed(boolean b)
-  {
-  }
-
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void overviewMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void printMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void findMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
-  {
-  }
-
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void deleteGroups_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void copy_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void cut_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void delete_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void pasteNew_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void pasteThis_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void createPNG(java.io.File f)
-  {
-  }
-
-  protected void font_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void seqLimit_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void seqDBRef_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void createEPS(java.io.File f)
-  {
-  }
-
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void jpred_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void scaleAbove_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void scaleLeft_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void scaleRight_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void modifyConservation_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  public void vamsasStore_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void vamsasLoad_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void showTranslation_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void featureSettings_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void fetchSequence_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void smoothFont_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void annotationColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void associatedData_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void autoCalculate_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void showAllSeqs_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void showAllColumns_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void hideSelSequences_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void hideSelColumns_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void hiddenMarkers_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void findPdbId_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void enterPdbId_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void pdbFile_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void invertColSel_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void tabSelectionChanged(int sel)
-  {
-
-  }
-
-  public void tabbedPane_mousePressed(MouseEvent e)
-  {
-
-  }
-
-  public void tabbedPane_focusGained(FocusEvent e)
-  {
-    requestFocus();
-  }
-
-  public void save_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void reload_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void newView_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void textColour_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void idRightAlign_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void expandViews_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void gatherViews_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void buildTreeMenu()
-  {
-
-  }
-
-  public void pageSetup_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void alignmentProperties()
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.jbgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.schemes.*;
+
+public class GAlignFrame
+    extends JInternalFrame
+{
+  protected JMenuBar alignFrameMenuBar = new JMenuBar();
+  protected JMenu fileMenu = new JMenu();
+  protected JMenuItem closeMenuItem = new JMenuItem();
+  protected JMenu editMenu = new JMenu();
+  protected JMenu viewMenu = new JMenu();
+  protected JMenu colourMenu = new JMenu();
+  protected JMenu calculateMenu = new JMenu();
+  protected JMenu webService = new JMenu();
+  protected JMenuItem webServiceNoServices;
+  protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+  protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+  protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+  protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+  protected JMenuItem remove2RightMenuItem = new JMenuItem();
+  protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+  protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+  protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+  protected JMenuItem sortIDMenuItem = new JMenuItem();
+  protected JMenuItem sortGroupMenuItem = new JMenuItem();
+  protected JMenu sortByAnnotScore = new JMenu();
+  protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+  protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+  protected JMenuItem PCAMenuItem = new JMenuItem();
+  protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+  protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+  BorderLayout borderLayout1 = new BorderLayout();
+  public JLabel statusBar = new JLabel();
+  protected JMenuItem saveAs = new JMenuItem();
+  protected JMenu outputTextboxMenu = new JMenu();
+  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+  JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+  JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+  JMenuItem htmlMenuItem = new JMenuItem();
+  JMenuItem overviewMenuItem = new JMenuItem();
+  protected JMenuItem undoMenuItem = new JMenuItem();
+  protected JMenuItem redoMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+  JMenuItem printMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  JMenuItem findMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+  JMenuItem deleteGroups = new JMenuItem();
+  JMenuItem delete = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem cut = new JMenuItem();
+  JMenu pasteMenu = new JMenu();
+  JMenuItem pasteNew = new JMenuItem();
+  JMenuItem pasteThis = new JMenuItem();
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  JMenuItem createPNG = new JMenuItem();
+  protected JMenuItem font = new JMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+  JMenuItem epsFile = new JMenuItem();
+  JMenuItem LoadtreeMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
+  protected JMenuItem modifyConservation = new JMenuItem();
+  protected JMenu sortByTreeMenu = new JMenu();
+  protected JMenu sort = new JMenu();
+  JMenu calculate = new JMenu();
+  JMenu jMenu2 = new JMenu();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
+  JMenuItem vamsasStore = new JMenuItem();
+  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenuItem extractScores = new JMenuItem();
+  public JMenuItem featureSettings = new JMenuItem();
+  JMenuItem fetchSequence = new JMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
+  JMenuItem exportAnnotations = new JMenuItem();
+  JMenuItem exportFeatures = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  JMenu jMenu3 = new JMenu();
+  JMenuItem showAllSeqs = new JMenuItem();
+  JMenuItem showAllColumns = new JMenuItem();
+  JMenu hideMenu = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
+  JMenuItem save = new JMenuItem();
+  protected JMenuItem reload = new JMenuItem();
+  JMenuItem newView = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu formatMenu = new JMenu();
+  JMenu selectMenu = new JMenu();
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+  protected JMenuItem gatherViews = new JMenuItem();
+  protected JMenuItem expandViews = new JMenuItem();
+  JMenuItem pageSetup = new JMenuItem();
+  JMenuItem alignmentProperties = new JMenuItem();
+  public GAlignFrame()
+  {
+    try
+    {
+      jbInit();
+      setJMenuBar(alignFrameMenuBar);
+
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      {
+        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
+                                       WRITEABLE_FORMATS[i]);
+
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            outputText_actionPerformed(e);
+          }
+        });
+
+        outputTextboxMenu.add(item);
+      }
+    }
+    catch (Exception e)
+    {
+    }
+
+    if (!System.getProperty("os.name").startsWith("Mac"))
+    {
+      closeMenuItem.setMnemonic('C');
+      outputTextboxMenu.setMnemonic('T');
+      undoMenuItem.setMnemonic('Z');
+      redoMenuItem.setMnemonic('0');
+      copy.setMnemonic('C');
+      cut.setMnemonic('U');
+      pasteMenu.setMnemonic('P');
+      reload.setMnemonic('R');
+    }
+
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+            userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+            {
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
+                  Desktop.desktop,
+                  "Remove from default list?",
+                  "Remove user defined colour",
+                  JOptionPane.YES_NO_OPTION);
+              if (option == JOptionPane.YES_OPTION)
+              {
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(
+                    radioItem.getText());
+                colourMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent evt)
+                  {
+                    userDefinedColour_actionPerformed(evt);
+                  }
+                });
+              }
+            }
+          }
+        });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
+
+    if (defaultColour != null)
+    {
+      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+      switch (index)
+      {
+        case ColourSchemeProperty.NONE:
+          noColourmenuItem.setSelected(true);
+          break;
+        case ColourSchemeProperty.CLUSTAL:
+          clustalColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BLOSUM:
+          BLOSUM62Colour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.PID:
+          PIDColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.ZAPPO:
+          zappoColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.TAYLOR:
+          taylorColour.setSelected(true);
+          break;
+
+        case ColourSchemeProperty.HYDROPHOBIC:
+          hydrophobicityColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.HELIX:
+          helixColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.STRAND:
+          strandColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.TURN:
+          turnColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BURIED:
+          buriedColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.NUCLEOTIDE:
+          nucleotideColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.USER_DEFINED:
+          userDefinedColour.setSelected(true);
+
+          break;
+      }
+    }
+
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    fileMenu.setText("File");
+    saveAs.setText("Save As...");
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
+    saveAs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAs_actionPerformed(e);
+      }
+    });
+    closeMenuItem.setText("Close");
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        closeMenuItem_actionPerformed(false);
+      }
+    });
+    editMenu.setText("Edit");
+    viewMenu.setText("View");
+    colourMenu.setText("Colour");
+    calculateMenu.setText("Calculate");
+    webService.setText("Web Service");
+    selectAllSequenceMenuItem.setText("Select All");
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        selectAllSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    deselectAllSequenceMenuItem.setText("Deselect All");
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                               getKeyStroke(
+        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deselectAllSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_I,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSequenceMenuItem_actionPerformed(e);
+      }
+    });
+    remove2LeftMenuItem.setText("Remove Left");
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_L,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2LeftMenuItem_actionPerformed(e);
+      }
+    });
+    remove2RightMenuItem.setText("Remove Right");
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_R,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        remove2RightMenuItem_actionPerformed(e);
+      }
+    });
+    removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                              getKeyStroke(java.awt.event.
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeGappedColumnMenuItem_actionPerformed(e);
+      }
+    });
+    removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_E,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
+    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeAllGapsMenuItem_actionPerformed(e);
+      }
+    });
+    viewBoxesMenuItem.setText("Boxes");
+    viewBoxesMenuItem.setState(true);
+    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewBoxesMenuItem_actionPerformed(e);
+      }
+    });
+    viewTextMenuItem.setText("Text");
+    viewTextMenuItem.setState(true);
+    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewTextMenuItem_actionPerformed(e);
+      }
+    });
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
+    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortPairwiseMenuItem_actionPerformed(e);
+      }
+    });
+    sortIDMenuItem.setText("by ID");
+    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortIDMenuItem_actionPerformed(e);
+      }
+    });
+    sortGroupMenuItem.setText("by Group");
+    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortGroupMenuItem_actionPerformed(e);
+      }
+    });
+    removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_D,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeRedundancyMenuItem_actionPerformed(e);
+      }
+    });
+    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pairwiseAlignmentMenuItem_actionPerformed(e);
+      }
+    });
+    PCAMenuItem.setText("Principal Component Analysis");
+    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PCAMenuItem_actionPerformed(e);
+      }
+    });
+    averageDistanceTreeMenuItem.setText(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        averageDistanceTreeMenuItem_actionPerformed(e);
+      }
+    });
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        neighbourTreeMenuItem_actionPerformed(e);
+      }
+    });
+    this.getContentPane().setLayout(borderLayout1);
+    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setBackground(Color.white);
+    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+    statusBar.setText("Status bar");
+    outputTextboxMenu.setText("Output to Textbox");
+    clustalColour.setText("Clustalx");
+
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed(e);
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed(e);
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed(e);
+      }
+    });
+    hydrophobicityColour.setText("Hydrophobicity");
+    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydrophobicityColour_actionPerformed(e);
+      }
+    });
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed(e);
+      }
+    });
+    strandColour.setText("Strand Propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed(e);
+      }
+    });
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed(e);
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed(e);
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed(e);
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62 Score");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed(e);
+      }
+    });
+    avDistanceTreeBlosumMenuItem.setText(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+        ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        avTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        njTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    annotationPanelMenuItem.setActionCommand("");
+    annotationPanelMenuItem.setText("Show Annotations");
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+        "SHOW_ANNOTATIONS", true));
+    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationPanelMenuItem_actionPerformed(e);
+      }
+    });
+    colourTextMenuItem.setText("Colour Text");
+    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        colourTextMenuItem_actionPerformed(e);
+      }
+    });
+    htmlMenuItem.setText("HTML");
+    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        htmlMenuItem_actionPerformed(e);
+      }
+    });
+    overviewMenuItem.setText("Overview Window");
+    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        overviewMenuItem_actionPerformed(e);
+      }
+    });
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setText("Undo");
+    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_Z,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoMenuItem_actionPerformed(e);
+      }
+    });
+    redoMenuItem.setEnabled(false);
+    redoMenuItem.setText("Redo");
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        redoMenuItem_actionPerformed(e);
+      }
+    });
+    conservationMenuItem.setText("By Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
+      }
+    });
+    wrapMenuItem.setText("Wrap");
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
+    printMenuItem.setText("Print ...");
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenuItem_actionPerformed(e);
+      }
+    });
+    renderGapsMenuItem.setText("Show Gaps");
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        renderGapsMenuItem_actionPerformed(e);
+      }
+    });
+    findMenuItem.setText("Find...");
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_F,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        findMenuItem_actionPerformed(e);
+      }
+    });
+    abovePIDThreshold.setText("Above Identity Threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(e);
+      }
+    });
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showSeqFeatures_actionPerformed(actionEvent);
+      }
+    });
+    nucleotideColour.setText("Nucleotide");
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideColour_actionPerformed(e);
+      }
+    });
+    deleteGroups.setText("Undefine groups");
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    deleteGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deleteGroups_actionPerformed(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_C,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+
+    copy.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    cut.setText("Cut");
+    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_X,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    cut.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    delete.setText("Delete");
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_BACK_SPACE, 0, false));
+    delete.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        delete_actionPerformed(e);
+      }
+    });
+    pasteMenu.setText("Paste");
+    pasteNew.setText("To New Alignment");
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteNew_actionPerformed(e);
+      }
+    });
+    pasteThis.setText("Add To This Alignment");
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteThis_actionPerformed(e);
+      }
+    });
+    applyToAllGroups.setText("Apply Colour To All Groups");
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(e);
+      }
+    });
+    createPNG.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createPNG(null);
+      }
+    });
+    createPNG.setActionCommand("Save As PNG Image");
+    createPNG.setText("PNG");
+    font.setText("Font...");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_actionPerformed(e);
+      }
+    });
+
+    seqLimits.setText("Show Sequence Limits");
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        seqLimit_actionPerformed(e);
+      }
+    });
+    epsFile.setText("EPS");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createEPS(null);
+      }
+    });
+    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+    LoadtreeMenuItem.setText("Load Associated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        LoadtreeMenuItem_actionPerformed(e);
+      }
+    });
+    scaleAbove.setVisible(false);
+    scaleAbove.setText("Scale Above");
+    scaleAbove.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleAbove_actionPerformed(e);
+      }
+    });
+    scaleLeft.setVisible(false);
+    scaleLeft.setSelected(true);
+    scaleLeft.setText("Scale Left");
+    scaleLeft.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleLeft_actionPerformed(e);
+      }
+    });
+    scaleRight.setVisible(false);
+    scaleRight.setSelected(true);
+    scaleRight.setText("Scale Right");
+    scaleRight.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleRight_actionPerformed(e);
+      }
+    });
+    modifyPID.setText("Modify Identity Threshold...");
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed(e);
+      }
+    });
+    modifyConservation.setText("Modify Conservation Threshold...");
+    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed(e);
+      }
+    });
+    sortByTreeMenu.setText("By Tree Order");
+    sort.setText("Sort");
+    sort.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        buildTreeMenu();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    sortByAnnotScore.setText("by Score");
+    sort.add(sortByAnnotScore);
+    sortByAnnotScore.addMenuListener(
+            new javax.swing.event.MenuListener() {
+              
+                public void menuCanceled(MenuEvent e)
+                {
+                }
+
+                public void menuDeselected(MenuEvent e)
+                {
+                }
+
+                public void menuSelected(MenuEvent e)
+                {
+                  buildSortByAnnotationScoresMenu();
+                }
+              }
+              );
+    sortByAnnotScore.setVisible(false);
+    
+    calculate.setText("Calculate Tree");
+
+    jMenu2.setText("Export Image");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
+      }
+    });
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStore_actionPerformed(e);
+      }
+    });
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showTranslation_actionPerformed(e);
+      }
+    });
+    extractScores.setText("Extract Scores...");
+    extractScores.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        extractScores_actionPerformed(e);
+      }
+    });
+    
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        featureSettings_actionPerformed(e);
+      }
+    });
+    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSequence_actionPerformed(e);
+      }
+    });
+
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    hideMenu.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Show Hidden Markers");
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_I,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+        | java.awt.event.KeyEvent.ALT_MASK,
+        false));
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        JTabbedPane pane = (JTabbedPane) evt.getSource();
+        int sel = pane.getSelectedIndex();
+        tabSelectionChanged(sel);
+      }
+    });
+    tabbedPane.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        tabbedPane_mousePressed(e);
+      }
+    });
+    tabbedPane.addFocusListener(new FocusAdapter()
+    {
+      public void focusGained(FocusEvent e)
+      {
+        tabbedPane_focusGained(e);
+      }
+    });
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save_actionPerformed(e);
+      }
+    });
+    reload.setEnabled(false);
+    reload.setText("Reload");
+    reload.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        reload_actionPerformed(e);
+      }
+    });
+    newView.setText("New View");
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    newView.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        newView_actionPerformed(e);
+      }
+    });
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+                              +
+        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    formatMenu.setText("Format");
+    selectMenu.setText("Select");
+    idRightAlign.setText("Right Align Sequence Id");
+    idRightAlign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        idRightAlign_actionPerformed(e);
+      }
+    });
+    gatherViews.setEnabled(false);
+    gatherViews.setText("Gather Views");
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_G, 0, false));
+    gatherViews.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        gatherViews_actionPerformed(e);
+      }
+    });
+    expandViews.setEnabled(false);
+    expandViews.setText("Expand Views");
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_X, 0, false));
+    expandViews.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        expandViews_actionPerformed(e);
+      }
+    });
+    pageSetup.setText("Page Setup ...");
+    pageSetup.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pageSetup_actionPerformed(e);
+      }
+    });
+    alignmentProperties.setText("Alignment Properties...");
+    alignmentProperties.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignmentProperties();
+      }
+    });
+
+    alignFrameMenuBar.add(fileMenu);
+    alignFrameMenuBar.add(editMenu);
+    alignFrameMenuBar.add(selectMenu);
+    alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
+    alignFrameMenuBar.add(colourMenu);
+    alignFrameMenuBar.add(calculateMenu);
+    alignFrameMenuBar.add(webService);
+    fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
+    fileMenu.add(save);
+    fileMenu.add(saveAs);
+    fileMenu.add(outputTextboxMenu);
+    fileMenu.add(pageSetup);
+    fileMenu.add(printMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(jMenu2);
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
+    fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
+    fileMenu.addSeparator();
+    fileMenu.add(closeMenuItem);
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(pasteMenu);
+    editMenu.add(delete);
+    editMenu.addSeparator();
+    editMenu.add(remove2LeftMenuItem);
+    editMenu.add(remove2RightMenuItem);
+    editMenu.add(removeGappedColumnMenuItem);
+    editMenu.add(removeAllGapsMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
+    viewMenu.add(newView);
+    viewMenu.add(expandViews);
+    viewMenu.add(gatherViews);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
+    viewMenu.addSeparator();
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.addSeparator();
+    viewMenu.add(showSeqFeatures);
+    viewMenu.add(featureSettings);
+    viewMenu.addSeparator();
+    viewMenu.add(alignmentProperties);
+    viewMenu.addSeparator();
+    viewMenu.add(overviewMenuItem);
+    colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
+    colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
+    colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
+    colourMenu.add(zappoColour);
+    colourMenu.add(taylorColour);
+    colourMenu.add(hydrophobicityColour);
+    colourMenu.add(helixColour);
+    colourMenu.add(strandColour);
+    colourMenu.add(turnColour);
+    colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideColour);
+    colourMenu.add(userDefinedColour);
+    colourMenu.addSeparator();
+    colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
+    calculateMenu.add(sort);
+    calculateMenu.add(calculate);
+    calculateMenu.addSeparator();
+    calculateMenu.add(pairwiseAlignmentMenuItem);
+    calculateMenu.add(PCAMenuItem);
+    calculateMenu.addSeparator();
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
+    calculateMenu.addSeparator();
+    calculateMenu.add(extractScores);
+    webServiceNoServices = new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);
+    pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
+    sort.add(sortIDMenuItem);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    sort.add(sortByTreeMenu);
+    calculate.add(averageDistanceTreeMenuItem);
+    calculate.add(neighbourTreeMenuItem);
+    calculate.add(avDistanceTreeBlosumMenuItem);
+    calculate.add(njTreeBlosumMenuItem);
+    jMenu2.add(htmlMenuItem);
+    jMenu2.add(epsFile);
+    jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+    jMenu3.add(showAllColumns);
+    jMenu3.add(showAllSeqs);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
+    formatMenu.add(font);
+    formatMenu.addSeparator();
+    formatMenu.add(wrapMenuItem);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(seqLimits);
+    formatMenu.add(idRightAlign);
+    formatMenu.add(hiddenMarkers);
+    formatMenu.add(viewBoxesMenuItem);
+    formatMenu.add(viewTextMenuItem);
+    formatMenu.add(colourTextMenuItem);
+    formatMenu.add(renderGapsMenuItem);
+    selectMenu.add(findMenuItem);
+    selectMenu.addSeparator();
+    selectMenu.add(selectAllSequenceMenuItem);
+    selectMenu.add(deselectAllSequenceMenuItem);
+    selectMenu.add(invertSequenceMenuItem);
+    selectMenu.add(invertColSel);
+    selectMenu.add(deleteGroups);
+  }
+
+  protected void buildSortByAnnotationScoresMenu()
+  {
+  }
+
+  protected void extractScores_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void outputText_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void closeMenuItem_actionPerformed(boolean b)
+  {
+  }
+
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void PCAMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void clustalColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void zappoColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void taylorColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void helixColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void strandColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void turnColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void buriedColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void PIDColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void printMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void copy_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void cut_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void createPNG(java.io.File f)
+  {
+  }
+
+  protected void font_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void seqDBRef_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void createEPS(java.io.File f)
+  {
+  }
+
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void saveAs_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showTranslation_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void findPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void enterPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void pdbFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void tabSelectionChanged(int sel)
+  {
+
+  }
+
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void reload_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void newView_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void expandViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void gatherViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void buildTreeMenu()
+  {
+
+  }
+  
+  public void pageSetup_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void alignmentProperties()
+  {
+
+  }
+}
-- 
1.7.10.2