X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=1b89d71c9848945444d28735db4be89efde76911;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=bb69a54dba0d2ed06b16a5c5dfc07176f43b68c2;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bb69a54..1b89d71 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) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,6 +21,7 @@ package jalview.jbgui;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
+import javax.swing.event.*;
 
 import jalview.schemes.*;
 
@@ -53,10 +54,9 @@ 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();
@@ -84,15 +84,14 @@ public class GAlignFrame
   JMenuItem printMenuItem = new JMenuItem();
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   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();
   JMenuItem copy = new JMenuItem();
   JMenuItem cut = new JMenuItem();
-  JMenu jMenu1 = new JMenu();
+  JMenu pasteMenu = new JMenu();
   JMenuItem pasteNew = new JMenuItem();
   JMenuItem pasteThis = new JMenuItem();
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
@@ -110,29 +109,55 @@ 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 JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
-  //protected JTabbedPane tabbedPane = new JTabbedPane();
+  protected JMenuItem showTranslation = new JMenuItem();
   public JMenuItem featureSettings = new JMenuItem();
   JMenuItem fetchSequence = new JMenuItem();
-
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
+  JMenuItem exportAnnotations = new JMenuItem();
+  JMenuItem exportFeatures = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  JMenu jMenu3 = new JMenu();
+  JMenuItem showAllSeqs = new JMenuItem();
+  JMenuItem showAllColumns = new JMenuItem();
+  JMenu hideMenu = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
+  JMenuItem save = new JMenuItem();
+  protected JMenuItem reload = new JMenuItem();
+  JMenuItem newView = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu formatMenu = new JMenu();
+  JMenu selectMenu = new JMenu();
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+  protected JMenuItem gatherViews = new JMenuItem();
+  protected JMenuItem expandViews = new JMenuItem();
+  JMenuItem pageSetup = new JMenuItem();
   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)
@@ -148,45 +173,61 @@ public class GAlignFrame
     {
     }
 
+    if (!System.getProperty("os.name").startsWith("Mac"))
+    {
+      closeMenuItem.setMnemonic('C');
+      outputTextboxMenu.setMnemonic('T');
+      undoMenuItem.setMnemonic('Z');
+      redoMenuItem.setMnemonic('0');
+      copy.setMnemonic('C');
+      cut.setMnemonic('U');
+      pasteMenu.setMnemonic('P');
+      reload.setMnemonic('R');
+    }
 
-    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
           getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+        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))
             {
-              public void mousePressed(MouseEvent 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
               {
-                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                radioItem.addActionListener(new ActionListener()
                 {
-                  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)
+                  public void actionPerformed(ActionEvent evt)
                   {
-                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
-                    colourMenu.remove(radioItem);
+                    userDefinedColour_actionPerformed(evt);
                   }
-                  else
-                    radioItem.addActionListener(new ActionListener()
-                    {
-                      public void actionPerformed(ActionEvent evt)
-                      {
-                        userDefinedColour_actionPerformed(evt);
-                      }
-                    });
-                }
+                });
               }
-            });
+            }
+          }
+        });
         radioItem.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -214,7 +255,6 @@ public class GAlignFrame
 
     setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 
-
   }
 
   public void setColourSelected(String defaultColour)
@@ -227,8 +267,8 @@ public class GAlignFrame
       switch (index)
       {
         case ColourSchemeProperty.NONE:
-              noColourmenuItem.setSelected(true);
-              break;
+          noColourmenuItem.setSelected(true);
+          break;
         case ColourSchemeProperty.CLUSTAL:
           clustalColour.setSelected(true);
 
@@ -295,26 +335,27 @@ 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,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_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)
       {
-        closeMenuItem_actionPerformed(e);
+        closeMenuItem_actionPerformed(false);
       }
     });
     editMenu.setText("Edit");
@@ -322,7 +363,7 @@ public class GAlignFrame
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
     webService.setText("Web Service");
-    selectAllSequenceMenuItem.setText("Select all");
+    selectAllSequenceMenuItem.setText("Select All");
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
         java.awt.event.KeyEvent.VK_A,
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
@@ -346,7 +387,10 @@ 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,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -355,6 +399,9 @@ 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)
@@ -363,6 +410,9 @@ 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)
@@ -371,6 +421,9 @@ 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()
     {
@@ -380,6 +433,10 @@ public class GAlignFrame
       }
     });
     removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_E,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -430,6 +487,9 @@ 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()
     {
@@ -479,7 +539,6 @@ public class GAlignFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText("Status bar");
-    outputTextboxMenu.setMnemonic('T');
     outputTextboxMenu.setText("Output to Textbox");
     clustalColour.setText("Clustalx");
 
@@ -590,7 +649,8 @@ public class GAlignFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+        "SHOW_ANNOTATIONS", true));
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -623,7 +683,6 @@ public class GAlignFrame
       }
     });
     undoMenuItem.setEnabled(false);
-    undoMenuItem.setMnemonic('Z');
     undoMenuItem.setText("Undo");
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
         java.awt.event.KeyEvent.VK_Z,
@@ -636,8 +695,9 @@ 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)
@@ -669,7 +729,9 @@ public class GAlignFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-    printMenuItem.setText("Print");
+    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)
@@ -697,8 +759,6 @@ public class GAlignFrame
         findMenuItem_actionPerformed(e);
       }
     });
-    searchMenu.setText("Search");
-
     abovePIDThreshold.setText("Above Identity Threshold");
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
     {
@@ -707,12 +767,12 @@ 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");
@@ -724,6 +784,8 @@ 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)
@@ -735,7 +797,6 @@ public class GAlignFrame
     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()
     {
@@ -748,7 +809,6 @@ public class GAlignFrame
     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()
     {
       public void actionPerformed(ActionEvent e)
@@ -757,6 +817,8 @@ 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)
@@ -764,12 +826,12 @@ public class GAlignFrame
         delete_actionPerformed(e);
       }
     });
-    jMenu1.setMnemonic('V');
-    jMenu1.setText("Paste");
+    pasteMenu.setText("Paste");
     pasteNew.setText("To New Alignment");
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
         java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
+        java.awt.event.KeyEvent.SHIFT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -778,6 +840,9 @@ public class GAlignFrame
       }
     });
     pasteThis.setText("Add To This Alignment");
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -786,7 +851,6 @@ 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)
@@ -813,7 +877,7 @@ public class GAlignFrame
     });
 
     seqLimits.setText("Show Sequence Limits");
-    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -830,7 +894,7 @@ 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)
@@ -885,10 +949,26 @@ public class GAlignFrame
     });
     sortByTreeMenu.setText("By Tree Order");
     sort.setText("Sort");
+    sort.addMenuListener(new MenuListener()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        buildTreeMenu();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
     calculate.setText("Calculate Tree");
 
-    jMenu2.setText("Export");
+    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)
@@ -914,15 +994,6 @@ public class GAlignFrame
       }
     });
 
-   /* tabbedPane.addChangeListener(new ChangeListener()
-        {
-          public void stateChanged(ChangeEvent ece)
-          {
-
-            tabSelected();
-          }
-        });*/
-    featureSettings.setEnabled(false);
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -931,7 +1002,7 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText("Fetch Sequence...");
+    fetchSequence.setText("Fetch Sequence(s)...");
     fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -939,35 +1010,266 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);
       }
     });
+
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    hideMenu.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Show Hidden Markers");
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_I,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+        | java.awt.event.KeyEvent.ALT_MASK,
+        false));
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        JTabbedPane pane = (JTabbedPane) evt.getSource();
+        int sel = pane.getSelectedIndex();
+        tabSelectionChanged(sel);
+      }
+    });
+    tabbedPane.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        tabbedPane_mousePressed(e);
+      }
+    });
+    tabbedPane.addFocusListener(new FocusAdapter()
+    {
+      public void focusGained(FocusEvent e)
+      {
+        tabbedPane_focusGained(e);
+      }
+    });
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        save_actionPerformed(e);
+      }
+    });
+    reload.setEnabled(false);
+    reload.setText("Reload");
+    reload.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        reload_actionPerformed(e);
+      }
+    });
+    newView.setText("New View");
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    newView.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        newView_actionPerformed(e);
+      }
+    });
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+                              +
+        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    formatMenu.setText("Format");
+    selectMenu.setText("Select");
+    idRightAlign.setText("Right Align Sequence Id");
+    idRightAlign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        idRightAlign_actionPerformed(e);
+      }
+    });
+    gatherViews.setEnabled(false);
+    gatherViews.setText("Gather Views");
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_G, 0, false));
+    gatherViews.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        gatherViews_actionPerformed(e);
+      }
+    });
+    expandViews.setEnabled(false);
+    expandViews.setText("Expand Views");
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_X, 0, false));
+    expandViews.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        expandViews_actionPerformed(e);
+      }
+    });
+    pageSetup.setText("Page Setup ...");
+    pageSetup.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pageSetup_actionPerformed(e);
+      }
+    });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(searchMenu);
+    alignFrameMenuBar.add(selectMenu);
     alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
     fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
+    fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
-    fileMenu.add(saveAlignmentMenu);
-    fileMenu.add(jMenu2);
+    fileMenu.add(save);
+    fileMenu.add(saveAs);
     fileMenu.add(outputTextboxMenu);
+    fileMenu.add(pageSetup);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(jMenu2);
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.add(cut);
     editMenu.add(copy);
-    editMenu.add(jMenu1);
+    editMenu.add(pasteMenu);
     editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(selectAllSequenceMenuItem);
-    editMenu.add(deselectAllSequenceMenuItem);
-    editMenu.add(invertSequenceMenuItem);
-    editMenu.add(deleteGroups);
-    editMenu.addSeparator();
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
     editMenu.add(removeGappedColumnMenuItem);
@@ -975,25 +1277,21 @@ public class GAlignFrame
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-    searchMenu.add(findMenuItem);
-    viewMenu.add(font);
+    viewMenu.add(newView);
+    viewMenu.add(expandViews);
+    viewMenu.add(gatherViews);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
     viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-    viewMenu.add(seqLimits);
-    viewMenu.add(scaleAbove);
-    viewMenu.add(scaleLeft);
-    viewMenu.add(scaleRight);
-    viewMenu.add(viewBoxesMenuItem);
-    viewMenu.add(viewTextMenuItem);
-    viewMenu.add(colourTextMenuItem);
-    viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(sequenceFeatures);
+    viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
     colourMenu.addSeparator();
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -1013,6 +1311,7 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1020,15 +1319,15 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
-    webServiceNoServices=new JMenuItem("<No Services>");
+    calculateMenu.add(autoCalculate);
+    webServiceNoServices = new JMenuItem("<No Services>");
     webService.add(webServiceNoServices);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    jMenu1.add(pasteNew);
-    jMenu1.add(pasteThis);
+    pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
+    sort.add(sortByTreeMenu);
     calculate.add(averageDistanceTreeMenuItem);
     calculate.add(neighbourTreeMenuItem);
     calculate.add(avDistanceTreeBlosumMenuItem);
@@ -1036,17 +1335,72 @@ 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);
+    formatMenu.add(font);
+    formatMenu.addSeparator();
+    formatMenu.add(wrapMenuItem);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(seqLimits);
+    formatMenu.add(idRightAlign);
+    formatMenu.add(hiddenMarkers);
+    formatMenu.add(viewBoxesMenuItem);
+    formatMenu.add(viewTextMenuItem);
+    formatMenu.add(colourTextMenuItem);
+    formatMenu.add(renderGapsMenuItem);
+    selectMenu.add(findMenuItem);
+    selectMenu.addSeparator();
+    selectMenu.add(selectAllSequenceMenuItem);
+    selectMenu.add(deselectAllSequenceMenuItem);
+    selectMenu.add(invertSequenceMenuItem);
+    selectMenu.add(invertColSel);
+    selectMenu.add(deleteGroups);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
   }
 
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  protected void closeMenuItem_actionPerformed(boolean b)
   {
   }
 
@@ -1218,7 +1572,7 @@ public class GAlignFrame
   {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -1271,7 +1625,6 @@ public class GAlignFrame
 
   }
 
-
   public void createEPS(java.io.File f)
   {
   }
@@ -1304,9 +1657,7 @@ public class GAlignFrame
   {
   }
 
-
-
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed(ActionEvent e)
   {
   }
 
@@ -1314,7 +1665,6 @@ public class GAlignFrame
   {
   }
 
-
   public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
@@ -1330,17 +1680,137 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void featureSettings_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void findPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void enterPdbId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void pdbFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void tabSelectionChanged(int sel)
+  {
+
+  }
+
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void reload_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void newView_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void expandViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void gatherViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void buildTreeMenu()
+  {
+
+  }
+
+  public void pageSetup_actionPerformed(ActionEvent e)
   {
 
   }