Formatting
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
index 81325d5..1b89d71 100755 (executable)
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
+ * 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 jalview.gui.Preferences;\r
-\r
-import jalview.schemes.ColourSchemeProperty;\r
-\r
 import java.awt.*;\r
 import java.awt.event.*;\r
-\r
 import javax.swing.*;\r
-import javax.swing.event.AncestorEvent;\r
-import javax.swing.event.AncestorListener;\r
-\r
-\r
-public class GAlignFrame extends JInternalFrame {\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 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
-    protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();\r
-    protected 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
-    protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
-    BorderLayout borderLayout1 = new BorderLayout();\r
-    public JLabel statusBar = new JLabel();\r
-    protected JMenuItem saveAlignmentMenu = 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 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
-    protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();\r
-    protected 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
-    protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-    JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
-    protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();\r
-    JMenuItem printMenuItem = new JMenuItem();\r
-    protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
-    JMenuItem findMenuItem = new JMenuItem();\r
-    JMenu searchMenu = new JMenu();\r
-    protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
-    protected JCheckBoxMenuItem sequenceFeatures = 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 jMenu1 = new JMenu();\r
-    JMenuItem pasteNew = new JMenuItem();\r
-    JMenuItem pasteThis = new JMenuItem();\r
-    protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
-    JMenuItem createPNG = new JMenuItem();\r
-    protected JMenuItem font = new JMenuItem();\r
-    protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
-    JMenuItem epsFile = new JMenuItem();\r
-    JMenuItem LoadtreeMenuItem = new JMenuItem();\r
-    JMenuItem jpred = new JMenuItem();\r
-    protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
-    protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
-    protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
-    JMenuItem modifyPID = new JMenuItem();\r
-    JMenuItem modifyConservation = new JMenuItem();\r
-    protected JMenu sortByTreeMenu = new JMenu();\r
-    protected JMenu sort = new JMenu();\r
-    JMenu calculate = new JMenu();\r
-    JMenuItem msaAlignMenuItem = new JMenuItem();\r
-    JMenu jMenu2 = new JMenu();\r
-    JMenuItem padGapsMenuitem = new JMenuItem();\r
-    JMenuItem ClustalRealign = new JMenuItem();\r
-\r
-    public GAlignFrame() {\r
-        ButtonGroup colours = new ButtonGroup();\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
-        noColourmenuItem.setSelected(true);\r
-\r
-        String defaultColour = Preferences.defaultColour;\r
-\r
-        if (defaultColour != null) {\r
-            int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);\r
-\r
-            switch (index) {\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.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
+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
+  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
-                break;\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
+\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(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
-            case ColourSchemeProperty.USER_DEFINED:\r
-                userDefinedColour.setSelected(true);\r
+  protected void viewTextMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-                break;\r
-            }\r
-        }\r
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-        try {\r
-            jbInit();\r
-            setJMenuBar(alignFrameMenuBar);\r
+  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-            JMenuItem item;\r
+  protected void overviewMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-            // dynamically fill save as menu with available formats\r
-            for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {\r
-                item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(\r
-                            i));\r
-                item.addActionListener(new java.awt.event.ActionListener() {\r
-                        public void actionPerformed(ActionEvent e) {\r
-                            outputText_actionPerformed(e);\r
-                        }\r
-                    });\r
+  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-                outputTextboxMenu.add(item);\r
-            }\r
-        } catch (Exception e) {\r
-            e.printStackTrace();\r
-        }\r
-    }\r
+  protected void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    private void jbInit() throws Exception {\r
-        fileMenu.setMnemonic('F');\r
-        fileMenu.setText("File");\r
-        saveAlignmentMenu.setMnemonic('L');\r
-        saveAlignmentMenu.setText("Save As");\r
-        saveAlignmentMenu.addActionListener(new ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    saveAlignmentMenu_actionPerformed(e);\r
-                }\r
-            });\r
-        closeMenuItem.setMnemonic('C');\r
-        closeMenuItem.setText("Close");\r
-        closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    closeMenuItem_actionPerformed(e);\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.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    selectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        deselectAllSequenceMenuItem.setText("Deselect All");\r
-        deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
-                java.awt.event.KeyEvent.VK_ESCAPE, 0, false));\r
-        deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    deselectAllSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        invertSequenceMenuItem.setText("Invert Selection");\r
-        invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    invertSequenceMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        remove2LeftMenuItem.setText("Remove Left");\r
-        remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2LeftMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        remove2RightMenuItem.setText("Remove Right");\r
-        remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    remove2RightMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
-        removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeGappedColumnMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeAllGapsMenuItem.setText("Remove All Gaps");\r
-        removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeAllGapsMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        viewBoxesMenuItem.setText("Boxes");\r
-        viewBoxesMenuItem.setState(true);\r
-        viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    viewBoxesMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        viewTextMenuItem.setText("Text");\r
-        viewTextMenuItem.setState(true);\r
-        viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    viewTextMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        sortPairwiseMenuItem.setText("by Pairwise Identity");\r
-        sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortPairwiseMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        sortIDMenuItem.setText("by ID");\r
-        sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortIDMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        sortGroupMenuItem.setText("by Group");\r
-        sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    sortGroupMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        removeRedundancyMenuItem.setText("Remove Redundancy...");\r
-        removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    removeRedundancyMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");\r
-        pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pairwiseAlignmentMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        PCAMenuItem.setText("Principal Component Analysis...");\r
-        PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PCAMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        averageDistanceTreeMenuItem.setText(\r
-            "Average Distance Using % Identity...");\r
-        averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    averageDistanceTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");\r
-        neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    neighbourTreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        clustalAlignMenuItem.setText("Clustal Alignment...");\r
-        clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    clustalAlignMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        this.getContentPane().setLayout(borderLayout1);\r
-        alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
-        alignFrameMenuBar.addAncestorListener(new AncestorListener() {\r
-                public void ancestorAdded(AncestorEvent event) {\r
-                    alignFrameMenuBar_ancestorAdded(event);\r
-                }\r
-\r
-                public void ancestorRemoved(AncestorEvent event) {\r
-                }\r
-\r
-                public void ancestorMoved(AncestorEvent event) {\r
-                }\r
-            });\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.setMnemonic('T');\r
-        outputTextboxMenu.setText("Output to Textbox");\r
-        clustalColour.setText("Clustalx");\r
-\r
-        clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    clustalColour_actionPerformed(e);\r
-                }\r
-            });\r
-        zappoColour.setText("Zappo");\r
-        zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    zappoColour_actionPerformed(e);\r
-                }\r
-            });\r
-        taylorColour.setText("Taylor");\r
-        taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    taylorColour_actionPerformed(e);\r
-                }\r
-            });\r
-        hydrophobicityColour.setText("Hydrophobicity");\r
-        hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    hydrophobicityColour_actionPerformed(e);\r
-                }\r
-            });\r
-        helixColour.setText("Helix Propensity");\r
-        helixColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    helixColour_actionPerformed(e);\r
-                }\r
-            });\r
-        strandColour.setText("Strand Propensity");\r
-        strandColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    strandColour_actionPerformed(e);\r
-                }\r
-            });\r
-        turnColour.setText("Turn Propensity");\r
-        turnColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    turnColour_actionPerformed(e);\r
-                }\r
-            });\r
-        buriedColour.setText("Buried Index");\r
-        buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    buriedColour_actionPerformed(e);\r
-                }\r
-            });\r
-        userDefinedColour.setText("User Defined...");\r
-        userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    userDefinedColour_actionPerformed(e);\r
-                }\r
-            });\r
-        PIDColour.setText("Percentage Identity");\r
-        PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    PIDColour_actionPerformed(e);\r
-                }\r
-            });\r
-        BLOSUM62Colour.setText("BLOSUM62 Score");\r
-        BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    BLOSUM62Colour_actionPerformed(e);\r
-                }\r
-            });\r
-        avDistanceTreeBlosumMenuItem.setText(\r
-            "Average Distance Using BLOSUM62...");\r
-        avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    avTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");\r
-        njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    njTreeBlosumMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        annotationPanelMenuItem.setActionCommand("");\r
-        annotationPanelMenuItem.setText("Show Annotations");\r
-        annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
-        annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    annotationPanelMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        colourTextMenuItem.setText("Colour Text");\r
-        colourTextMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    colourTextMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        htmlMenuItem.setText("HTML");\r
-        htmlMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    htmlMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        overviewMenuItem.setText("Overview Window...");\r
-        overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    overviewMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        undoMenuItem.setEnabled(false);\r
-        undoMenuItem.setMnemonic('Z');\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
-                public void actionPerformed(ActionEvent e) {\r
-                    undoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        redoMenuItem.setEnabled(false);\r
-        redoMenuItem.setMnemonic('0');\r
-        redoMenuItem.setText("Redo");\r
-        redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    redoMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        conservationMenuItem.setText("By Conservation");\r
-        conservationMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    conservationMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        noColourmenuItem.setText("None");\r
-        noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    noColourmenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        wrapMenuItem.setText("Wrap");\r
-        wrapMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    wrapMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        printMenuItem.setText("Print");\r
-        printMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    printMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        renderGapsMenuItem.setText("Show Gaps");\r
-        renderGapsMenuItem.setState(true);\r
-        renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\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
-                public void actionPerformed(ActionEvent e) {\r
-                    findMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        searchMenu.setText("Search");\r
-\r
-        abovePIDThreshold.setText("Above Identity Threshold");\r
-        abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    abovePIDThreshold_actionPerformed(e);\r
-                }\r
-            });\r
-        sequenceFeatures.setText("Sequence Features");\r
-        sequenceFeatures.addActionListener(new ActionListener() {\r
-                public void actionPerformed(ActionEvent actionEvent) {\r
-                    sequenceFeatures_actionPerformed(actionEvent);\r
-                }\r
-            });\r
-        nucleotideColour.setText("Nucleotide");\r
-        nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    nucleotideColour_actionPerformed(e);\r
-                }\r
-            });\r
-        deleteGroups.setText("Undefine groups");\r
-        deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\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
-        copy.setMnemonic(KeyEvent.VK_C);\r
-\r
-        copy.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\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.setMnemonic(KeyEvent.VK_X);\r
-        cut.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    cut_actionPerformed(e);\r
-                }\r
-            });\r
-        delete.setText("Delete");\r
-        delete.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    delete_actionPerformed(e);\r
-                }\r
-            });\r
-        jMenu1.setMnemonic('V');\r
-        jMenu1.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(), false));\r
-        pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteNew_actionPerformed(e);\r
-                }\r
-            });\r
-        pasteThis.setText("Add To This Alignment");\r
-        pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    pasteThis_actionPerformed(e);\r
-                }\r
-            });\r
-        applyToAllGroups.setText("Apply Colour To All Groups");\r
-        applyToAllGroups.setState(true);\r
-        applyToAllGroups.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    applyToAllGroups_actionPerformed(e);\r
-                }\r
-            });\r
-        createPNG.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    createPNG_actionPerformed(e);\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
-                public void actionPerformed(ActionEvent e) {\r
-                    font_actionPerformed(e);\r
-                }\r
-            });\r
-        fullSeqId.setText("Show Full Sequence ID");\r
-        fullSeqId.setState(true);\r
-        fullSeqId.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    fullSeqId_actionPerformed(e);\r
-                }\r
-            });\r
-        epsFile.setText("EPS");\r
-        epsFile.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    epsFile_actionPerformed(e);\r
-                }\r
-            });\r
-        LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
-        LoadtreeMenuItem.setText("Load Assocated Tree");\r
-        LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    LoadtreeMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        jpred.setText("JPred...");\r
-        jpred.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    jpred_actionPerformed(e);\r
-                }\r
-            });\r
-        scaleAbove.setVisible(false);\r
-        scaleAbove.setText("Scale Above");\r
-        scaleAbove.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\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
-                public void actionPerformed(ActionEvent e) {\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
-                public void actionPerformed(ActionEvent e) {\r
-                    scaleRight_actionPerformed(e);\r
-                }\r
-            });\r
-        modifyPID.setText("Modify Identity Threshold...");\r
-        modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyPID_actionPerformed(e);\r
-                }\r
-            });\r
-        modifyConservation.setText("Modify Conservation Threshold...");\r
-        modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    modifyConservation_actionPerformed(e);\r
-                }\r
-            });\r
-        sortByTreeMenu.setText("By Tree Order");\r
-        sort.setText("Sort");\r
-        calculate.setText("Calculate Tree");\r
-        msaAlignMenuItem.setText("Muscle Alignment...");\r
-        msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    msaAlignMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        jMenu2.setText("Export");\r
-        padGapsMenuitem.setText("Pad Gaps");\r
-        padGapsMenuitem.addActionListener(new ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    padGapsMenuitem_actionPerformed(e);\r
-                }\r
-            });\r
-        ClustalRealign.setText("Clustal Realign...");\r
-        ClustalRealign.addActionListener(new ActionListener() {\r
-                public void actionPerformed(ActionEvent e) {\r
-                    ClustalRealign_actionPerformed(e);\r
-                }\r
-            });\r
-        alignFrameMenuBar.add(fileMenu);\r
-        alignFrameMenuBar.add(editMenu);\r
-        alignFrameMenuBar.add(searchMenu);\r
-        alignFrameMenuBar.add(viewMenu);\r
-        alignFrameMenuBar.add(colourMenu);\r
-        alignFrameMenuBar.add(calculateMenu);\r
-        fileMenu.add(saveAlignmentMenu);\r
-        fileMenu.add(jMenu2);\r
-        fileMenu.add(outputTextboxMenu);\r
-        fileMenu.add(printMenuItem);\r
-        fileMenu.addSeparator();\r
-        fileMenu.add(LoadtreeMenuItem);\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(jMenu1);\r
-        editMenu.add(delete);\r
-        editMenu.addSeparator();\r
-        editMenu.add(selectAllSequenceMenuItem);\r
-        editMenu.add(deselectAllSequenceMenuItem);\r
-        editMenu.add(invertSequenceMenuItem);\r
-        editMenu.add(deleteGroups);\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
-        searchMenu.add(findMenuItem);\r
-        viewMenu.add(font);\r
-        viewMenu.addSeparator();\r
-        viewMenu.add(wrapMenuItem);\r
-        viewMenu.add(fullSeqId);\r
-        viewMenu.add(scaleAbove);\r
-        viewMenu.add(scaleLeft);\r
-        viewMenu.add(scaleRight);\r
-        viewMenu.add(viewBoxesMenuItem);\r
-        viewMenu.add(viewTextMenuItem);\r
-        viewMenu.add(colourTextMenuItem);\r
-        viewMenu.add(renderGapsMenuItem);\r
-        viewMenu.add(annotationPanelMenuItem);\r
-        viewMenu.add(sequenceFeatures);\r
-        viewMenu.addSeparator();\r
-        viewMenu.add(overviewMenuItem);\r
-        colourMenu.add(applyToAllGroups);\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
-        calculateMenu.add(sort);\r
-        calculateMenu.add(calculate);\r
-        calculateMenu.addSeparator();\r
-        calculateMenu.add(pairwiseAlignmentMenuItem);\r
-        calculateMenu.add(PCAMenuItem);\r
-        calculateMenu.addSeparator();\r
-        calculateMenu.add(webService);\r
-        webService.add(clustalAlignMenuItem);\r
-        webService.add(msaAlignMenuItem);\r
-        webService.add(jpred);\r
-        webService.add(ClustalRealign);\r
-        this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-        jMenu1.add(pasteNew);\r
-        jMenu1.add(pasteThis);\r
-        sort.add(sortIDMenuItem);\r
-        sort.add(sortGroupMenuItem);\r
-        sort.add(sortPairwiseMenuItem);\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
-    }\r
+  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void outputText_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void PCAMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void clustalColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void zappoColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void taylorColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void helixColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void strandColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void turnColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void buriedColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void PIDColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void printMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void findMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
+  {\r
+  }\r
 \r
-    protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void nucleotideColour_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void deleteGroups_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void copy_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void cut_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void clustalColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void delete_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void zappoColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void pasteNew_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void taylorColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void pasteThis_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void helixColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void createPNG(java.io.File f)\r
+  {\r
+  }\r
 \r
-    protected void strandColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void font_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void turnColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void seqLimit_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void buriedColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void seqDBRef_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void PIDColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void createEPS(java.io.File f)\r
+  {\r
+  }\r
 \r
-    protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void jpred_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void scaleAbove_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void printMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void scaleLeft_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void scaleRight_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void findMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void modifyPID_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void modifyConservation_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
-    }\r
+  protected void saveAs_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
-    }\r
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    protected void deleteGroups_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void vamsasStore_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void copy_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void cut_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void vamsasLoad_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void delete_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void pasteNew_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void showTranslation_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void pasteThis_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void featureSettings_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void createPNG_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void font_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void fullSeqId_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void epsFile_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void smoothFont_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void jpred_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void annotationColour_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void scaleAbove_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void scaleLeft_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void associatedData_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void scaleRight_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void modifyPID_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void modifyConservation_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void preferences_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void showAllSeqs_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event) {\r
-    }\r
+  public void showAllColumns_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void saveAlignmentMenu_actionPerformed(ActionEvent e) {\r
-    }\r
+  }\r
 \r
-    protected void padGapsMenuitem_actionPerformed(ActionEvent e) {\r
-    }\r
+  public void hideSelSequences_actionPerformed(ActionEvent e)\r
+  {\r
 \r
-    protected void ClustalRealign_actionPerformed(ActionEvent e) {\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