X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b03e19b687bceecb291538f7450a59184f6259e;hb=32a259190463ee06a81886db9d7843b565dea6df;hp=73709958944496aaba067e7841e821891a61ed14;hpb=a7eff74f18498e209c422b7cd090e294b36806dc;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 7370995..1b03e19 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,23 +1,32 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
 
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import javax.swing.event.AncestorListener;
-import javax.swing.event.AncestorEvent;
+import jalview.schemes.*;
+import java.awt.BorderLayout;
 
-public class GAlignFrame extends JInternalFrame
+public class GAlignFrame
+    extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
   protected JMenu fileMenu = new JMenu();
@@ -27,6 +36,7 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
   protected JMenu webService = new JMenu();
+  protected JMenuItem webServiceNoServices;
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
@@ -34,8 +44,8 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
   protected JMenuItem sortIDMenuItem = new JMenuItem();
   protected JMenuItem sortGroupMenuItem = new JMenuItem();
@@ -52,7 +62,8 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
@@ -62,21 +73,21 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
   JMenuItem overviewMenuItem = new JMenuItem();
   protected JMenuItem undoMenuItem = new JMenuItem();
   protected JMenuItem redoMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
   JMenuItem printMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -85,60 +96,50 @@ public class GAlignFrame extends JInternalFrame
   JMenu jMenu1 = new JMenu();
   JMenuItem pasteNew = new JMenuItem();
   JMenuItem pasteThis = new JMenuItem();
-  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
   JMenuItem createPNG = new JMenuItem();
   protected JMenuItem font = new JMenuItem();
-  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
   JMenuItem epsFile = new JMenuItem();
   JMenuItem LoadtreeMenuItem = new JMenuItem();
-  JMenuItem jpred = new JMenuItem();
-  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-  JMenuItem modifyPID = new JMenuItem();
-  JMenuItem modifyConservation = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
+  protected JMenuItem modifyConservation = new JMenuItem();
   protected JMenu sortByTreeMenu = new JMenu();
-  JMenu sort = new JMenu();
+  protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
-  JMenuItem msaAlignMenuItem = new JMenuItem();
   JMenu jMenu2 = new JMenu();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
+  JMenuItem vamsasStore = new JMenuItem();
+  protected JMenuItem showTranslation = new JMenuItem();
+  public JMenuItem featureSettings = new JMenuItem();
+  JMenuItem fetchSequence = new JMenuItem();
+  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
+  JMenuItem exportAnnotations = new JMenuItem();
+  JMenuItem exportFeatures = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  JMenu jMenu3 = new JMenu();
+  JMenuItem showAllSeqs = new JMenuItem();
+  JMenuItem showAllColumns = new JMenuItem();
+  JMenu jMenu4 = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+
   public GAlignFrame()
   {
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(nucleotideColour);
-
-   noColourmenuItem.setSelected(true);
-   String defaultColour = Preferences.defaultColour;
-   if(defaultColour!=null)
-   {
-   int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
-   switch(index)
-   {
-     case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
-     case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
-     case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
-     case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
-     case ColourSchemeProperty.HYDROPHOBIC: hydrophobicityColour.setSelected(true); break;
-     case ColourSchemeProperty.HELIX: helixColour.setSelected(true); break;
-     case ColourSchemeProperty.STRAND: strandColour.setSelected(true); break;
-     case ColourSchemeProperty.TURN : turnColour.setSelected(true); break;
-     case ColourSchemeProperty.BURIED: buriedColour.setSelected(true); break;
-     case ColourSchemeProperty.NUCLEOTIDE: nucleotideColour.setSelected(true); break;
-     case ColourSchemeProperty.USER_DEFINED : userDefinedColour.setSelected(true); break;
-   }
-   }
 
 
     try
@@ -146,10 +147,11 @@ public class GAlignFrame extends JInternalFrame
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
-      JMenuItem item;
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) {
-        item = new JMenuItem((String) jalview.io.FormatAdapter.formats.elementAt(i));
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      {
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -158,22 +160,166 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
+    }
+    catch (Exception e)
+    {
+    }
 
+
+    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
     }
-    catch(Exception e)
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
+
+    if (defaultColour != null)
     {
-      e.printStackTrace();
+      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+      switch (index)
+      {
+        case ColourSchemeProperty.NONE:
+              noColourmenuItem.setSelected(true);
+              break;
+        case ColourSchemeProperty.CLUSTAL:
+          clustalColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BLOSUM:
+          BLOSUM62Colour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.PID:
+          PIDColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.ZAPPO:
+          zappoColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.TAYLOR:
+          taylorColour.setSelected(true);
+          break;
+
+        case ColourSchemeProperty.HYDROPHOBIC:
+          hydrophobicityColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.HELIX:
+          helixColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.STRAND:
+          strandColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.TURN:
+          turnColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.BURIED:
+          buriedColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.NUCLEOTIDE:
+          nucleotideColour.setSelected(true);
+
+          break;
+
+        case ColourSchemeProperty.USER_DEFINED:
+          userDefinedColour.setSelected(true);
+
+          break;
+      }
     }
 
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     fileMenu.setMnemonic('F');
     fileMenu.setText("File");
     saveAlignmentMenu.setMnemonic('L');
     saveAlignmentMenu.setText("Save As");
+    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
     saveAlignmentMenu.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -197,8 +343,10 @@ public class GAlignFrame extends JInternalFrame
     webService.setText("Web Service");
     selectAllSequenceMenuItem.setText("Select all");
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -207,16 +355,17 @@ public class GAlignFrame extends JInternalFrame
     });
     deselectAllSequenceMenuItem.setText("Deselect All");
     deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                               getKeyStroke(java.awt.event.
-        KeyEvent.VK_ESCAPE, 0, false));
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+                                               getKeyStroke(
+        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert Selection");
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -241,7 +390,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -274,7 +424,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("By Pairwise Identity");
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -282,7 +432,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText("By ID");
+    sortIDMenuItem.setText("by ID");
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -290,7 +440,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("By Group");
+    sortGroupMenuItem.setText("by Group");
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -299,7 +449,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -307,14 +458,15 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    PCAMenuItem.setText("Principal Component Analysis...");
+    PCAMenuItem.setText("Principal Component Analysis");
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -322,15 +474,17 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    averageDistanceTreeMenuItem.setText(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         averageDistanceTreeMenuItem_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -338,31 +492,8 @@ public class GAlignFrame extends JInternalFrame
         neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal Alignment...");
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalAlignMenuItem_actionPerformed(e);
-      }
-    });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    alignFrameMenuBar.addAncestorListener(new AncestorListener()
-    {
-      public void ancestorAdded(AncestorEvent event)
-      {
-        alignFrameMenuBar_ancestorAdded(event);
-      }
-
-      public void ancestorRemoved(AncestorEvent event)
-      {
-      }
-
-      public void ancestorMoved(AncestorEvent event)
-      {
-      }
-    });
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
@@ -458,15 +589,17 @@ public class GAlignFrame extends JInternalFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    avDistanceTreeBlosumMenuItem.setText(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+        ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         avTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -476,7 +609,7 @@ public class GAlignFrame extends JInternalFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
+    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -500,7 +633,7 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview Window...");
+    overviewMenuItem.setText("Overview Window");
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -511,8 +644,9 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setMnemonic('Z');
     undoMenuItem.setText("Undo");
-    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_Z,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -572,8 +706,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     findMenuItem.setText("Find...");
-    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_F,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     findMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -584,17 +719,19 @@ public class GAlignFrame extends JInternalFrame
     searchMenu.setText("Search");
 
     abovePIDThreshold.setText("Above Identity Threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    sequenceFeatures.setText("Sequence Features");
-    sequenceFeatures.addActionListener(new ActionListener()
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        sequenceFeatures_actionPerformed(actionEvent);
+        showSeqFeatures_actionPerformed(actionEvent);
       }
     });
     nucleotideColour.setText("Nucleotide");
@@ -614,8 +751,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     copy.setText("Copy");
-    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_C, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_C,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     copy.setMnemonic(KeyEvent.VK_C);
 
     copy.addActionListener(new java.awt.event.ActionListener()
@@ -626,8 +764,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     cut.setText("Cut");
-    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_X, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_X,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     cut.setMnemonic(KeyEvent.VK_X);
     cut.addActionListener(new java.awt.event.ActionListener()
     {
@@ -646,9 +785,10 @@ public class GAlignFrame extends JInternalFrame
     });
     jMenu1.setMnemonic('V');
     jMenu1.setText("Paste");
-    pasteNew.setText("to new alignment");
-    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteNew.setText("To New Alignment");
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -656,7 +796,7 @@ public class GAlignFrame extends JInternalFrame
         pasteNew_actionPerformed(e);
       }
     });
-    pasteThis.setText("add to this alignment");
+    pasteThis.setText("Add To This Alignment");
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -677,7 +817,7 @@ public class GAlignFrame extends JInternalFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        createPNG_actionPerformed(e);
+        createPNG(null);
       }
     });
     createPNG.setActionCommand("Save As PNG Image");
@@ -690,12 +830,14 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show Full Sequence ID");
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+    seqLimits.setText("Show Sequence Limits");
+    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+    seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fullSeqId_actionPerformed(e);
+        seqLimit_actionPerformed(e);
       }
     });
     epsFile.setText("EPS");
@@ -703,23 +845,16 @@ public class GAlignFrame extends JInternalFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        epsFile_actionPerformed(e);
+        createEPS(null);
       }
     });
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Assocated Tree");
-    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e)
-      {
-        LoadtreeMenuItem_actionPerformed(e);
-      }
-    });
-    jpred.setText("JPred...");
-    jpred.addActionListener(new java.awt.event.ActionListener()
+    LoadtreeMenuItem.setText("Load Associated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        jpred_actionPerformed(e);
+        LoadtreeMenuItem_actionPerformed(e);
       }
     });
     scaleAbove.setVisible(false);
@@ -770,25 +905,207 @@ public class GAlignFrame extends JInternalFrame
     sortByTreeMenu.setText("By Tree Order");
     sort.setText("Sort");
     calculate.setText("Calculate Tree");
-    msaAlignMenuItem.setText("Muscle Alignment...");
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        msaAlignMenuItem_actionPerformed(e);
+
+    jMenu2.setText("Export");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
       }
     });
-    jMenu2.setText("Export");
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStore_actionPerformed(e);
+      }
+    });
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showTranslation_actionPerformed(e);
+      }
+    });
+
+   /* tabbedPane.addChangeListener(new ChangeListener()
+        {
+          public void stateChanged(ChangeEvent ece)
+          {
+
+            tabSelected();
+          }
+        });*/
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        featureSettings_actionPerformed(e);
+      }
+    });
+    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSequence_actionPerformed(e);
+      }
+    });
+    smoothFont.setText("Smooth Fonts");
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    jMenu4.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Hidden Markers");
+    hiddenMarkers.setState(true);
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
+    alignFrameMenuBar.add(webService);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(fetchSequence);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -801,6 +1118,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
+    editMenu.add(invertColSel);
     editMenu.add(deleteGroups);
     editMenu.addSeparator();
     editMenu.add(remove2LeftMenuItem);
@@ -808,26 +1126,34 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
-    viewMenu.add(fullSeqId);
+    viewMenu.add(smoothFont);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(jMenu4);
+    viewMenu.add(hiddenMarkers);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
+    viewMenu.add(seqLimits);
     viewMenu.add(scaleAbove);
     viewMenu.add(scaleLeft);
     viewMenu.add(scaleRight);
-    viewMenu.addSeparator();
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
     viewMenu.add(colourTextMenuItem);
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
-    viewMenu.add(sequenceFeatures);
+    viewMenu.addSeparator();
+    viewMenu.add(showSeqFeatures);
+    viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
-    colourMenu.add(noColourmenuItem);
     colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
     colourMenu.add(PIDColour);
@@ -845,21 +1171,19 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
-    calculateMenu.add(webService);
-    webService.add(clustalAlignMenuItem);
-    webService.add(jpred);
-    webService.add(msaAlignMenuItem);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
+    webServiceNoServices=new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
-    sort.add(sortByTreeMenu);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
     calculate.add(averageDistanceTreeMenuItem);
@@ -869,372 +1193,407 @@ public class GAlignFrame extends JInternalFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    jMenu3.add(showAllColumns);
+    jMenu3.add(showAllSeqs);
+    jMenu4.add(hideSelColumns);
+    jMenu4.add(hideSelSequences);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
+  }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  public void addFromText_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
 
-  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  public void exportFeatures_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  public void exportAnnotations_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void closeMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void overviewMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void zappoColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void taylorColour_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void helixColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void strandColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void turnColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void buriedColour_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void printMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+  {
   }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void cut_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void createPNG(java.io.File f)
+  {
   }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  protected void font_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
+  public void seqDBRef_actionPerformed(ActionEvent e)
   {
 
   }
 
- protected void copy_actionPerformed(ActionEvent e)
+
+  public void createEPS(java.io.File f)
   {
+  }
 
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void cut_actionPerformed(ActionEvent e)
+  protected void scaleAbove_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  protected void scaleRight_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
+  protected void modifyConservation_actionPerformed(ActionEvent e)
   {
+  }
+
+
 
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
+  }
+
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  public void vamsasLoad_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void font_actionPerformed(ActionEvent e)
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  protected void jpred_actionPerformed(ActionEvent e)
+
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
+  public void showAllSeqs_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
+  public void showAllColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  public void hideSelSequences_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  public void hideSelColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void preferences_actionPerformed(ActionEvent e)
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+  public void findPdbId_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  public void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  public void enterPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void pdbFile_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
 }