X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=7fb94f9afa3e7c3a74e6eb5a5b97c6943b24f48a;hb=4a3f84f077dde7be327e3fa679cd58addc5f4ea3;hp=ddb2bcd954a15a1231874818257f579eb1a408ff;hpb=ab6be38b4baaf8fc26fc19b2e514a6c40d6118f3;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index ddb2bcd..7fb94f9 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -24,6 +24,10 @@ import javax.swing.*;
 import javax.swing.event.*;
 
 import jalview.schemes.*;
+import java.awt.BorderLayout;
+
+
+
 
 public class GAlignFrame
     extends JInternalFrame
@@ -54,10 +58,9 @@ public class GAlignFrame
   protected JMenuItem PCAMenuItem = new JMenuItem();
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-  protected JMenuItem clustalAlignMenuItem = new JMenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public JLabel statusBar = new JLabel();
-  protected JMenuItem saveAlignmentMenu = new JMenuItem();
+  protected JMenuItem saveAs = new JMenuItem();
   protected JMenu outputTextboxMenu = new JMenu();
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
@@ -87,7 +90,7 @@ public class GAlignFrame
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -99,7 +102,7 @@ public class GAlignFrame
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
   JMenuItem createPNG = new JMenuItem();
   protected JMenuItem font = new JMenuItem();
-  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
   JMenuItem epsFile = new JMenuItem();
   JMenuItem LoadtreeMenuItem = new JMenuItem();
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -111,24 +114,48 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenu jMenu2 = new JMenu();
-  JMenuItem padGapsMenuitem = new JMenuItem();
+  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 hideMenu = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
+  JMenuItem save = new JMenuItem();
+  JMenuItem jMenuItem1 = new JMenuItem();
+  JMenuItem reload = new JMenuItem();
   public GAlignFrame()
   {
-
-
     try
     {
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
-        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                             elementAt(
-                                 i));
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -291,21 +318,21 @@ public class GAlignFrame
   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()
+    saveAs.setText("Save As ...");
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_MASK, false));
+    saveAs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        saveAlignmentMenu_actionPerformed(e);
+        saveAs_actionPerformed(e);
       }
     });
     closeMenuItem.setMnemonic('C');
     closeMenuItem.setText("Close");
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -342,7 +369,10 @@ public class GAlignFrame
         deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert Selection");
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_I,
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -351,6 +381,8 @@ public class GAlignFrame
       }
     });
     remove2LeftMenuItem.setText("Remove Left");
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -359,6 +391,8 @@ public class GAlignFrame
       }
     });
     remove2RightMenuItem.setText("Remove Right");
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -367,6 +401,9 @@ public class GAlignFrame
       }
     });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                              getKeyStroke(java.awt.event.
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeGappedColumnMenuItem.addActionListener(new java.awt.event.
                                                  ActionListener()
     {
@@ -376,6 +413,8 @@ public class GAlignFrame
       }
     });
     removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -426,6 +465,8 @@ public class GAlignFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeRedundancyMenuItem.addActionListener(new java.awt.event.
                                                ActionListener()
     {
@@ -471,21 +512,6 @@ public class GAlignFrame
     });
     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));
@@ -649,6 +675,8 @@ public class GAlignFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setMnemonic('0');
     redoMenuItem.setText("Redo");
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -681,6 +709,8 @@ public class GAlignFrame
       }
     });
     printMenuItem.setText("Print");
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -718,12 +748,12 @@ public class GAlignFrame
         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");
@@ -735,6 +765,8 @@ public class GAlignFrame
       }
     });
     deleteGroups.setText("Undefine groups");
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -768,6 +800,8 @@ public class GAlignFrame
       }
     });
     delete.setText("Delete");
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_BACK_SPACE, 0, false));
     delete.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -797,7 +831,6 @@ public class GAlignFrame
       }
     });
     applyToAllGroups.setText("Apply Colour To All Groups");
-    applyToAllGroups.setState(true);
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -822,13 +855,14 @@ public class GAlignFrame
         font_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show Full Sequence ID");
-    fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));
-    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");
@@ -840,7 +874,7 @@ public class GAlignFrame
       }
     });
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Assocated Tree");
+    LoadtreeMenuItem.setText("Load Associated Tree");
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -897,8 +931,9 @@ public class GAlignFrame
     sort.setText("Sort");
     calculate.setText("Calculate Tree");
 
-    jMenu2.setText("Export");
+    jMenu2.setText("Export Image");
     padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -906,6 +941,214 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);
       }
     });
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStore_actionPerformed(e);
+      }
+    });
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showTranslation_actionPerformed(e);
+      }
+    });
+
+
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        featureSettings_actionPerformed(e);
+      }
+    });
+    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSequence_actionPerformed(e);
+      }
+    });
+    smoothFont.setText("Smooth Fonts");
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    hideMenu.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Hidden Markers");
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+    {
+        public void stateChanged(ChangeEvent evt)
+        {
+            JTabbedPane pane = (JTabbedPane)evt.getSource();
+            int sel = pane.getSelectedIndex();
+            tabSelectionChanged(sel);
+        }
+    });
+    tabbedPane.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        tabbedPane_mousePressed(e);
+      }
+    });
+    tabbedPane.addFocusListener(new FocusAdapter()
+    {
+      public void focusGained(FocusEvent e)
+      {
+        tabbedPane_focusGained(e);
+      }
+    });
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save_actionPerformed(e);
+      }
+    });
+    reload.setMnemonic('R');
+    reload.setText("Reload");
+   // reload.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+  //      KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    reload.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        reload_actionPerformed(e);
+      }
+    });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -913,12 +1156,21 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
-    fileMenu.add(saveAlignmentMenu);
-    fileMenu.add(jMenu2);
+    fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
+    fileMenu.add(save);
+    fileMenu.add(saveAs);
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(jMenu2);
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -931,6 +1183,7 @@ public class GAlignFrame
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
+    editMenu.add(invertColSel);
     editMenu.add(deleteGroups);
     editMenu.addSeparator();
     editMenu.add(remove2LeftMenuItem);
@@ -942,9 +1195,14 @@ public class GAlignFrame
     editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
+    viewMenu.add(smoothFont);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
+    viewMenu.add(hiddenMarkers);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
-    viewMenu.add(fullSeqId);
+    viewMenu.add(seqLimits);
     viewMenu.add(scaleAbove);
     viewMenu.add(scaleLeft);
     viewMenu.add(scaleRight);
@@ -953,7 +1211,9 @@ public class GAlignFrame
     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);
@@ -976,15 +1236,17 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
+    calculateMenu.addSeparator();
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -996,12 +1258,47 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+    jMenu3.add(showAllColumns);
+    jMenu3.add(showAllSeqs);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
   }
 
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -1110,10 +1407,6 @@ public class GAlignFrame
   {
   }
 
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void clustalColour_actionPerformed(ActionEvent e)
   {
   }
@@ -1182,7 +1475,7 @@ public class GAlignFrame
   {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -1226,10 +1519,16 @@ public class GAlignFrame
   {
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void seqDBRef_actionPerformed(ActionEvent e)
   {
+
   }
 
+
   public void createEPS(java.io.File f)
   {
   }
@@ -1262,27 +1561,130 @@ public class GAlignFrame
   {
   }
 
-  protected void preferences_actionPerformed(ActionEvent e)
+
+
+  protected void saveAs_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  public void vamsasLoad_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void findPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void enterPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void pdbFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void tabSelectionChanged(int sel)
+  {
+
+  }
+
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
   {
+
   }
 
-  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  public void reload_actionPerformed(ActionEvent e)
   {
+
   }
 }