X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=77c3b6acac1cf21985075a1967c47957e5c80bdb;hb=59d682209891099d46b960509907c79e3fb276fe;hp=2e6ea520d9cc36b90a79628e16b083ceb5bfc2de;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2e6ea52..77c3b6a 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview 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 
@@ -17,25 +17,113 @@
  */
 package jalview.gui;
 
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.MenuEvent;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.NJTree;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HTMLOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.ws.jws1.Discoverer;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
 
 /**
  * DOCUMENT ME!
@@ -199,7 +287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
-    if (viewport.conservation == null)
+    if (viewport.getAlignmentConservationAnnotation() == null)
     {
       BLOSUM62Colour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
@@ -225,7 +313,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
       addServiceListeners();
-      setGUINucleotide(viewport.alignment.isNucleotide());
+      setGUINucleotide(viewport.getAlignment().isNucleotide());
     }
 
     setMenusFromViewport(viewport);
@@ -264,6 +352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         if (viewport.cursorMode
@@ -319,6 +408,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           break;
 
+        // case KeyEvent.VK_A:
+        // if (viewport.cursorMode)
+        // {
+        // alignPanel.seqPanel.insertNucAtCursor(false,"A");
+        // //System.out.println("A");
+        // }
+        // break;
+        /*
+         * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
+         * System.out.println("closing bracket"); } break;
+         */
         case KeyEvent.VK_DELETE:
         case KeyEvent.VK_BACK_SPACE:
           if (!viewport.cursorMode)
@@ -433,6 +533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
+      @Override
       public void keyReleased(KeyEvent evt)
       {
         switch (evt.getKeyCode())
@@ -485,12 +586,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (newPanel)
     {
-      if (ap.av.padGaps)
+      if (ap.av.isPadGaps())
       {
-        ap.av.alignment.padGaps();
+        ap.av.getAlignment().padGaps();
       }
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
+      ap.av.updateStrucConsensus(ap);
     }
   }
 
@@ -513,32 +615,51 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   private void addServiceListeners()
   {
     final java.beans.PropertyChangeListener thisListener;
-    // Do this once to get current state
-    BuildWebServiceMenu();
-    Desktop.discoverer
-            .addPropertyChangeListener(thisListener = new java.beans.PropertyChangeListener()
+    Desktop.instance.addJalviewPropertyChangeListener("services",
+            thisListener = new java.beans.PropertyChangeListener()
             {
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // System.out.println("Discoverer property change.");
-                if (evt.getPropertyName().equals("services"))
+                // // System.out.println("Discoverer property change.");
+                // if (evt.getPropertyName().equals("services"))
                 {
-                  // System.out.println("Rebuilding web service menu");
-                  BuildWebServiceMenu();
+                  SwingUtilities.invokeLater(new Runnable()
+                  {
+
+                    @Override
+                    public void run()
+                    {
+                      System.err
+                              .println("Rebuild WS Menu for service change");
+                      BuildWebServiceMenu();
+                    }
+
+                  });
                 }
               }
             });
-
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        // System.out.println("deregistering discoverer listener");
-        Desktop.discoverer.removePropertyChangeListener(thisListener);
+        System.out.println("deregistering discoverer listener");
+        Desktop.instance.removeJalviewPropertyChangeListener("services",
+                thisListener);
         closeMenuItem_actionPerformed(true);
       };
     });
+    // Finally, build the menu once to get current service state
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        BuildWebServiceMenu();
+      }
+    }).start();
   }
 
   public void setGUINucleotide(boolean nucleotide)
@@ -547,11 +668,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
+    rnahelicesColour.setEnabled(nucleotide);
+    purinePyrimidineColour.setEnabled(nucleotide);
     // Remember AlignFrame always starts as protein
-    if (!nucleotide)
-    {
-      calculateMenu.remove(calculateMenu.getItemCount() - 2);
-    }
+    // if (!nucleotide)
+    // {
+    // showTr
+    // calculateMenu.remove(calculateMenu.getItemCount() - 2);
+    // }
   }
 
   /**
@@ -573,7 +697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void setMenusFromViewport(AlignViewport av)
   {
-    padGapsMenuitem.setSelected(av.padGaps);
+    padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.showColourText);
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
     conservationMenuItem.setSelected(av.getConservationSelected());
@@ -588,25 +712,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     annotationPanelMenuItem.setState(av.showAnnotation);
     viewBoxesMenuItem.setSelected(av.showBoxes);
     viewTextMenuItem.setSelected(av.showText);
-    showUnconservedMenuItem.setSelected(av.showUnconserved);
-    showGroupConsensus.setSelected(av.showGroupConsensus);
-    showGroupConservation.setSelected(av.showGroupConservation);
-    showConsensusHistogram.setSelected(av.showConsensusHistogram);
-    showSequenceLogo.setSelected(av.showSequenceLogo);
+    showNonconservedMenuItem.setSelected(av.getShowUnconserved());
+    showGroupConsensus.setSelected(av.isShowGroupConsensus());
+    showGroupConservation.setSelected(av.isShowGroupConservation());
+    showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
+    showSequenceLogo.setSelected(av.isShowSequenceLogo());
+    normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
     showSeqFeatures.setSelected(av.showSequenceFeatures);
     hiddenMarkers.setState(av.showHiddenMarkers);
-    applyToAllGroups.setState(av.colourAppliesToAllGroups);
+    applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
-
+    autoCalculate.setSelected(av.autoCalculateConsensus);
+    sortByTree.setSelected(av.sortByTree);
+    listenToViewSelections.setSelected(av.followSelection);
+    rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
+    rnahelicesColour
+            .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
 
     updateEditMenuBar();
   }
 
+  // methods for implementing IProgressIndicator
+  // need to refactor to a reusable stub class
   Hashtable progressBars, progressBarHandlers;
 
   /*
@@ -614,6 +747,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+  @Override
   public void setProgressBar(String message, long id)
   {
     if (progressBars == null)
@@ -657,10 +791,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBars.put(lId, progressPanel);
     }
     // update GUI
-    setMenusForViewport();
+    // setMenusForViewport();
     validate();
   }
 
+  @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
@@ -678,11 +813,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       cancel.addActionListener(new ActionListener()
       {
 
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
-          us.setProgressBar("Cancelled "
-                  + ((JLabel) progressPanel.getComponent(0)).getText(), id);
+          us.setProgressBar(
+                  "Cancelled "
+                          + ((JLabel) progressPanel.getComponent(0))
+                                  .getText(), id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
@@ -693,6 +831,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if any progress bars are still active
    */
+  @Override
   public boolean operationInProgress()
   {
     if (progressBars != null && progressBars.size() > 0)
@@ -715,20 +854,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
   }
 
+  @Override
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
 
+  @Override
   public void addFromFile_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
     if (fileName != null)
     {
+      // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+      // originating file's format
       // TODO: work out how to recover feature settings for correct view(s) when
       // file is reloaded.
       if (currentFileFormat.equals("Jalview"))
@@ -737,6 +881,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         for (int i = 0; i < frames.length; i++)
         {
           if (frames[i] instanceof AlignFrame && frames[i] != this
+                  && ((AlignFrame) frames[i]).fileName != null
                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
           {
             try
@@ -774,6 +919,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           final FeatureSettings nfs = newframe.featureSettings;
           SwingUtilities.invokeLater(new Runnable()
           {
+            @Override
             public void run()
             {
               nfs.frame.setBounds(fspos);
@@ -787,16 +933,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void addFromURL_actionPerformed(ActionEvent e)
   {
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+  @Override
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null
@@ -818,10 +967,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"),
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
             currentFileFormat, false);
@@ -892,7 +1042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       String[] omitHidden = null;
 
-      if (viewport.hasHiddenColumns)
+      if (viewport.hasHiddenColumns())
       {
         int reply = JOptionPane
                 .showInternalConfirmDialog(
@@ -910,9 +1060,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       FormatAdapter f = new FormatAdapter();
       String output = f.formatSequences(format,
-              (Alignment) viewport.alignment, // class cast exceptions will
+              viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
-              omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
+              omitHidden, f.getCacheSuffixDefault(format),
+              viewport.getColumnSelection());
 
       if (output == null)
       {
@@ -968,11 +1119,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
     String[] omitHidden = null;
 
-    if (viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns())
     {
       int reply = JOptionPane
               .showInternalConfirmDialog(
@@ -991,11 +1143,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap, "Alignment output - "
-            + e.getActionCommand(), 600, 500);
 
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-            viewport.alignment, omitHidden, viewport.colSel));
+    try
+    {
+      cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+              viewport.getAlignment(), omitHidden,
+              viewport.getColumnSelection()));
+      Desktop.addInternalFrame(cap,
+              "Alignment output - " + e.getActionCommand(), 600, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+      cap.dispose();
+    }
+
   }
 
   /**
@@ -1004,11 +1165,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(alignPanel, alignPanel.seqPanel.seqCanvas
-            .getSequenceRenderer(), alignPanel.seqPanel.seqCanvas
-            .getFeatureRenderer());
+    new HTMLOutput(alignPanel,
+            alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
+            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
   }
 
   public void createImageMap(File file, String image)
@@ -1022,6 +1184,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createPNG(File f)
   {
     alignPanel.makePNG(f);
@@ -1033,11 +1196,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void createEPS(File f)
   {
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -1050,6 +1215,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
     // Putting in a thread avoids Swing painting problems
@@ -1057,25 +1223,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     thread.start();
   }
 
+  @Override
   public void exportFeatures_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+  @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(alignPanel,
-            viewport.showAnnotation ? viewport.alignment
-                    .getAlignmentAnnotation() : null, viewport.alignment
-                    .getGroups(),
-            ((Alignment) viewport.alignment).alignmentProperties);
+            viewport.showAnnotation ? viewport.getAlignment()
+                    .getAlignmentAnnotation() : null, viewport
+                    .getAlignment().getGroups(), ((Alignment) viewport
+                    .getAlignment()).alignmentProperties);
   }
 
+  @Override
   public void associatedData_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Load Jalview Annotations or Features File");
     chooser.setToolTipText("Load Jalview Annotations / Features file");
@@ -1086,7 +1255,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      loadJalviewDataFile(choice);
+      loadJalviewDataFile(choice, null, null, null);
     }
 
   }
@@ -1097,6 +1266,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param closeAllTabs
    */
+  @Override
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
     if (alignPanels != null && alignPanels.size() < 2)
@@ -1206,9 +1376,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.historyList.push(command);
       viewport.redoList.clear();
       updateEditMenuBar();
-      viewport.hasHiddenColumns = (viewport.colSel != null
-              && viewport.colSel.getHiddenColumns() != null && viewport.colSel
-              .getHiddenColumns().size() > 0);
+      viewport.updateHiddenColumns();
+      // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
+      // && viewport.getColumnSelection().getHiddenColumns() != null &&
+      // viewport.getColumnSelection()
+      // .getHiddenColumns().size() > 0);
     }
   }
 
@@ -1231,7 +1403,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport != null)
     {
       return new AlignmentI[]
-      { viewport.alignment };
+      { viewport.getAlignment() };
     }
     return null;
   }
@@ -1242,6 +1414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.historyList.empty())
@@ -1255,11 +1428,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (originalSource != null)
     {
-      originalSource.hasHiddenColumns = (viewport.colSel != null
-              && viewport.colSel.getHiddenColumns() != null && viewport.colSel
-              .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.alignment.getSequences());
+      if (originalSource != viewport)
+      {
+        Cache.log
+                .warn("Implementation worry: mismatch of viewport origin for undo");
+      }
+      originalSource.updateHiddenColumns();
+      // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+      // null
+      // && viewport.getColumnSelection().getHiddenColumns() != null &&
+      // viewport.getColumnSelection()
+      // .getHiddenColumns().size() > 0);
+      originalSource.firePropertyChange("alignment", null, originalSource
+              .getAlignment().getSequences());
     }
   }
 
@@ -1269,6 +1450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.redoList.size() < 1)
@@ -1285,11 +1467,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (originalSource != null)
     {
-      originalSource.hasHiddenColumns = (viewport.colSel != null
-              && viewport.colSel.getHiddenColumns() != null && viewport.colSel
-              .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.alignment.getSequences());
+
+      if (originalSource != viewport)
+      {
+        Cache.log
+                .warn("Implementation worry: mismatch of viewport origin for redo");
+      }
+      originalSource.updateHiddenColumns();
+      // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
+      // null
+      // && viewport.getColumnSelection().getHiddenColumns() != null &&
+      // viewport.getColumnSelection()
+      // .getHiddenColumns().size() > 0);
+      originalSource.firePropertyChange("alignment", null, originalSource
+              .getAlignment().getSequences());
     }
   }
 
@@ -1311,7 +1502,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
         {
-          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
           {
             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
             break;
@@ -1326,7 +1517,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // the current view against the closed view first
       if (al != null)
       {
-        PaintRefresher.validateSequences(al, viewport.alignment);
+        PaintRefresher.validateSequences(al, viewport.getAlignment());
       }
 
       originalSource = viewport;
@@ -1349,69 +1540,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-
-    if (up)
-    {
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
-      }
-    }
-    else
-    {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
-      {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-
-        if (!sg.getSequences(null).contains(seq))
-        {
-          continue;
-        }
-
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-
-        if (sg.getSequences(null).contains(temp))
-        {
-          continue;
-        }
-
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
-      }
-    }
-
+    viewport.getAlignment().moveSelectedSequencesByOne(sg,
+            viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true);
   }
 
   synchronized void slideSequences(boolean right, int size)
   {
-    Vector sg = new Vector();
+    List<SequenceI> sg = new Vector();
     if (viewport.cursorMode)
     {
-      sg.addElement(viewport.alignment
-              .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
+      sg.add(viewport.getAlignment().getSequenceAt(
+              alignPanel.seqPanel.seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport.alignment
-                    .getHeight())
+            && viewport.getSelectionGroup().getSize() != viewport
+                    .getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup().getSequences(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
     }
 
     if (sg.size() < 1)
@@ -1421,15 +1568,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     Vector invertGroup = new Vector();
 
-    for (int i = 0; i < viewport.alignment.getHeight(); i++)
+    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
-      if (!sg.contains(viewport.alignment.getSequenceAt(i)))
-        invertGroup.add(viewport.alignment.getSequenceAt(i));
+      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+        invertGroup.add(viewport.getAlignment().getSequenceAt(i));
     }
 
-    SequenceI[] seqs1 = new SequenceI[sg.size()];
-    for (int i = 0; i < sg.size(); i++)
-      seqs1[i] = (SequenceI) sg.elementAt(i);
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
 
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
@@ -1488,6 +1633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
     System.gc();
@@ -1500,7 +1646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
     String[] omitHidden = null;
 
-    if (viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns())
     {
       omitHidden = viewport.getViewAsString(true);
     }
@@ -1515,11 +1661,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       jalview.gui.Desktop.internalCopy = true;
       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
-      Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
-              new StringSelection(""), null);
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+              .setContents(new StringSelection(""), null);
 
-      Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
-              Desktop.instance);
+      Toolkit.getDefaultToolkit().getSystemClipboard()
+              .setContents(ss, Desktop.instance);
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("copying region", er);
@@ -1527,23 +1673,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     Vector hiddenColumns = null;
-    if (viewport.hasHiddenColumns)
+    if (viewport.hasHiddenColumns())
     {
       hiddenColumns = new Vector();
-      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
+              .getSelectionGroup().getEndRes();
       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
               .size(); i++)
       {
         int[] region = (int[]) viewport.getColumnSelection()
                 .getHiddenColumns().elementAt(i);
-
-        hiddenColumns.addElement(new int[]
-        { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
+        {
+          hiddenColumns.addElement(new int[]
+          { region[0] - hiddenOffset, region[1] - hiddenOffset });
+        }
       }
     }
 
     Desktop.jalviewClipboard = new Object[]
-    { seqs, viewport.alignment.getDataset(), hiddenColumns };
+    { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
     statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
   }
 
@@ -1553,6 +1702,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
     paste(true);
@@ -1564,6 +1714,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
     paste(false);
@@ -1632,6 +1783,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
 
       int alwidth = 0;
+      ArrayList<Integer> newGraphGroups = new ArrayList<Integer>();
+      int fgroup = -1;
 
       if (newAlignment)
       {
@@ -1699,6 +1852,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           newDs.clear(); // tidy up
         }
+        if (alignment.getAlignmentAnnotation() != null)
+        {
+          for (AlignmentAnnotation alan : alignment
+                  .getAlignmentAnnotation())
+          {
+            if (alan.graphGroup > fgroup)
+            {
+              fgroup = alan.graphGroup;
+            }
+          }
+        }
         if (pastedal.getAlignmentAnnotation() != null)
         {
           // Add any annotation attached to alignment.
@@ -1709,6 +1873,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
             {
               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+
               newann.padAnnotation(alwidth);
               alignment.addAnnotation(newann);
             }
@@ -1728,11 +1908,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (sequences[i].getAnnotation() != null)
         {
+          AlignmentAnnotation newann;
           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
           {
             annotationAdded = true;
-            sequences[i].getAnnotation()[a].adjustForAlignment();
-            sequences[i].getAnnotation()[a].padAnnotation(alwidth);
+            newann = sequences[i].getAnnotation()[a];
+            newann.adjustForAlignment();
+            newann.padAnnotation(alwidth);
+            if (newann.graphGroup > -1)
+            {
+              if (newann.graphGroup > -1)
+              {
+                if (newGraphGroups.size() <= newann.graphGroup
+                        || newGraphGroups.get(newann.graphGroup) == null)
+                {
+                  for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++)
+                  {
+                    newGraphGroups.add(q, null);
+                  }
+                  newGraphGroups.set(newann.graphGroup, new Integer(
+                          ++fgroup));
+                }
+                newann.graphGroup = newGraphGroups.get(newann.graphGroup)
+                        .intValue();
+              }
+            }
             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
             // was
             // duplicated
@@ -1772,6 +1972,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   newann.padAnnotation(avwidth);
                   alview[avnum].addAnnotation(newann); // annotation was
                   // duplicated earlier
+                  // TODO JAL-1145 graphGroups are not updated for sequence
+                  // annotation added to several views. This may cause
+                  // strangeness
                   alview[avnum].setAnnotationIndex(newann, a);
                 }
               }
@@ -1779,8 +1982,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           buildSortByAnnotationScoresMenu();
         }
-        viewport.firePropertyChange("alignment", null, alignment
-                .getSequences());
+        viewport.firePropertyChange("alignment", null,
+                alignment.getSequences());
+        if (alignPanels != null)
+        {
+          for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+          {
+            ap.validateAnnotationDimensions(false);
+          }
+        }
+        else
+        {
+          alignPanel.validateAnnotationDimensions(false);
+        }
 
       }
       else
@@ -1844,6 +2058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void cut_actionPerformed(ActionEvent e)
   {
     copy_actionPerformed(null);
@@ -1856,6 +2071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void delete_actionPerformed(ActionEvent evt)
   {
 
@@ -1874,7 +2090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     // If the cut affects all sequences, remove highlighted columns
-    if (sg.getSize() == viewport.alignment.getHeight())
+    if (sg.getSize() == viewport.getAlignment().getHeight())
     {
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
@@ -1891,11 +2107,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
-            viewport.alignment));
+            viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
     viewport.sendSelection();
-    viewport.alignment.deleteGroup(sg);
+    viewport.getAlignment().deleteGroup(sg);
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -1916,9 +2132,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-    viewport.alignment.deleteAllGroups();
+    viewport.getAlignment().deleteAllGroups();
     viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
@@ -1932,6 +2149,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = new SequenceGroup();
@@ -1941,7 +2159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
 
-    sg.setEndRes(viewport.alignment.getWidth() - 1);
+    sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
     viewport.sendSelection();
     alignPanel.paintAlignment(true);
@@ -1954,6 +2172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     if (viewport.cursorMode)
@@ -1968,6 +2187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
   }
 
   /**
@@ -1976,6 +2196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -1993,14 +2214,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.paintAlignment(true);
-    viewport.sendSelection();
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+    viewport.sendSelection();
   }
 
+  @Override
   public void invertColSel_actionPerformed(ActionEvent e)
   {
     viewport.invertColumnSelection();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   /**
@@ -2009,6 +2232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(true);
@@ -2020,6 +2244,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
     trimAlignment(false);
@@ -2045,11 +2270,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (viewport.getSelectionGroup() != null)
       {
         seqs = viewport.getSelectionGroup().getSequencesAsArray(
-                viewport.hiddenRepSequences);
+                viewport.getHiddenRepSequences());
       }
       else
       {
-        seqs = viewport.alignment.getSequencesArray();
+        seqs = viewport.getAlignment().getSequencesArray();
       }
 
       TrimRegionCommand trimRegion;
@@ -2057,32 +2282,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left",
                 TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.alignment, viewport.colSel,
-                viewport.selectionGroup);
+                viewport.getAlignment(), viewport.getColumnSelection(),
+                viewport.getSelectionGroup());
         viewport.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right",
                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.alignment, viewport.colSel,
-                viewport.selectionGroup);
+                viewport.getAlignment(), viewport.getColumnSelection(),
+                viewport.getSelectionGroup());
       }
 
       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
-      Vector groups = viewport.alignment.getGroups();
-
-      for (int i = 0; i < groups.size(); i++)
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
-        SequenceGroup sg = (SequenceGroup) groups.get(i);
-
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
-          viewport.alignment.deleteGroup(sg);
+          viewport.getAlignment().deleteGroup(sg);
         }
       }
 
@@ -2097,25 +2318,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
       seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
     {
-      seqs = viewport.alignment.getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
 
     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
-            "Remove Gapped Columns", seqs, start, end, viewport.alignment);
+            "Remove Gapped Columns", seqs, start, end,
+            viewport.getAlignment());
 
     addHistoryItem(removeGapCols);
 
@@ -2124,7 +2347,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
@@ -2143,30 +2366,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
       seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
     {
-      seqs = viewport.alignment.getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.alignment));
+            viewport.getAlignment()));
 
     viewport.setStartRes(seq.findIndex(startRes) - 1);
 
@@ -2181,9 +2405,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
-    viewport.padGaps = padGapsMenuitem.isSelected();
+    viewport.setPadGaps(padGapsMenuitem.isSelected());
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
   }
@@ -2204,15 +2429,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     new Finder();
   }
 
+  @Override
   public void newView_actionPerformed(ActionEvent e)
   {
+    newView(true);
+  }
+
+  /**
+   * 
+   * @param copyAnnotation
+   *          if true then duplicate all annnotation, groups and settings
+   * @return new alignment panel, already displayed.
+   */
+  public AlignmentPanel newView(boolean copyAnnotation)
+  {
+    return newView(null, copyAnnotation);
+  }
+
+  /**
+   * 
+   * @param viewTitle
+   *          title of newly created view
+   * @return new alignment panel, already displayed.
+   */
+  public AlignmentPanel newView(String viewTitle)
+  {
+    return newView(viewTitle, true);
+  }
+
+  /**
+   * 
+   * @param viewTitle
+   *          title of newly created view
+   * @param copyAnnotation
+   *          if true then duplicate all annnotation, groups and settings
+   * @return new alignment panel, already displayed.
+   */
+  public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+  {
     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
             true);
+    if (!copyAnnotation)
+    {
+      // just remove all the current annotation except for the automatic stuff
+      newap.av.getAlignment().deleteAllGroups();
+      for (AlignmentAnnotation alan : newap.av.getAlignment()
+              .getAlignmentAnnotation())
+      {
+        if (!alan.autoCalculated)
+        {
+          newap.av.getAlignment().deleteAnnotation(alan);
+        }
+        ;
+      }
+    }
 
     newap.av.gatherViewsHere = false;
 
@@ -2225,8 +2501,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.redoList = viewport.redoList;
 
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
-    String newViewName = "View " + index;
-
+    // make sure the new view has a unique name - this is essential for Jalview
+    // 2 archives
+    boolean addFirstIndex = false;
+    if (viewTitle == null || viewTitle.trim().length() == 0)
+    {
+      viewTitle = "View";
+      addFirstIndex = true;
+    }
+    else
+    {
+      index = 1;// we count from 1 if given a specific name
+    }
+    String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
     Vector comps = (Vector) PaintRefresher.components.get(viewport
             .getSequenceSetId());
     Vector existingNames = new Vector();
@@ -2244,7 +2531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     while (existingNames.contains(newViewName))
     {
-      newViewName = "View " + (++index);
+      newViewName = viewTitle + " " + (++index);
     }
 
     newap.av.viewName = newViewName;
@@ -2256,13 +2543,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport.gatherViewsHere = true;
     }
     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+    return newap;
   }
 
+  @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
     Desktop.instance.explodeViews(this);
   }
 
+  @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
     Desktop.instance.gatherViews(this);
@@ -2274,6 +2564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void font_actionPerformed(ActionEvent e)
   {
     new FontChooser(alignPanel);
@@ -2285,6 +2576,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
@@ -2294,12 +2586,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
     viewport.rightAlignIds = idRightAlign.isSelected();
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
@@ -2311,6 +2605,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
+  @Override
   protected void followHighlight_actionPerformed()
   {
     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
@@ -2326,6 +2621,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setColourText(colourTextMenuItem.isSelected());
@@ -2338,6 +2634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
     scaleAbove.setVisible(wrapMenuItem.isSelected());
@@ -2347,17 +2644,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
   }
 
+  @Override
   public void showAllSeqs_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenSeqs();
   }
 
+  @Override
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
     repaint();
   }
 
+  @Override
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
@@ -2380,8 +2680,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
-              .getSelected().size() > 0)
+      if ((viewport.getColumnSelection() != null
+              && viewport.getColumnSelection().getSelected() != null && viewport
+              .getColumnSelection().getSelected().size() > 0)
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -2404,12 +2705,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (toggleSeqs)
     {
-      if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+      if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
       {
         hideSelSequences_actionPerformed(null);
         hide = true;
       }
-      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
+              .size() > 0))
       {
         showAllSeqs_actionPerformed(null);
       }
@@ -2417,12 +2719,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (toggleCols)
     {
-      if (viewport.colSel.getSelected().size() > 0)
+      if (viewport.getColumnSelection().getSelected().size() > 0)
       {
         hideSelColumns_actionPerformed(null);
         if (!toggleSeqs)
         {
-          viewport.selectionGroup = sg;
+          viewport.setSelectionGroup(sg);
         }
       }
       else if (!hide)
@@ -2439,6 +2741,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
    */
+  @Override
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
@@ -2451,6 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   public void hideAllSelection_actionPerformed(ActionEvent e)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -2467,6 +2771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   public void showAllhidden_actionPerformed(ActionEvent e)
   {
     viewport.showAllHiddenColumns();
@@ -2474,12 +2779,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void hiddenMarkers_actionPerformed(ActionEvent e)
   {
     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
@@ -2492,6 +2799,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
@@ -2504,6 +2812,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
@@ -2516,6 +2825,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
@@ -2528,6 +2838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
@@ -2540,6 +2851,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowText(viewTextMenuItem.isSelected());
@@ -2552,6 +2864,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
@@ -2560,6 +2873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureSettings featureSettings;
 
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -2582,6 +2896,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
@@ -2598,6 +2913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
@@ -2621,68 +2937,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
   }
 
+  @Override
   public void alignmentProperties()
   {
     JEditorPane editPane = new JEditorPane("text/html", "");
     editPane.setEditable(false);
-    StringBuffer contents = new StringBuffer("<html>");
-
-    float avg = 0;
-    int min = Integer.MAX_VALUE, max = 0;
-    for (int i = 0; i < viewport.alignment.getHeight(); i++)
-    {
-      int size = viewport.alignment.getSequenceAt(i).getEnd()
-              - viewport.alignment.getSequenceAt(i).getStart();
-      avg += size;
-      if (size > max)
-        max = size;
-      if (size < min)
-        min = size;
-    }
-    avg = avg / (float) viewport.alignment.getHeight();
-
-    contents.append("<br>Sequences: " + viewport.alignment.getHeight());
-    contents.append("<br>Minimum Sequence Length: " + min);
-    contents.append("<br>Maximum Sequence Length: " + max);
-    contents.append("<br>Average Length: " + (int) avg);
-
-    if (((Alignment) viewport.alignment).getProperties() != null)
-    {
-      Hashtable props = ((Alignment) viewport.alignment).getProperties();
-      Enumeration en = props.keys();
-      contents.append("<br><br><table border=\"1\">");
-      while (en.hasMoreElements())
-      {
-        String key = en.nextElement().toString();
-        StringBuffer val = new StringBuffer();
-        String vals = props.get(key).toString();
-        int pos = 0, npos;
-        do
-        {
-          npos = vals.indexOf("\n", pos);
-          if (npos == -1)
-          {
-            val.append(vals.substring(pos));
-          }
-          else
-          {
-            val.append(vals.substring(pos, npos));
-            val.append("<br>");
-          }
-          pos = npos + 1;
-        } while (npos != -1);
-        contents
-                .append("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
-      }
-      contents.append("</table>");
-    }
-    editPane.setText(contents.toString() + "</html>");
+    StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+            .formatAsHtml();
+    editPane.setText("<html>" + contents.toString() + "</html>");
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
@@ -2696,6 +2965,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
     if (alignPanel.overviewPanel != null)
@@ -2706,23 +2976,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     JInternalFrame frame = new JInternalFrame();
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
-    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame
-            .getWidth(), frame.getHeight());
+    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+            frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    frame
-            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-            {
-              public void internalFrameClosed(
-                      javax.swing.event.InternalFrameEvent evt)
-              {
-                alignPanel.setOverviewPanel(null);
-              };
-            });
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(
+              javax.swing.event.InternalFrameEvent evt)
+      {
+        alignPanel.setOverviewPanel(null);
+      };
+    });
 
     alignPanel.setOverviewPanel(overview);
   }
 
+  @Override
   public void textColour_actionPerformed(ActionEvent e)
   {
     new TextColourChooser().chooseColour(alignPanel, null);
@@ -2734,6 +3005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
     changeColour(null);
@@ -2745,11 +3017,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    changeColour(new ClustalxColourScheme(
-            viewport.alignment.getSequences(), viewport.alignment
-                    .getWidth()));
+    changeColour(new ClustalxColourScheme(viewport.getAlignment(),
+            viewport.getHiddenRepSequences()));
   }
 
   /**
@@ -2758,6 +3030,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void zappoColour_actionPerformed(ActionEvent e)
   {
     changeColour(new ZappoColourScheme());
@@ -2769,6 +3042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void taylorColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TaylorColourScheme());
@@ -2780,6 +3054,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HydrophobicColourScheme());
@@ -2791,6 +3066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void helixColour_actionPerformed(ActionEvent e)
   {
     changeColour(new HelixColourScheme());
@@ -2802,6 +3078,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void strandColour_actionPerformed(ActionEvent e)
   {
     changeColour(new StrandColourScheme());
@@ -2813,6 +3090,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void turnColour_actionPerformed(ActionEvent e)
   {
     changeColour(new TurnColourScheme());
@@ -2824,6 +3102,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void buriedColour_actionPerformed(ActionEvent e)
   {
     changeColour(new BuriedColourScheme());
@@ -2835,22 +3114,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void nucleotideColour_actionPerformed(ActionEvent e)
   {
     changeColour(new NucleotideColourScheme());
   }
 
+  @Override
+  public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new PurinePyrimidineColourScheme());
+  }
+
+  /*
+   * public void covariationColour_actionPerformed(ActionEvent e) {
+   * changeColour(new
+   * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
+   * ()[0])); }
+   */
+  @Override
   public void annotationColour_actionPerformed(ActionEvent e)
   {
     new AnnotationColourChooser(viewport, alignPanel);
   }
 
+  @Override
+  public void rnahelicesColour_actionPerformed(ActionEvent e)
+  {
+    new RNAHelicesColourChooser(viewport, alignPanel);
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
@@ -2864,6 +3164,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void changeColour(ColourSchemeI cs)
   {
+    // TODO: compare with applet and pull up to model method
     int threshold = 0;
 
     if (cs != null)
@@ -2885,13 +3186,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (viewport.getConservationSelected())
       {
 
-        Alignment al = (Alignment) viewport.alignment;
+        Alignment al = (Alignment) viewport.getAlignment();
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
 
         c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
+        c.verdict(false, viewport.getConsPercGaps());
 
         cs.setConservation(c);
 
@@ -2903,19 +3204,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.hconsensus);
+      cs.setConsensus(viewport.getSequenceConsensusHash());
     }
 
     viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
-      Vector groups = viewport.alignment.getGroups();
 
-      for (int i = 0; i < groups.size(); i++)
+      for (SequenceGroup sg : viewport.getAlignment().getGroups())
       {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-
         if (cs == null)
         {
           sg.cs = null;
@@ -2924,8 +3222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg
-                  .getSequences(viewport.hiddenRepSequences), sg.getWidth());
+          sg.cs = new ClustalxColourScheme(sg,
+                  viewport.getHiddenRepSequences());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -2935,7 +3233,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           try
           {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+            sg.cs = cs.getClass().newInstance();
           } catch (Exception ex)
           {
           }
@@ -2947,9 +3245,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
 
-          sg.cs.setConsensus(AAFrequency.calculate(sg
-                  .getSequences(viewport.hiddenRepSequences), sg
-                  .getStartRes(), sg.getEndRes() + 1));
+          sg.cs.setConsensus(AAFrequency.calculate(
+                  sg.getSequences(viewport.getHiddenRepSequences()),
+                  sg.getStartRes(), sg.getEndRes() + 1));
         }
         else
         {
@@ -2959,11 +3257,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (viewport.getConservationSelected())
         {
           Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg
-                          .getSequences(viewport.hiddenRepSequences), sg
-                          .getStartRes(), sg.getEndRes() + 1);
+                  ResidueProperties.propHash, 3, sg.getSequences(viewport
+                          .getHiddenRepSequences()), sg.getStartRes(),
+                  sg.getEndRes() + 1);
           c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
+          c.verdict(false, viewport.getConsPercGaps());
           sg.cs.setConservation(c);
         }
         else
@@ -2987,13 +3285,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
     if (viewport.getAbovePIDThreshold()
-            && viewport.globalColourScheme != null)
+            && viewport.getGlobalColourScheme() != null)
     {
-      SliderPanel.setPIDSliderSource(alignPanel, viewport
-              .getGlobalColourScheme(), "Background");
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getGlobalColourScheme(), "Background");
       SliderPanel.showPIDSlider();
     }
   }
@@ -3004,13 +3303,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
     if (viewport.getConservationSelected()
-            && viewport.globalColourScheme != null)
+            && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.globalColourScheme, "Background");
+              viewport.getGlobalColourScheme(), "Background");
       SliderPanel.showConservationSlider();
     }
   }
@@ -3021,6 +3321,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
@@ -3039,6 +3340,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
@@ -3057,6 +3359,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     if (e.getActionCommand().equals("User Defined..."))
@@ -3098,13 +3401,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
+          @Override
           public void mousePressed(MouseEvent evt)
           {
             if (evt.isControlDown()
                     || SwingUtilities.isRightMouseButton(evt))
             {
-              radioItem
-                      .removeActionListener(radioItem.getActionListeners()[0]);
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
@@ -3121,6 +3424,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 radioItem.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent evt)
                   {
                     userDefinedColour_actionPerformed(evt);
@@ -3132,6 +3436,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         });
         radioItem.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent evt)
           {
             userDefinedColour_actionPerformed(evt);
@@ -3150,6 +3455,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PIDColour_actionPerformed(ActionEvent e)
   {
     changeColour(new PIDColourScheme());
@@ -3161,6 +3467,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
     changeColour(new Blosum62ColourScheme());
@@ -3172,13 +3479,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
             .getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -3188,11 +3496,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -3202,12 +3512,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -3217,12 +3528,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
 
     alignPanel.paintAlignment(true);
   }
@@ -3233,6 +3545,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
     new RedundancyPanel(alignPanel, this);
@@ -3244,6 +3557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ((viewport.getSelectionGroup() == null)
@@ -3267,6 +3581,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if (((viewport.getSelectionGroup() != null)
@@ -3286,6 +3601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new PCAPanel(alignPanel);
   }
 
+  @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
     viewport.autoCalculateConsensus = autoCalculate.isSelected();
@@ -3296,12 +3612,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
+  {
+    viewport.sortByTree = sortByTree.isSelected();
+  }
+
+  @Override
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    viewport.followSelection = listenToViewSelections.isSelected();
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "PID", "Average distance tree using PID");
@@ -3313,6 +3642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
@@ -3324,6 +3654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
@@ -3335,6 +3666,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
@@ -3354,7 +3686,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     TreePanel tp;
 
-    if (viewport.getSelectionGroup() != null)
+    if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() > 0)
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
@@ -3366,14 +3699,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      int s = 0;
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.getSize())
+      for (SequenceI _s : sg.getSequences())
       {
-        if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
-                .getEndRes())
+        if (_s.getLength() < sg.getEndRes())
         {
           JOptionPane
                   .showMessageDialog(
@@ -3394,7 +3725,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       // are the visible sequences aligned?
-      if (!viewport.alignment.isAligned(false))
+      if (!viewport.getAlignment().isAligned(false))
       {
         JOptionPane
                 .showMessageDialog(
@@ -3408,7 +3739,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      if (viewport.alignment.getHeight() < 2)
+      if (viewport.getAlignment().getHeight() < 2)
       {
         return;
       }
@@ -3443,6 +3774,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3451,8 +3783,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // pointers
         AlignmentSorter.sortBy(viewport.getAlignment(), order);
 
-        addHistoryItem(new OrderCommand(order.getName(), oldOrder,
-                viewport.alignment));
+        addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
+                .getAlignment()));
 
         alignPanel.paintAlignment(true);
       }
@@ -3475,13 +3807,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport
-                .getAlignment());// ,viewport.getSelectionGroup());
+        AlignmentSorter.sortByAnnotationScore(scoreLabel,
+                viewport.getAlignment());// ,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
-                viewport.alignment));
+                viewport.getAlignment()));
         alignPanel.paintAlignment(true);
       }
     });
@@ -3499,23 +3832,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * rebuilding in subsequence calls.
    * 
    */
+  @Override
   public void buildSortByAnnotationScoresMenu()
   {
-    if (viewport.alignment.getAlignmentAnnotation() == null)
+    if (viewport.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
 
-    if (viewport.alignment.getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
+    if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
     {
       sortByAnnotScore.removeAll();
       // almost certainly a quicker way to do this - but we keep it simple
       Hashtable scoreSorts = new Hashtable();
       AlignmentAnnotation aann[];
-      Enumeration sq = viewport.alignment.getSequences().elements();
-      while (sq.hasMoreElements())
+      for (SequenceI sqa : viewport.getAlignment().getSequences())
       {
-        aann = ((SequenceI) sq.nextElement()).getAnnotation();
+        aann = sqa.getAnnotation();
         for (int i = 0; aann != null && i < aann.length; i++)
         {
           if (aann[i].hasScore() && aann[i].sequenceRef != null)
@@ -3527,13 +3860,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       Enumeration labels = scoreSorts.keys();
       while (labels.hasMoreElements())
       {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore, (String) labels
-                .nextElement());
+        addSortByAnnotScoreMenuItem(sortByAnnotScore,
+                (String) labels.nextElement());
       }
       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
       scoreSorts.clear();
 
-      _annotationScoreVectorHash = viewport.alignment
+      _annotationScoreVectorHash = viewport.getAlignment()
               .getAlignmentAnnotation().hashCode();
     }
   }
@@ -3550,6 +3883,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param title
    *          SortBy menu item title.
    */
+  @Override
   public void buildTreeMenu()
   {
     sortByTreeMenu.removeAll();
@@ -3578,21 +3912,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     for (i = 0; i < treePanels.size(); i++)
     {
-      TreePanel tp = (TreePanel) treePanels.elementAt(i);
+      final TreePanel tp = (TreePanel) treePanels.elementAt(i);
       final JMenuItem item = new JMenuItem(tp.getTitle());
       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
       item.addActionListener(new java.awt.event.ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent e)
         {
-          SequenceI[] oldOrder = viewport.getAlignment()
-                  .getSequencesArray();
-          AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
-
-          addHistoryItem(new OrderCommand("Tree Sort", oldOrder,
-                  viewport.alignment));
+          tp.sortByTree_actionPerformed(null);
+          addHistoryItem(tp.sortAlignmentIn(alignPanel));
 
-          alignPanel.paintAlignment(true);
         }
       });
 
@@ -3600,6 +3930,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  public boolean sortBy(AlignmentOrder alorder, String undoname)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+    if (undoname != null)
+    {
+      addHistoryItem(new OrderCommand(undoname, oldOrder,
+              viewport.getAlignment()));
+    }
+    alignPanel.paintAlignment(true);
+    return true;
+  }
+
   /**
    * Work out whether the whole set of sequences or just the selected set will
    * be submitted for multiple alignment.
@@ -3661,9 +4004,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     // limit sequences - JBPNote in future - could spawn multiple prediction
     // jobs
-    // TODO: viewport.alignment.isAligned is a global state - the local
+    // TODO: viewport.getAlignment().isAligned is a global state - the local
     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
-    if (!viewport.alignment.isAligned(false))
+    if (!viewport.getAlignment().isAligned(false))
     {
       seqs.setSequences(new SeqCigar[]
       { seqs.getSequences()[0] });
@@ -3680,11 +4023,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Select a newick-like tree file");
     chooser.setToolTipText("Load a tree file");
@@ -3708,13 +4052,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop, fin
-                .getWarningMessage(), "Possible problem with tree file",
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                fin.getWarningMessage(), "Possible problem with tree file",
                 JOptionPane.WARNING_MESSAGE);
       }
     }
   }
 
+  @Override
+  protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+  {
+    changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+  }
+
   public TreePanel ShowNewickTree(NewickFile nf, String title)
   {
     return ShowNewickTree(nf, title, 600, 500, 4, 5);
@@ -3782,99 +4132,197 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return tp;
   }
 
+  private boolean buildingMenu = false;
+
   /**
    * Generates menu items and listener event actions for web service clients
    * 
    */
   public void BuildWebServiceMenu()
   {
-    // TODO: add support for context dependent disabling of services based on
-    // alignment and current selection
-    // TODO: add additional serviceHandle parameter to specify abstract handler
-    // class independently of AbstractName
-    // TODO: add in rediscovery GUI function to restart discoverer
-    // TODO: group services by location as well as function and/or introduce
-    // object broker mechanism.
-    if ((Discoverer.services != null) && (Discoverer.services.size() > 0))
-    {
-      // TODO: refactor to allow list of AbstractName/Handler bindings to be
-      // stored or retrieved from elsewhere
-      Vector msaws = (Vector) Discoverer.services.get("MsaWS");
-      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
-      Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
-      // TODO: move GUI generation code onto service implementation - so a
-      // client instance attaches itself to the GUI with method call like
-      // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
-      // alignframe)
-      Vector wsmenu = new Vector();
-      final IProgressIndicator af = this;
-      if (msaws != null)
+    while (buildingMenu)
+    {
+      try
       {
-        // Add any Multiple Sequence Alignment Services
-        final JMenu msawsmenu = new JMenu("Alignment");
-        for (int i = 0, j = msaws.size(); i < j; i++)
-        {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
-                  .get(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer
-                  .getServiceClient(sh);
-          impl.attachWSMenuEntry(msawsmenu, this);
-
-        }
-        wsmenu.add(msawsmenu);
-      }
-      if (secstrpr != null)
+        System.err.println("Waiting for building menu to finish.");
+        Thread.sleep(10);
+      } catch (Exception e)
       {
-        // Add any secondary structure prediction services
-        final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
-        for (int i = 0, j = secstrpr.size(); i < j; i++)
-        {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
-                  .get(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer
-                  .getServiceClient(sh);
-          impl.attachWSMenuEntry(secstrmenu, this);
-        }
-        wsmenu.add(secstrmenu);
       }
-      if (seqsrch != null)
+      ;
+    }
+    final AlignFrame me = this;
+    buildingMenu = true;
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        // Add any sequence search services
-        final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
-        for (int i = 0, j = seqsrch.size(); i < j; i++)
+        try
+        {
+          System.err.println("Building ws menu again "
+                  + Thread.currentThread());
+          // TODO: add support for context dependent disabling of services based
+          // on
+          // alignment and current selection
+          // TODO: add additional serviceHandle parameter to specify abstract
+          // handler
+          // class independently of AbstractName
+          // TODO: add in rediscovery GUI function to restart discoverer
+          // TODO: group services by location as well as function and/or
+          // introduce
+          // object broker mechanism.
+          final Vector<JMenu> wsmenu = new Vector<JMenu>();
+          final IProgressIndicator af = me;
+          final JMenu msawsmenu = new JMenu("Alignment");
+          final JMenu secstrmenu = new JMenu(
+                  "Secondary Structure Prediction");
+          final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
+          final JMenu analymenu = new JMenu("Analysis");
+          final JMenu dismenu = new JMenu("Protein Disorder");
+          // JAL-940 - only show secondary structure prediction services from
+          // the legacy server
+          if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
+              // &&
+          Discoverer.services != null && (Discoverer.services.size() > 0))
+          {
+            // TODO: refactor to allow list of AbstractName/Handler bindings to
+            // be
+            // stored or retrieved from elsewhere
+            Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
+            Vector secstrpr = (Vector) Discoverer.services
+                    .get("SecStrPred");
+            Vector seqsrch = null; // (Vector)
+                                   // Discoverer.services.get("SeqSearch");
+            // TODO: move GUI generation code onto service implementation - so a
+            // client instance attaches itself to the GUI with method call like
+            // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
+            // alignframe)
+            if (msaws != null)
+            {
+              // Add any Multiple Sequence Alignment Services
+              for (int i = 0, j = msaws.size(); i < j; i++)
+              {
+                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
+                        .get(i);
+                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+                        .getServiceClient(sh);
+                impl.attachWSMenuEntry(msawsmenu, me);
+
+              }
+            }
+            if (secstrpr != null)
+            {
+              // Add any secondary structure prediction services
+              for (int i = 0, j = secstrpr.size(); i < j; i++)
+              {
+                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+                        .get(i);
+                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+                        .getServiceClient(sh);
+                impl.attachWSMenuEntry(secstrmenu, me);
+              }
+            }
+            if (seqsrch != null)
+            {
+              // Add any sequence search services
+              for (int i = 0, j = seqsrch.size(); i < j; i++)
+              {
+                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
+                        .elementAt(i);
+                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
+                        .getServiceClient(sh);
+                impl.attachWSMenuEntry(seqsrchmenu, me);
+              }
+            }
+          }
+
+          // Add all submenus in the order they should appear on the web
+          // services menu
+          wsmenu.add(msawsmenu);
+          wsmenu.add(secstrmenu);
+          wsmenu.add(dismenu);
+          wsmenu.add(analymenu);
+          // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
+          // submens.add(msawsmenu);
+          // submens.add(secstrmenu);
+          // submens.add(dismenu);
+          // submens.add(analymenu);
+
+          // No search services yet
+          // wsmenu.add(seqsrchmenu);
+
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            @Override
+            public void run()
+            {
+              try
+              {
+                webService.removeAll();
+                // first, add discovered services onto the webservices menu
+                if (wsmenu.size() > 0)
+                {
+                  for (int i = 0, j = wsmenu.size(); i < j; i++)
+                  {
+                    webService.add(wsmenu.get(i));
+                  }
+                }
+                else
+                {
+                  webService.add(me.webServiceNoServices);
+                }
+                // TODO: move into separate menu builder class.
+                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+                {
+                  Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+                  if (jws2servs != null)
+                  {
+                    if (jws2servs.hasServices())
+                    {
+                      jws2servs.attachWSMenuEntry(webService, me);
+                    }
+                    if (jws2servs.isRunning())
+                    {
+                      JMenuItem tm = new JMenuItem(
+                              "Still discovering JABA Services");
+                      tm.setEnabled(false);
+                      webService.add(tm);
+                    }
+                  }
+                }
+
+                build_urlServiceMenu(me.webService);
+                build_fetchdbmenu(webService);
+                for (JMenu item : wsmenu)
+                {
+                  if (item.getItemCount() == 0)
+                  {
+                    item.setEnabled(false);
+                  }
+                  else
+                  {
+                    item.setEnabled(true);
+                  }
+                }
+              } catch (Exception e)
+              {
+                Cache.log
+                        .debug("Exception during web service menu building process.",
+                                e);
+              }
+              ;
+            }
+          });
+        } catch (Exception e)
         {
-          final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
-                  .elementAt(i);
-          jalview.ws.WSClient impl = jalview.ws.Discoverer
-                  .getServiceClient(sh);
-          impl.attachWSMenuEntry(seqsrchmenu, this);
         }
-        wsmenu.add(seqsrchmenu);
-      }
-      // finally, add the whole shebang onto the webservices menu
-      resetWebServiceMenu();
-      for (int i = 0, j = wsmenu.size(); i < j; i++)
-      {
-        webService.add((JMenu) wsmenu.get(i));
+        ;
+
+        buildingMenu = false;
       }
-    }
-    else
-    {
-      resetWebServiceMenu();
-      this.webService.add(this.webServiceNoServices);
-    }
-  }
+    }).start();
 
-  /**
-   * empty the web service menu and add any ad-hoc functions not dynamically
-   * discovered.
-   * 
-   */
-  private void resetWebServiceMenu()
-  {
-    webService.removeAll();
-    build_fetchdbmenu(webService);
-    build_urlServiceMenu(webService);
   }
 
   /**
@@ -3884,8 +4332,37 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   private void build_urlServiceMenu(JMenu webService)
   {
-    jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
-            webService, this);
+    // TODO: remove this code when 2.7 is released
+    // DEBUG - alignmentView
+    /*
+     * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
+     * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
+     * 
+     * @Override public void actionPerformed(ActionEvent e) {
+     * jalview.datamodel.AlignmentView
+     * .testSelectionViews(af.viewport.getAlignment(),
+     * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
+     * 
+     * }); webService.add(testAlView);
+     */
+    // TODO: refactor to RestClient discoverer and merge menu entries for
+    // rest-style services with other types of analysis/calculation service
+    // SHmmr test client - still being implemented.
+    // DEBUG - alignmentView
+
+    for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+            .getRestClients())
+    {
+      client.attachWSMenuEntry(
+              JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+              this);
+    }
+
+    if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
+    {
+      jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
+              webService, this);
+    }
   }
 
   /*
@@ -3955,6 +4432,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         xtype.addActionListener(new ActionListener()
         {
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             // TODO: new thread for this call with vis-delay
@@ -3970,8 +4448,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception e)
     {
       jalview.bin.Cache.log
-              .warn(
-                      "canTranslate threw an exception - please report to help@jalview.org",
+              .warn("canTranslate threw an exception - please report to help@jalview.org",
                       e);
       return false;
     }
@@ -3989,13 +4466,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Runnable foo = new Runnable()
     {
 
+      @Override
       public void run()
       {
         final long sttime = System.currentTimeMillis();
         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
         try
         {
-          Alignment ds = ths.getViewport().alignment.getDataset(); // update
+          Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
           // our local
           // dataset
           // reference
@@ -4061,18 +4539,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // old way
     try
     {
-      return (jalview.analysis.Dna.canTranslate(selection, viewport
-              .getViewAsVisibleContigs(true)));
+      return (jalview.analysis.Dna.canTranslate(selection,
+              viewport.getViewAsVisibleContigs(true)));
     } catch (Exception e)
     {
       jalview.bin.Cache.log
-              .warn(
-                      "canTranslate threw an exception - please report to help@jalview.org",
+              .warn("canTranslate threw an exception - please report to help@jalview.org",
                       e);
       return false;
     }
   }
 
+  @Override
   public void showProducts_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4106,6 +4584,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void showTranslation_actionPerformed(ActionEvent e)
   {
     // /////////////////////////////
@@ -4118,8 +4597,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
               viewport.getViewAsVisibleContigs(true), viewport
-                      .getGapCharacter(), viewport.alignment
-                      .getAlignmentAnnotation(), viewport.alignment
+                      .getGapCharacter(), viewport.getAlignment()
+                      .getAlignmentAnnotation(), viewport.getAlignment()
                       .getWidth(), viewport.getAlignment().getDataset());
     } catch (Exception ex)
     {
@@ -4156,9 +4635,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment
-              .getDataset(), alignPanel.seqPanel.seqCanvas
-              .getFeatureRenderer().featureColours, false);
+      featuresFile = new FeaturesFile(file, type).parse(viewport
+              .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().featureColours, false,
+              jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -4183,22 +4663,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return featuresFile;
   }
 
+  @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dragExit(DropTargetEvent evt)
   {
   }
 
+  @Override
   public void dragOver(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dropActionChanged(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void drop(DropTargetDropEvent evt)
   {
     Transferable t = evt.getTransferable();
@@ -4253,10 +4738,127 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       try
       {
-
+        // check to see if any of these files have names matching sequences in
+        // the alignment
+        SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+                .getAlignment().getSequencesArray());
+        /**
+         * Object[] { String,SequenceI}
+         */
+        ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
+        ArrayList<String> filesnotmatched = new ArrayList<String>();
         for (int i = 0; i < files.size(); i++)
         {
-          loadJalviewDataFile(files.get(i).toString());
+          String file = files.get(i).toString();
+          String pdbfn = "";
+          String protocol = FormatAdapter.checkProtocol(file);
+          if (protocol == jalview.io.FormatAdapter.FILE)
+          {
+            File fl = new File(file);
+            pdbfn = fl.getName();
+          }
+          else if (protocol == jalview.io.FormatAdapter.URL)
+          {
+            URL url = new URL(file);
+            pdbfn = url.getFile();
+          }
+          if (pdbfn.length() > 0)
+          {
+            // attempt to find a match in the alignment
+            SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
+            int l = 0, c = pdbfn.indexOf(".");
+            while (mtch == null && c != -1)
+            {
+              do
+              {
+                l = c;
+              } while ((c = pdbfn.indexOf(".", l)) > l);
+              if (l > -1)
+              {
+                pdbfn = pdbfn.substring(0, l);
+              }
+              mtch = idm.findAllIdMatches(pdbfn);
+            }
+            if (mtch != null)
+            {
+              String type = null;
+              try
+              {
+                type = new IdentifyFile().Identify(file, protocol);
+              } catch (Exception ex)
+              {
+                type = null;
+              }
+              if (type != null)
+              {
+                if (type.equalsIgnoreCase("PDB"))
+                {
+                  filesmatched.add(new Object[]
+                  { file, protocol, mtch });
+                  continue;
+                }
+              }
+            }
+            // File wasn't named like one of the sequences or wasn't a PDB file.
+            filesnotmatched.add(file);
+          }
+        }
+        int assocfiles = 0;
+        if (filesmatched.size() > 0)
+        {
+          if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
+                  || JOptionPane
+                          .showConfirmDialog(
+                                  this,
+                                  "Do you want to automatically associate the "
+                                          + filesmatched.size()
+                                          + " PDB files with sequences in the alignment that have the same name ?",
+                                  "Automatically Associate PDB files by name",
+                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+
+          {
+            for (Object[] fm : filesmatched)
+            {
+              // try and associate
+              // TODO: may want to set a standard ID naming formalism for
+              // associating PDB files which have no IDs.
+              for (SequenceI toassoc : (SequenceI[]) fm[2])
+              {
+                PDBEntry pe = new AssociatePdbFileWithSeq()
+                        .associatePdbWithSeq((String) fm[0],
+                                (String) fm[1], toassoc, false);
+                if (pe != null)
+                {
+                  System.err.println("Associated file : "
+                          + ((String) fm[0]) + " with "
+                          + toassoc.getDisplayId(true));
+                  assocfiles++;
+                }
+              }
+              alignPanel.paintAlignment(true);
+            }
+          }
+        }
+        if (filesnotmatched.size() > 0)
+        {
+          if (assocfiles > 0
+                  && (Cache.getDefault(
+                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+                          .showConfirmDialog(
+                                  this,
+                                  "<html>Do you want to <em>ignore</em> the "
+                                          + filesnotmatched.size()
+                                          + " files whose names did not match any sequence IDs ?</html>",
+                                  "Ignore unmatched dropped files ?",
+                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+          {
+            return;
+          }
+          for (String fn : filesnotmatched)
+          {
+            loadJalviewDataFile(fn, null, null, null);
+          }
+
         }
       } catch (Exception ex)
       {
@@ -4274,47 +4876,117 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    *          either a filename or a URL string.
    */
-  public void loadJalviewDataFile(String file)
+  public void loadJalviewDataFile(String file, String protocol,
+          String format, SequenceI assocSeq)
   {
     try
     {
-      String protocol = jalview.io.FormatAdapter.FILE;
-      String f = file.toLowerCase();
-      if (f.indexOf("http:") == 0 || f.indexOf("https:") == 0
-              || f.indexOf("file:") == 0)
+      if (protocol == null)
       {
-        protocol = jalview.io.FormatAdapter.URL;
+        protocol = jalview.io.FormatAdapter.checkProtocol(file);
       }
-
-      boolean isAnnotation = new AnnotationFile().readAnnotationFile(
-              viewport.alignment, file, protocol);
+      // if the file isn't identified, or not positively identified as some
+      // other filetype (PFAM is default unidentified alignment file type) then
+      // try to parse as annotation.
+      boolean isAnnotation = (format == null || format
+              .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
+              .readAnnotationFile(viewport.getAlignment(), file, protocol)
+              : false;
 
       if (!isAnnotation)
       {
-        // try to see if its a JNet 'concise' style annotation file *before* we
-        // try to parse it as a features file
-        String format = new IdentifyFile().Identify(file, protocol);
-        if (format.equalsIgnoreCase("JnetFile"))
+        // first see if its a T-COFFEE score file
+        TCoffeeScoreFile tcf = null;
+        try
         {
-          jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
-                  protocol);
-          new JnetAnnotationMaker().add_annotation(predictions, viewport
-                  .getAlignment(), 0, false);
-          isAnnotation = true;
+          tcf = new TCoffeeScoreFile(file, protocol);
+          if (tcf.isValid())
+          {
+            if (tcf.annotateAlignment(viewport.getAlignment(), true))
+            {
+              tcoffeeColour.setEnabled(true);
+              tcoffeeColour.setSelected(true);
+              changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+              isAnnotation = true;
+              statusBar
+                      .setText("Successfully pasted T-Coffee scores to alignment.");
+            }
+            else
+            {
+              // some problem - if no warning its probable that the ID matching
+              // process didn't work
+              JOptionPane
+                      .showMessageDialog(
+                              Desktop.desktop,
+                              tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment."
+                                      : tcf.getWarningMessage(),
+                              "Problem reading T-COFFEE score file",
+                              JOptionPane.WARNING_MESSAGE);
+            }
+          }
+          else
+          {
+            tcf = null;
+          }
+        } catch (Exception x)
+        {
+          Cache.log
+                  .debug("Exception when processing data source as T-COFFEE score file",
+                          x);
+          tcf = null;
         }
-        else
+        if (tcf == null)
         {
+          // try to see if its a JNet 'concise' style annotation file *before*
+          // we
           // try to parse it as a features file
-          boolean isGroupsFile = parseFeaturesFile(file, protocol);
-          // if it wasn't a features file then we just treat it as a general
-          // alignment file to load into the current view.
-          if (!isGroupsFile)
+          if (format == null)
+          {
+            format = new IdentifyFile().Identify(file, protocol);
+          }
+          if (format.equalsIgnoreCase("JnetFile"))
           {
-            new FileLoader().LoadFile(viewport, file, protocol, format);
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+                    file, protocol);
+            new JnetAnnotationMaker().add_annotation(predictions,
+                    viewport.getAlignment(), 0, false);
+            isAnnotation = true;
           }
           else
           {
-            alignPanel.paintAlignment(true);
+            /*
+             * if (format.equalsIgnoreCase("PDB")) {
+             * 
+             * String pdbfn = ""; // try to match up filename with sequence id
+             * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+             * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+             * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+             * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+             * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+             * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+             * // attempt to find a match in the alignment SequenceI mtch =
+             * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+             * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+             * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+             * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+             * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+             * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+             * { System.err.println("Associated file : " + file + " with " +
+             * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+             * TODO: maybe need to load as normal otherwise return; } }
+             */
+            // try to parse it as a features file
+            boolean isGroupsFile = parseFeaturesFile(file, protocol);
+            // if it wasn't a features file then we just treat it as a general
+            // alignment file to load into the current view.
+            if (!isGroupsFile)
+            {
+              new FileLoader().LoadFile(viewport, file, protocol, format);
+            }
+            else
+            {
+              alignPanel.paintAlignment(true);
+            }
           }
         }
       }
@@ -4329,9 +5001,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     } catch (Exception ex)
     {
       ex.printStackTrace();
+    } catch (OutOfMemoryError oom)
+    {
+      try
+      {
+        System.gc();
+      } catch (Exception x)
+      {
+      }
+      ;
+      new OOMWarning(
+              "loading data "
+                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
+                              : "using " + protocol + " from " + file)
+                              : ".")
+                      + (format != null ? "(parsing as '" + format
+                              + "' file)" : ""), oom, Desktop.desktop);
     }
   }
 
+  @Override
   public void tabSelectionChanged(int index)
   {
     if (index > -1)
@@ -4342,6 +5031,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
     if (SwingUtilities.isRightMouseButton(e))
@@ -4366,10 +5056,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Open the dialog for regex description parsing.
    */
+  @Override
   protected void extractScores_actionPerformed(ActionEvent e)
   {
     ParseProperties pp = new jalview.analysis.ParseProperties(
-            viewport.alignment);
+            viewport.getAlignment());
     // TODO: verify regex and introduce GUI dialog for version 2.5
     // if (pp.getScoresFromDescription("col", "score column ",
     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
@@ -4388,6 +5079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+  @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
@@ -4399,6 +5091,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+  @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
@@ -4439,22 +5132,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // TODO We probably want to store a sequence database checklist in
     // preferences and have checkboxes.. rather than individual sources selected
     // here
-    JMenu rfetch = new JMenu("Fetch DB References");
-    rfetch
-            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+    final JMenu rfetch = new JMenu("Fetch DB References");
+    rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
     webService.add(rfetch);
 
     JMenuItem fetchr = new JMenuItem("Standard Databases");
-    fetchr
-            .setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+    fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
     fetchr.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         new Thread(new Runnable()
         {
 
+          @Override
           public void run()
           {
             new jalview.ws.DBRefFetcher(alignPanel.av
@@ -4467,62 +5160,193 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     });
     rfetch.add(fetchr);
-    JMenu dfetch = new JMenu();
-    rfetch.add(dfetch);
-    jalview.ws.SequenceFetcher sf = SequenceFetcher
-            .getSequenceFetcherSingleton(this);
-    String[] otherdb = sf.getOrderedSupportedSources();
-    // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
-    // jalview.util.QuickSort.sort(otherdb, otherdb);
-    int comp = 0, mcomp = 15;
-    String mname = null;
-    if (otherdb != null && otherdb.length > 0)
-    {
-      for (int i = 0; i < otherdb.length; i++)
+    final AlignFrame me = this;
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        String dbname = sf.getSourceProxy(otherdb[i]).getDbName();
-        if (mname == null)
-        {
-          mname = "from '" + dbname + "'";
-        }
-        fetchr = new JMenuItem(otherdb[i]);
-        final String[] dassource = new String[]
-        { otherdb[i] };
-        fetchr.addActionListener(new ActionListener()
+        final jalview.ws.SequenceFetcher sf = SequenceFetcher
+                .getSequenceFetcherSingleton(me);
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-
-          public void actionPerformed(ActionEvent e)
+          @Override
+          public void run()
           {
-            new Thread(new Runnable()
+            String[] dbclasses = sf.getOrderedSupportedSources();
+            // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+            // jalview.util.QuickSort.sort(otherdb, otherdb);
+            List<DbSourceProxy> otherdb;
+            JMenu dfetch = new JMenu();
+            JMenu ifetch = new JMenu();
+            JMenuItem fetchr = null;
+            int comp = 0, icomp = 0, mcomp = 15;
+            String mname = null;
+            int dbi = 0;
+            for (String dbclass : dbclasses)
             {
+              otherdb = sf.getSourceProxy(dbclass);
+              // add a single entry for this class, or submenu allowing 'fetch
+              // all' or pick one
+              if (otherdb == null || otherdb.size() < 1)
+              {
+                continue;
+              }
+              // List<DbSourceProxy> dbs=otherdb;
+              // otherdb=new ArrayList<DbSourceProxy>();
+              // for (DbSourceProxy db:dbs)
+              // {
+              // if (!db.isA(DBRefSource.ALIGNMENTDB)
+              // }
+              if (mname == null)
+              {
+                mname = "From " + dbclass;
+              }
+              if (otherdb.size() == 1)
+              {
+                final DbSourceProxy[] dassource = otherdb
+                        .toArray(new DbSourceProxy[0]);
+                DbSourceProxy src = otherdb.get(0);
+                fetchr = new JMenuItem(src.getDbSource());
+                fetchr.addActionListener(new ActionListener()
+                {
+
+                  @Override
+                  public void actionPerformed(ActionEvent e)
+                  {
+                    new Thread(new Runnable()
+                    {
+
+                      @Override
+                      public void run()
+                      {
+                        new jalview.ws.DBRefFetcher(alignPanel.av
+                                .getSequenceSelection(),
+                                alignPanel.alignFrame, dassource)
+                                .fetchDBRefs(false);
+                      }
+                    }).start();
+                  }
 
-              public void run()
+                });
+                fetchr.setToolTipText("<html>"
+                        + JvSwingUtils.wrapTooltip("Retrieve from "
+                                + src.getDbName()) + "<html>");
+                dfetch.add(fetchr);
+                comp++;
+              }
+              else
+              {
+                final DbSourceProxy[] dassource = otherdb
+                        .toArray(new DbSourceProxy[0]);
+                // fetch all entry
+                DbSourceProxy src = otherdb.get(0);
+                fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
+                        + "'");
+                fetchr.addActionListener(new ActionListener()
+                {
+                  @Override
+                  public void actionPerformed(ActionEvent e)
+                  {
+                    new Thread(new Runnable()
+                    {
+
+                      @Override
+                      public void run()
+                      {
+                        new jalview.ws.DBRefFetcher(alignPanel.av
+                                .getSequenceSelection(),
+                                alignPanel.alignFrame, dassource)
+                                .fetchDBRefs(false);
+                      }
+                    }).start();
+                  }
+                });
+
+                fetchr.setToolTipText("<html>"
+                        + JvSwingUtils.wrapTooltip("Retrieve from all "
+                                + otherdb.size() + " sources in "
+                                + src.getDbSource() + "<br>First is :"
+                                + src.getDbName()) + "<html>");
+                dfetch.add(fetchr);
+                comp++;
+                // and then build the rest of the individual menus
+                ifetch = new JMenu("Sources from " + src.getDbSource());
+                icomp = 0;
+                String imname = null;
+                int i = 0;
+                for (DbSourceProxy sproxy : otherdb)
+                {
+                  String dbname = sproxy.getDbName();
+                  String sname = dbname.length() > 5 ? dbname.substring(0,
+                          5) + "..." : dbname;
+                  String msname = dbname.length() > 10 ? dbname.substring(
+                          0, 10) + "..." : dbname;
+                  if (imname == null)
+                  {
+                    imname = "from '" + sname + "'";
+                  }
+                  fetchr = new JMenuItem(msname);
+                  final DbSourceProxy[] dassrc =
+                  { sproxy };
+                  fetchr.addActionListener(new ActionListener()
+                  {
+
+                    @Override
+                    public void actionPerformed(ActionEvent e)
+                    {
+                      new Thread(new Runnable()
+                      {
+
+                        @Override
+                        public void run()
+                        {
+                          new jalview.ws.DBRefFetcher(alignPanel.av
+                                  .getSequenceSelection(),
+                                  alignPanel.alignFrame, dassrc)
+                                  .fetchDBRefs(false);
+                        }
+                      }).start();
+                    }
+
+                  });
+                  fetchr.setToolTipText("<html>"
+                          + JvSwingUtils.wrapTooltip("Retrieve from "
+                                  + dbname) + "</html>");
+                  ifetch.add(fetchr);
+                  ++i;
+                  if (++icomp >= mcomp || i == (otherdb.size()))
+                  {
+                    ifetch.setText(imname + " to '" + sname + "'");
+                    dfetch.add(ifetch);
+                    ifetch = new JMenu();
+                    imname = null;
+                    icomp = 0;
+                    comp++;
+                  }
+                }
+              }
+              ++dbi;
+              if (comp >= mcomp || dbi >= (dbclasses.length))
               {
-                new jalview.ws.DBRefFetcher(alignPanel.av
-                        .getSequenceSelection(), alignPanel.alignFrame,
-                        dassource).fetchDBRefs(false);
+                dfetch.setText(mname + " to '" + dbclass + "'");
+                rfetch.add(dfetch);
+                dfetch = new JMenu();
+                mname = null;
+                comp = 0;
               }
-            }).start();
+            }
           }
-
         });
-        fetchr.setToolTipText("Retrieve from " + dbname);
-        dfetch.add(fetchr);
-        if (comp++ == mcomp || i == (otherdb.length - 1))
-        {
-          dfetch.setText(mname + " to '" + dbname + "'");
-          rfetch.add(dfetch);
-          dfetch = new JMenu();
-          mname = null;
-          comp = 0;
-        }
       }
-    }
+    }).start();
+
   }
 
   /**
    * Left justify the whole alignment.
    */
+  @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -4533,6 +5357,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Right justify the whole alignment.
    */
+  @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
     AlignmentI al = viewport.getAlignment();
@@ -4553,9 +5378,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
    */
+  @Override
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowUnconserved(showUnconservedMenuItem.getState());
+    viewport.setShowUnconserved(showNonconservedMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -4566,6 +5392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConsensus(showGroupConsensus.getState());
@@ -4580,6 +5407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
     viewport.setShowGroupConservation(showGroupConservation.getState());
@@ -4593,6 +5421,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
   {
     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
@@ -4606,12 +5435,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void showSequenceLogo_actionPerformed(ActionEvent e)
   {
     viewport.setShowSequenceLogo(showSequenceLogo.getState());
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
   }
 
+  @Override
+  protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    showSequenceLogo.setState(true);
+    viewport.setShowSequenceLogo(true);
+    viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
+    alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
+  }
+
+  @Override
   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
   {
     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
@@ -4624,37 +5464,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+  @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
     if (viewport.getSelectionGroup() != null)
     {
       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(), viewport.getAlignmentView(
-                      true).getSequenceStrings(viewport.getGapCharacter()),
-              viewport.alignment.getGroups());
-      viewport.alignment.deleteAllGroups();
+              viewport.getSequenceSelection(),
+              viewport.getAlignmentView(true).getSequenceStrings(
+                      viewport.getGapCharacter()), viewport.getAlignment()
+                      .getGroups());
+      viewport.getAlignment().deleteAllGroups();
       viewport.sequenceColours = null;
       viewport.setSelectionGroup(null);
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
-        gps[g].setShowunconserved(viewport.getShowUnconserved());
-        gps[g].setIncludeAllConsSymbols(viewport
-                .isIncludeAllConsensusSymbols());
-        viewport.alignment.addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255), (int) (Math
-                .random() * 255), (int) (Math.random() * 255));
+        gps[g].setShowNonconserved(viewport.getShowUnconserved());
+        gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
+        viewport.getAlignment().addGroup(gps[g]);
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
-                .hasMoreElements(); viewport.setSequenceColour(
-                (SequenceI) sq.nextElement(), col))
-          ;
+        for (SequenceI s : gps[g].getSequences())
+          viewport.setSequenceColour(s, col);
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
       alignPanel.paintAlignment(true);
     }
   }
+
+  /**
+   * make the given alignmentPanel the currently selected tab
+   * 
+   * @param alignmentPanel
+   */
+  public void setDisplayedView(AlignmentPanel alignmentPanel)
+  {
+    if (!viewport.getSequenceSetId().equals(
+            alignmentPanel.av.getSequenceSetId()))
+    {
+      throw new Error(
+              "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+    }
+    if (tabbedPane != null
+            & alignPanels.indexOf(alignmentPanel) != tabbedPane
+                    .getSelectedIndex())
+    {
+      tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
+    }
+  }
 }
 
 class PrintThread extends Thread
@@ -4668,6 +5528,7 @@ class PrintThread extends Thread
 
   static PageFormat pf;
 
+  @Override
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();