added/tested sort by scores menu and added basic extractScores function.

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