X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d161cfd4fcd59170d418679ffe009e54300eb8f0;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=b19e54fd440c9baa78150c791862361439faffbc;hpb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b19e54f..cf6a901 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,19 +20,23 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
-import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
-import jalview.analysis.NJTree;
+import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
+import jalview.api.SplitContainerI;
+import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -44,48 +48,46 @@ import jalview.commands.TrimRegionCommand;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
 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.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
 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.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -93,7 +95,6 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
 import java.awt.Component;
-import java.awt.GridLayout;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
@@ -107,34 +108,34 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 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.io.FileWriter;
+import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
-import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 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;
 
@@ -145,27 +146,28 @@ import javax.swing.SwingUtilities;
  * @version $Revision$
  */
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
-        IProgressIndicator, AlignViewControllerGuiI
+        IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
-  /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
 
-  /** DOCUMENT ME!! */
   public static final int DEFAULT_HEIGHT = 500;
 
+  /*
+   * The currently displayed panel (selected tabbed view if more than one)
+   */
   public AlignmentPanel alignPanel;
 
   AlignViewport viewport;
 
   public AlignViewControllerI avc;
 
-  Vector alignPanels = new Vector();
+  List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
 
   /**
    * Last format used to load or save alignments in this window
    */
-  String currentFileFormat = null;
+  FileFormatI currentFileFormat = null;
 
   /**
    * Current filename for this alignment
@@ -277,7 +279,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     alignPanel = new AlignmentPanel(this, viewport);
 
+    addAlignmentPanel(alignPanel, true);
+    init();
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection hiddenColumns, int width, int height)
+  {
+    setSize(width, height);
+
+    if (al.getDataset() == null)
+    {
+      al.setDataset(null);
+    }
+
+    viewport = new AlignViewport(al, hiddenColumns);
 
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+    }
+    alignPanel = new AlignmentPanel(this, viewport);
     addAlignmentPanel(alignPanel, true);
     init();
   }
@@ -304,11 +326,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    if (!Jalview.isHeadlessMode())
+    {
+      progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+    }
+
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
-      BLOSUM62Colour.setEnabled(false);
+      // BLOSUM62Colour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
       modifyConservation.setEnabled(false);
       // PIDColour.setEnabled(false);
@@ -328,18 +355,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sortPairwiseMenuItem_actionPerformed(null);
     }
 
+    this.alignPanel.av
+            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+
+    setMenusFromViewport(viewport);
+    buildSortByAnnotationScoresMenu();
+    buildTreeMenu();
+    buildColourMenu();
+
     if (Desktop.desktop != null)
     {
       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
       addServiceListeners();
-      setGUINucleotide(viewport.getAlignment().isNucleotide());
+      setGUINucleotide();
     }
 
-    setMenusFromViewport(viewport);
-    buildSortByAnnotationScoresMenu();
-    buildTreeMenu();
-    
-    if (viewport.wrapAlignment)
+    if (viewport.getWrapAlignment())
     {
       wrapMenuItem_actionPerformed(null);
     }
@@ -351,6 +382,90 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addKeyListener();
 
+    final List<AlignmentPanel> selviews = new ArrayList<AlignmentPanel>();
+    final List<AlignmentPanel> origview = new ArrayList<AlignmentPanel>();
+    final String menuLabel = MessageManager
+            .getString("label.copy_format_from");
+    ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
+            new ViewSetProvider()
+            {
+
+              @Override
+              public AlignmentPanel[] getAllAlignmentPanels()
+              {
+                origview.clear();
+                origview.add(alignPanel);
+                // make an array of all alignment panels except for this one
+                List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>(
+                        Arrays.asList(Desktop.getAlignmentPanels(null)));
+                aps.remove(AlignFrame.this.alignPanel);
+                return aps.toArray(new AlignmentPanel[aps.size()]);
+              }
+            }, selviews, new ItemListener()
+            {
+
+              @Override
+              public void itemStateChanged(ItemEvent e)
+              {
+                if (origview.size() > 0)
+                {
+                  final AlignmentPanel ap = origview.get(0);
+
+                  /*
+                   * Copy the ViewStyle of the selected panel to 'this one'.
+                   * Don't change value of 'scaleProteinAsCdna' unless copying
+                   * from a SplitFrame.
+                   */
+                  ViewStyleI vs = selviews.get(0).getAlignViewport()
+                          .getViewStyle();
+                  boolean fromSplitFrame = selviews.get(0)
+                          .getAlignViewport().getCodingComplement() != null;
+                  if (!fromSplitFrame)
+                  {
+                    vs.setScaleProteinAsCdna(ap.getAlignViewport()
+                            .getViewStyle().isScaleProteinAsCdna());
+                  }
+                  ap.getAlignViewport().setViewStyle(vs);
+
+                  /*
+                   * Also rescale ViewStyle of SplitFrame complement if there is
+                   * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
+                   * the whole ViewStyle (allow cDNA protein to have different
+                   * fonts)
+                   */
+                  AlignViewportI complement = ap.getAlignViewport()
+                          .getCodingComplement();
+                  if (complement != null && vs.isScaleProteinAsCdna())
+                  {
+                    AlignFrame af = Desktop.getAlignFrameFor(complement);
+                    ((SplitFrame) af.getSplitViewContainer())
+                            .adjustLayout();
+                    af.setMenusForViewport();
+                  }
+
+                  ap.updateLayout();
+                  ap.setSelected(true);
+                  ap.alignFrame.setMenusForViewport();
+
+                }
+              }
+            });
+    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+            .indexOf("devel") > -1
+            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+                    .indexOf("test") > -1)
+    {
+      formatMenu.add(vsel);
+    }
+    addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusGained(FocusEvent e)
+      {
+        Jalview.setCurrentAlignFrame(AlignFrame.this);
+      }
+    });
+
   }
 
   /**
@@ -362,13 +477,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
-  public void setFileName(String file, String format)
+  public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
-    currentFileFormat = format;
+    setFileFormat(format);
     reload.setEnabled(true);
   }
 
+  /**
+   * Add a KeyListener with handlers for various KeyPressed and KeyReleased
+   * events
+   */
   void addKeyListener()
   {
     addKeyListener(new KeyAdapter()
@@ -442,8 +561,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_SPACE:
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
-                    || evt.isShiftDown() || evt.isAltDown());
+            alignPanel.getSeqPanel().insertGapAtCursor(
+                    evt.isControlDown() || evt.isShiftDown()
+                            || evt.isAltDown());
           }
           break;
 
@@ -466,8 +586,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
-                    || evt.isShiftDown() || evt.isAltDown());
+            alignPanel.getSeqPanel().deleteGapAtCursor(
+                    evt.isControlDown() || evt.isShiftDown()
+                            || evt.isAltDown());
           }
 
           break;
@@ -515,8 +636,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_F2:
           viewport.cursorMode = !viewport.cursorMode;
           statusBar.setText(MessageManager.formatMessage(
-                  "label.keyboard_editing_mode", new String[]
-                  { (viewport.cursorMode ? "on" : "off") }));
+                  "label.keyboard_editing_mode",
+                  new String[] { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
             alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
@@ -541,8 +662,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           toggleHiddenRegions(toggleSeqs, toggleCols);
           break;
         }
+        case KeyEvent.VK_B:
+        {
+          boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
+          boolean modifyExisting = true; // always modify, don't clear
+                                         // evt.isShiftDown();
+          boolean invertHighlighted = evt.isAltDown();
+          avc.markHighlightedColumns(invertHighlighted, modifyExisting,
+                  toggleSel);
+          break;
+        }
         case KeyEvent.VK_PAGE_UP:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(true);
           }
@@ -553,7 +684,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(false);
           }
@@ -597,7 +728,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
 
-    alignPanels.addElement(ap);
+    alignPanels.add(ap);
 
     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 
@@ -640,7 +771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     expandViews.setEnabled(true);
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
-    AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
+    AlignmentPanel first = alignPanels.get(0);
     tabbedPane.addTab(first.av.viewName, first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
@@ -684,7 +815,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        System.out.println("deregistering discoverer listener");
+        // System.out.println("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -701,27 +832,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }).start();
   }
 
-  public void setGUINucleotide(boolean nucleotide)
+  /**
+   * Configure menu items that vary according to whether the alignment is
+   * nucleotide or protein
+   */
+  public void setGUINucleotide()
   {
+    AlignmentI al = getViewport().getAlignment();
+    boolean nucleotide = al.isNucleotide();
+
     showTranslation.setVisible(nucleotide);
+    showReverse.setVisible(nucleotide);
+    showReverseComplement.setVisible(nucleotide);
     conservationMenuItem.setEnabled(!nucleotide);
-    modifyConservation.setEnabled(!nucleotide);
+    modifyConservation.setEnabled(!nucleotide
+            && conservationMenuItem.isSelected());
     showGroupConservation.setEnabled(!nucleotide);
-    rnahelicesColour.setEnabled(nucleotide);
-    purinePyrimidineColour.setEnabled(nucleotide);
-    // Remember AlignFrame always starts as protein
-    // if (!nucleotide)
-    // {
-    // showTr
-    // calculateMenu.remove(calculateMenu.getItemCount() - 2);
-    // }
+
+    showComplementMenuItem.setText(nucleotide ? MessageManager
+            .getString("label.protein") : MessageManager
+            .getString("label.nucleotide"));
   }
 
   /**
-   * set up menus for the currently viewport. This may be called after any
+   * set up menus for the current viewport. This may be called after any
    * operation that affects the data in the current view (selection changed,
    * etc) to update the menus to reflect the new state.
    */
+  @Override
   public void setMenusForViewport()
   {
     setMenusFromViewport(viewport);
@@ -737,17 +875,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
-    colourTextMenuItem.setSelected(av.showColourText);
+    colourTextMenuItem.setSelected(av.isShowColourText());
     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    modifyPID.setEnabled(abovePIDThreshold.isSelected());
     conservationMenuItem.setSelected(av.getConservationSelected());
+    modifyConservation.setEnabled(conservationMenuItem.isSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
     idRightAlign.setSelected(av.isRightAlignIds());
-    centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
-    renderGapsMenuItem.setSelected(av.renderGaps);
-    wrapMenuItem.setSelected(av.wrapAlignment);
-    scaleAbove.setVisible(av.wrapAlignment);
-    scaleLeft.setVisible(av.wrapAlignment);
-    scaleRight.setVisible(av.wrapAlignment);
+    centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
+    renderGapsMenuItem.setSelected(av.isRenderGaps());
+    wrapMenuItem.setSelected(av.getWrapAlignment());
+    scaleAbove.setVisible(av.getWrapAlignment());
+    scaleLeft.setVisible(av.getWrapAlignment());
+    scaleRight.setVisible(av.getWrapAlignment());
     annotationPanelMenuItem.setState(av.isShowAnnotation());
     /*
      * Show/hide annotations only enabled if annotation panel is shown
@@ -756,8 +896,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    viewBoxesMenuItem.setSelected(av.showBoxes);
-    viewTextMenuItem.setSelected(av.showText);
+    viewBoxesMenuItem.setSelected(av.getShowBoxes());
+    viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
     showGroupConsensus.setSelected(av.isShowGroupConsensus());
     showGroupConservation.setSelected(av.isShowGroupConservation());
@@ -765,27 +905,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 
-    setColourSelected(ColourSchemeProperty.getColourName(av
-            .getGlobalColourScheme()));
+    ColourMenuHelper.setColourSelected(colourMenu,
+            av.getGlobalColourScheme());
 
     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
-    hiddenMarkers.setState(av.showHiddenMarkers);
+    hiddenMarkers.setState(av.getShowHiddenMarkers());
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
-    showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
-    showDbRefsMenuitem.setSelected(av.isShowDbRefs());
+    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();
+
+    showProducts.setEnabled(canShowProducts());
+    setGroovyEnabled(Desktop.getGroovyConsole() != null);
+
     updateEditMenuBar();
   }
 
-  // methods for implementing IProgressIndicator
-  // need to refactor to a reusable stub class
-  Hashtable progressBars, progressBarHandlers;
+  /**
+   * Set the enabled state of the 'Run Groovy' option in the Calculate menu
+   * 
+   * @param b
+   */
+  public void setGroovyEnabled(boolean b)
+  {
+    runGroovy.setEnabled(b);
+  }
+
+  private IProgressIndicator progressBar;
 
   /*
    * (non-Javadoc)
@@ -795,78 +943,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setProgressBar(String message, long id)
   {
-    if (progressBars == null)
-    {
-      progressBars = new Hashtable();
-      progressBarHandlers = new Hashtable();
-    }
-
-    JPanel progressPanel;
-    Long lId = new Long(id);
-    GridLayout layout = (GridLayout) statusPanel.getLayout();
-    if (progressBars.get(lId) != null)
-    {
-      progressPanel = (JPanel) progressBars.get(new Long(id));
-      statusPanel.remove(progressPanel);
-      progressBars.remove(lId);
-      progressPanel = null;
-      if (message != null)
-      {
-        statusBar.setText(message);
-      }
-      if (progressBarHandlers.contains(lId))
-      {
-        progressBarHandlers.remove(lId);
-      }
-      layout.setRows(layout.getRows() - 1);
-    }
-    else
-    {
-      progressPanel = new JPanel(new BorderLayout(10, 5));
-
-      JProgressBar progressBar = new JProgressBar();
-      progressBar.setIndeterminate(true);
-
-      progressPanel.add(new JLabel(message), BorderLayout.WEST);
-      progressPanel.add(progressBar, BorderLayout.CENTER);
-
-      layout.setRows(layout.getRows() + 1);
-      statusPanel.add(progressPanel);
-
-      progressBars.put(lId, progressPanel);
-    }
-    // update GUI
-    // setMenusForViewport();
-    validate();
+    progressBar.setProgressBar(message, id);
   }
 
   @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
-    {
-      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
-    }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
-    if (handler.canCancel())
-    {
-      JButton cancel = new JButton(
-              MessageManager.getString("action.cancel"));
-      final IProgressIndicator us = this;
-      cancel.addActionListener(new ActionListener()
-      {
-
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          handler.cancelActivity(id);
-          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
-        }
-      });
-      progressPanel.add(cancel, BorderLayout.EAST);
-    }
+    progressBar.registerHandler(id, handler);
   }
 
   /**
@@ -876,18 +960,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public boolean operationInProgress()
   {
-    if (progressBars != null && progressBars.size() > 0)
-    {
-      return true;
-    }
-    return false;
+    return progressBar.operationInProgress();
   }
 
   @Override
   public void setStatus(String text)
   {
     statusBar.setText(text);
-  };
+  }
 
   /*
    * Added so Castor Mapping file can obtain Jalview Version
@@ -905,7 +985,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
-    new SequenceFetcher(this);
+    new jalview.gui.SequenceFetcher(this);
   }
 
   @Override
@@ -923,7 +1003,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // originating file's format
       // TODO: work out how to recover feature settings for correct view(s) when
       // file is reloaded.
-      if (currentFileFormat.equals("Jalview"))
+      if (FileFormat.Jalview.equals(currentFileFormat))
       {
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
         for (int i = 0; i < frames.length; i++)
@@ -945,7 +1025,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
       else
@@ -953,7 +1034,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Rectangle bounds = this.getBounds();
 
         FileLoader loader = new FileLoader();
-        String protocol = fileName.startsWith("http:") ? "URL" : "File";
+        DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL
+                : DataSourceType.FILE;
         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
                 protocol, currentFileFormat);
 
@@ -984,7 +1066,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+            .getAlignPanel());
   }
 
   @Override
@@ -996,9 +1079,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void save_actionPerformed(ActionEvent e)
   {
-    if (fileName == null
-            || (currentFileFormat == null || !jalview.io.FormatAdapter
-                    .isValidIOFormat(currentFileFormat, true))
+    if (fileName == null || (currentFileFormat == null)
             || fileName.startsWith("http"))
     {
       saveAs_actionPerformed(null);
@@ -1018,14 +1099,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void saveAs_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
-            currentFileFormat, false);
+    String format = currentFileFormat == null ? null : currentFileFormat
+            .getName();
+    JalviewFileChooser chooser = JalviewFileChooser.forWrite(
+            Cache.getProperty("LAST_DIRECTORY"), format);
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_alignment_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -1033,40 +1114,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       currentFileFormat = chooser.getSelectedFormat();
-      if (currentFileFormat == null)
+      while (currentFileFormat == null)
       {
-        JOptionPane
+        JvOptionPane
                 .showInternalMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.select_file_format_before_saving"),
                         MessageManager
                                 .getString("label.file_format_not_specified"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
+        currentFileFormat = chooser.getSelectedFormat();
         value = chooser.showSaveDialog(this);
-        return;
+        if (value != JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
       }
 
       fileName = chooser.getSelectedFile().getPath();
 
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-              currentFileFormat);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
-      if (currentFileFormat.indexOf(" ") > -1)
-      {
-        currentFileFormat = currentFileFormat.substring(0,
-                currentFileFormat.indexOf(" "));
-      }
+      Cache.setProperty("LAST_DIRECTORY", fileName);
       saveAlignment(fileName, currentFileFormat);
     }
   }
 
-  public boolean saveAlignment(String file, String format)
+  public boolean saveAlignment(String file, FileFormatI format)
   {
     boolean success = true;
 
-    if (format.equalsIgnoreCase("Jalview"))
+    if (FileFormat.Jalview.equals(format))
     {
       String shortName = title;
 
@@ -1076,48 +1155,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 .lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().SaveAlignment(this, file, shortName);
+      success = new Jalview2XML().saveAlignment(this, file, shortName);
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.successfully_saved_to_file_in_format", new String[]
-              { fileName, format }));
+              "label.successfully_saved_to_file_in_format", new Object[] {
+                  fileName, format }));
 
     }
     else
     {
-      if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+      AlignmentExportData exportData = getAlignmentForExport(format,
+              viewport, null);
+      if (exportData.getSettings().isCancelled())
       {
-        warningMessage("Cannot save file " + fileName + " using format "
-                + format, "Alignment output format not supported");
-        saveAs_actionPerformed(null);
-        // JBPNote need to have a raise_gui flag here
         return false;
       }
-
-      String[] omitHidden = null;
-
-      if (viewport.hasHiddenColumns())
-      {
-        int reply = JOptionPane
-                .showInternalConfirmDialog(
-                        Desktop.desktop,
-                        MessageManager
-                                .getString("label.alignment_contains_hidden_columns"),
-                        MessageManager
-                                .getString("action.save_omit_hidden_columns"),
-                        JOptionPane.YES_NO_OPTION,
-                        JOptionPane.QUESTION_MESSAGE);
-
-        if (reply == JOptionPane.YES_OPTION)
-        {
-          omitHidden = viewport.getViewAsString(false);
-        }
-      }
-      FormatAdapter f = new FormatAdapter();
-      String output = f.formatSequences(format,
-              viewport.getAlignment(), // class cast exceptions will
+      FormatAdapter f = new FormatAdapter(alignPanel,
+              exportData.getSettings());
+      String output = f.formatSequences(
+              format,
+              exportData.getAlignment(), // class cast exceptions will
               // occur in the distant future
-              omitHidden, f.getCacheSuffixDefault(format),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
+              f.getCacheSuffixDefault(format),
               viewport.getColumnSelection());
 
       if (output == null)
@@ -1128,16 +1188,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         try
         {
-          java.io.PrintWriter out = new java.io.PrintWriter(
-                  new java.io.FileWriter(file));
+          PrintWriter out = new PrintWriter(new FileWriter(file));
 
           out.print(output);
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format",
-                  new String[]
-                  { fileName, format }));
+                  new Object[] { fileName, format.getName() }));
         } catch (Exception ex)
         {
           success = false;
@@ -1148,11 +1206,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!success)
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new String[]
-              { fileName }), MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
+              .formatMessage("label.couldnt_save_file",
+                      new Object[] { fileName }), MessageManager
               .getString("label.error_saving_file"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
 
     return success;
@@ -1167,8 +1225,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      JOptionPane.showInternalMessageDialog(this, warning, title,
-              JOptionPane.WARNING_MESSAGE);
+      JvOptionPane.showInternalMessageDialog(this, warning, title,
+              JvOptionPane.WARNING_MESSAGE);
     }
     return;
   }
@@ -1182,37 +1240,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    String[] omitHidden = null;
-
-    if (viewport.hasHiddenColumns())
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
+    AlignmentExportData exportData = getAlignmentForExport(fileFormat,
+            viewport, null);
+    if (exportData.getSettings().isCancelled())
     {
-      int reply = JOptionPane
-              .showInternalConfirmDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.alignment_contains_hidden_columns"),
-                      MessageManager
-                              .getString("action.save_omit_hidden_columns"),
-                      JOptionPane.YES_NO_OPTION,
-                      JOptionPane.QUESTION_MESSAGE);
-
-      if (reply == JOptionPane.YES_OPTION)
-      {
-        omitHidden = viewport.getViewAsString(false);
-      }
+      return;
     }
-
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-
     try
     {
-      cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-              viewport.getAlignment(), omitHidden,
-              viewport.getColumnSelection()));
+      FileFormatI format = fileFormat;
+      cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
+              .formatSequences(format, exportData.getAlignment(),
+                      exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(),
+                      viewport.getColumnSelection()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.alignment_output_command", new String[]
-              { e.getActionCommand() }), 600, 500);
+              "label.alignment_output_command",
+              new Object[] { e.getActionCommand() }), 600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
@@ -1221,6 +1269,50 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  public static AlignmentExportData getAlignmentForExport(
+          FileFormatI format, AlignViewportI viewport,
+          AlignExportSettingI exportSettings)
+  {
+    AlignmentI alignmentToExport = null;
+    AlignExportSettingI settings = exportSettings;
+    String[] omitHidden = null;
+
+    HiddenSequences hiddenSeqs = viewport.getAlignment()
+            .getHiddenSequences();
+
+    alignmentToExport = viewport.getAlignment();
+
+    boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
+    if (settings == null)
+    {
+      settings = new AlignExportSettings(hasHiddenSeqs,
+              viewport.hasHiddenColumns(), format);
+    }
+    // settings.isExportAnnotations();
+
+    if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
+    {
+      omitHidden = viewport.getViewAsString(false,
+              settings.isExportHiddenSequences());
+    }
+
+    int[] alignmentStartEnd = new int[2];
+    if (hasHiddenSeqs && settings.isExportHiddenSequences())
+    {
+      alignmentToExport = hiddenSeqs.getFullAlignment();
+    }
+    else
+    {
+      alignmentToExport = viewport.getAlignment();
+    }
+    alignmentStartEnd = alignmentToExport
+            .getVisibleStartAndEndIndex(viewport.getColumnSelection()
+                    .getHiddenColumns());
+    AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
+            omitHidden, alignmentStartEnd, settings);
+    return ed;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1230,18 +1322,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    // new HTMLOutput(alignPanel,
-    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
-    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
-    new HtmlSvgOutput(null, alignPanel);
+    HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
+    htmlSVG.exportHTML(null);
   }
 
   @Override
   public void bioJSMenuItem_actionPerformed(ActionEvent e)
   {
-    new BioJsHTMLOutput(alignPanel,
-            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+    bjs.exportHTML(null);
   }
+
   public void createImageMap(File file, String image)
   {
     alignPanel.makePNGImageMap(file, image);
@@ -1271,10 +1362,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.makeEPS(f);
   }
 
+  @Override
   public void createSVG(File f)
   {
     alignPanel.makeSVG(f);
   }
+
   @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
@@ -1357,7 +1450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // setClosed(true) is called
             for (int i = 0; i < alignPanels.size(); i++)
             {
-              AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+              AlignmentPanel ap = alignPanels.get(i);
               ap.closePanel();
             }
           }
@@ -1370,6 +1463,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (closeAllTabs)
       {
+        /*
+         * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+         * be called recursively, with the frame now in 'closed' state
+         */
         this.setClosed(true);
       }
     } catch (Exception ex)
@@ -1379,22 +1476,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * close alignPanel2 and shuffle tabs appropriately.
+   * Close the specified panel and close up tabs appropriately.
    * 
-   * @param alignPanel2
+   * @param panelToClose
    */
-  public void closeView(AlignmentPanel alignPanel2)
+  public void closeView(AlignmentPanel panelToClose)
   {
     int index = tabbedPane.getSelectedIndex();
-    int closedindex = tabbedPane.indexOfComponent(alignPanel2);
-    alignPanels.removeElement(alignPanel2);
-    // Unnecessary
-    // if (viewport == alignPanel2.av)
-    // {
-    // viewport = null;
-    // }
-    alignPanel2.closePanel();
-    alignPanel2 = null;
+    int closedindex = tabbedPane.indexOfComponent(panelToClose);
+    alignPanels.remove(panelToClose);
+    panelToClose.closePanel();
+    panelToClose = null;
 
     tabbedPane.removeTabAt(closedindex);
     tabbedPane.validate();
@@ -1414,13 +1506,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   void updateEditMenuBar()
   {
 
-    if (viewport.historyList.size() > 0)
+    if (viewport.getHistoryList().size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = viewport.historyList.peek();
+      CommandI command = viewport.getHistoryList().peek();
       undoMenuItem.setText(MessageManager.formatMessage(
-              "label.undo_command", new String[]
-              { command.getDescription() }));
+              "label.undo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1428,14 +1520,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       undoMenuItem.setText(MessageManager.getString("action.undo"));
     }
 
-    if (viewport.redoList.size() > 0)
+    if (viewport.getRedoList().size() > 0)
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = viewport.redoList.peek();
+      CommandI command = viewport.getRedoList().peek();
       redoMenuItem.setText(MessageManager.formatMessage(
-              "label.redo_command", new String[]
-              { command.getDescription() }));
+              "label.redo_command",
+              new Object[] { command.getDescription() }));
     }
     else
     {
@@ -1444,12 +1536,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  @Override
   public void addHistoryItem(CommandI command)
   {
     if (command.getSize() > 0)
     {
-      viewport.historyList.push(command);
-      viewport.redoList.clear();
+      viewport.addToHistoryList(command);
+      viewport.clearRedoList();
       updateEditMenuBar();
       viewport.updateHiddenColumns();
       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
@@ -1467,18 +1560,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (alignPanels != null)
     {
-      Enumeration e = alignPanels.elements();
       AlignmentI[] als = new AlignmentI[alignPanels.size()];
-      for (int i = 0; e.hasMoreElements(); i++)
+      int i = 0;
+      for (AlignmentPanel ap : alignPanels)
       {
-        als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
+        als[i++] = ap.av.getAlignment();
       }
       return als;
     }
     if (viewport != null)
     {
-      return new AlignmentI[]
-      { viewport.getAlignment() };
+      return new AlignmentI[] { viewport.getAlignment() };
     }
     return null;
   }
@@ -1492,15 +1584,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    if (viewport.historyList.empty())
+    if (viewport.getHistoryList().isEmpty())
     {
       return;
     }
-    CommandI command = viewport.historyList.pop();
-    viewport.redoList.push(command);
+    CommandI command = viewport.getHistoryList().pop();
+    viewport.addToRedoList(command);
     command.undoCommand(getViewAlignments());
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
     if (originalSource != null)
@@ -1530,16 +1622,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    if (viewport.redoList.size() < 1)
+    if (viewport.getRedoList().size() < 1)
     {
       return;
     }
 
-    CommandI command = viewport.redoList.pop();
-    viewport.historyList.push(command);
+    CommandI command = viewport.getRedoList().pop();
+    viewport.addToHistoryList(command);
     command.doCommand(getViewAlignments());
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     updateEditMenuBar();
 
     if (originalSource != null)
@@ -1561,9 +1653,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  AlignViewport getOriginatingSource(CommandI command)
+  AlignmentViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = null;
+    AlignmentViewport originalSource = null;
     // For sequence removal and addition, we need to fire
     // the property change event FROM the viewport where the
     // original alignment was altered
@@ -1572,16 +1664,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       EditCommand editCommand = (EditCommand) command;
       al = editCommand.getAlignment();
-      Vector comps = (Vector) PaintRefresher.components.get(viewport
+      List<Component> comps = PaintRefresher.components.get(viewport
               .getSequenceSetId());
 
-      for (int i = 0; i < comps.size(); i++)
+      for (Component comp : comps)
       {
-        if (comps.elementAt(i) instanceof AlignmentPanel)
+        if (comp instanceof AlignmentPanel)
         {
-          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
+          if (al == ((AlignmentPanel) comp).av.getAlignment())
           {
-            originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
+            originalSource = ((AlignmentPanel) comp).av;
             break;
           }
         }
@@ -1624,7 +1716,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    List<SequenceI> sg = new Vector();
+    List<SequenceI> sg = new ArrayList<SequenceI>();
     if (viewport.cursorMode)
     {
       sg.add(viewport.getAlignment().getSequenceAt(
@@ -1643,13 +1735,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector invertGroup = new Vector();
+    List<SequenceI> invertGroup = new ArrayList<SequenceI>();
 
-    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
+    for (SequenceI seq : viewport.getAlignment().getSequences())
     {
-      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+      if (!sg.contains(seq))
       {
-        invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+        invertGroup.add(seq);
       }
     }
 
@@ -1658,7 +1750,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
     for (int i = 0; i < invertGroup.size(); i++)
     {
-      seqs2[i] = (SequenceI) invertGroup.elementAt(i);
+      seqs2[i] = invertGroup.get(i);
     }
 
     SlideSequencesCommand ssc;
@@ -1705,12 +1797,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
     }
 
+    /*
+     * just extend the last slide command if compatible; but not if in
+     * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
+     */
     boolean appendHistoryItem = false;
-    if (viewport.historyList != null && viewport.historyList.size() > 0
-            && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    Deque<CommandI> historyList = viewport.getHistoryList();
+    boolean inSplitFrame = getSplitViewContainer() != null;
+    if (!inSplitFrame && historyList != null && historyList.size() > 0
+            && historyList.peek() instanceof SlideSequencesCommand)
     {
       appendHistoryItem = ssc
-              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+              .appendSlideCommand((SlideSequencesCommand) historyList
                       .peek());
     }
 
@@ -1746,8 +1844,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       omitHidden = viewport.getViewAsString(true);
     }
 
-    String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden);
+    String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
+            seqs, omitHidden, null);
 
     StringSelection ss = new StringSelection(output);
 
@@ -1767,30 +1865,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector hiddenColumns = null;
+    ArrayList<int[]> hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new ArrayList<int[]>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
               .getSelectionGroup().getEndRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
+      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
         {
-          hiddenColumns.addElement(new int[]
-          { region[0] - hiddenOffset, region[1] - hiddenOffset });
+          hiddenColumns.add(new int[] { region[0] - hiddenOffset,
+              region[1] - hiddenOffset });
         }
       }
     }
 
-    Desktop.jalviewClipboard = new Object[]
-    { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
+    Desktop.jalviewClipboard = new Object[] { seqs,
+        viewport.getAlignment().getDataset(), hiddenColumns };
     statusBar.setText(MessageManager.formatMessage(
-            "label.copied_sequences_to_clipboard", new String[]
-            { Integer.valueOf(seqs.length).toString() }));
+            "label.copied_sequences_to_clipboard", new Object[] { Integer
+                    .valueOf(seqs.length).toString() }));
   }
 
   /**
@@ -1836,7 +1931,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return;
       }
 
-      String str, format;
+      String str;
+      FileFormatI format;
       try
       {
         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
@@ -1845,7 +1941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           return;
         }
 
-        format = new IdentifyFile().Identify(str, "Paste");
+        format = new IdentifyFile().identify(str, DataSourceType.PASTE);
 
       } catch (OutOfMemoryError er)
       {
@@ -1875,7 +1971,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       else
       {
         // parse the clipboard as an alignment.
-        alignment = new FormatAdapter().readFile(str, "Paste", format);
+        alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
+                format);
         sequences = alignment.getSequencesArray();
       }
 
@@ -1999,8 +2096,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         //
         addHistoryItem(new EditCommand(
                 MessageManager.getString("label.add_sequences"),
-                Action.PASTE,
-                sequences, 0, alignment.getWidth(), alignment));
+                Action.PASTE, sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
       for (int i = 0; i < sequences.length; i++)
@@ -2087,7 +2183,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignment.getSequences());
         if (alignPanels != null)
         {
-          for (AlignmentPanel ap : ((Vector<AlignmentPanel>) alignPanels))
+          for (AlignmentPanel ap : alignPanels)
           {
             ap.validateAnnotationDimensions(false);
           }
@@ -2107,10 +2203,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          Vector hc = (Vector) Desktop.jalviewClipboard[2];
-          for (int i = 0; i < hc.size(); i++)
+          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+          for (int[] region : hc)
           {
-            int[] region = (int[]) hc.elementAt(i);
             af.viewport.hideColumns(region[0], region[1]);
           }
         }
@@ -2119,7 +2214,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // found!!<<<
         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .transferSettings(
-                        alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+                        alignPanel.getSeqPanel().seqCanvas
+                                .getFeatureRenderer());
 
         // TODO: maintain provenance of an alignment, rather than just make the
         // title a concatenation of operations.
@@ -2167,10 +2263,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        Vector hc = (Vector) Desktop.jalviewClipboard[2];
-        for (int i = 0; i < hc.size(); i++)
+        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
+        for (int region[] : hc)
         {
-          int[] region = (int[]) hc.elementAt(i);
           af.viewport.hideColumns(region[0], region[1]);
         }
       }
@@ -2179,7 +2274,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // found!!<<<
       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(
-                      alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+                      alignPanel.getSeqPanel().seqCanvas
+                              .getFeatureRenderer());
 
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
@@ -2236,40 +2332,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    List<SequenceI> seqs = new ArrayList<SequenceI>(sg.getSize());
-    SequenceI seq;
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      seq = sg.getSequenceAt(i);
-      seqs.add(seq);
-    }
-
-    // If the cut affects all sequences, warn, remove highlighted columns
+    /*
+     * If the cut affects all sequences, warn, remove highlighted columns
+     */
     if (sg.getSize() == viewport.getAlignment().getHeight())
     {
-      int confirm = JOptionPane.showConfirmDialog(this,
-              MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
-              MessageManager.getString("label.delete_all"), // $NON-NLS-1$
-              JOptionPane.OK_CANCEL_OPTION);
-
-      if (confirm == JOptionPane.CANCEL_OPTION
-              || confirm == JOptionPane.CLOSED_OPTION)
+      boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+              .getAlignment().getWidth()) ? true : false;
+      if (isEntireAlignWidth)
       {
-        return;
+        int confirm = JvOptionPane.showConfirmDialog(this,
+                MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+                MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+                JvOptionPane.OK_CANCEL_OPTION);
+
+        if (confirm == JvOptionPane.CANCEL_OPTION
+                || confirm == JvOptionPane.CLOSED_OPTION)
+        {
+          return;
+        }
       }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
+    SequenceI[] cut = sg.getSequences()
+            .toArray(new SequenceI[sg.getSize()]);
 
-    SequenceI[] cut = new SequenceI[seqs.size()];
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      cut[i] = seqs.get(i);
-    }
-
-    /*
-     * //ADD HISTORY ITEM
-     */
     addHistoryItem(new EditCommand(
             MessageManager.getString("label.cut_sequences"), Action.CUT,
             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
@@ -2328,7 +2416,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
     viewport.sendSelection();
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
   }
 
@@ -2351,7 +2442,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setSelectionGroup(null);
     alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2378,6 +2472,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
     }
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
 
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@@ -2421,7 +2518,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {
@@ -2446,23 +2543,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
-        trimRegion = new TrimRegionCommand("Remove Left",
-                TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+                column, viewport.getAlignment());
         viewport.setStartRes(0);
       }
       else
       {
-        trimRegion = new TrimRegionCommand("Remove Right",
-                TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+                column, viewport.getAlignment());
       }
 
       statusBar.setText(MessageManager.formatMessage(
-              "label.removed_columns", new String[]
-              { Integer.valueOf(trimRegion.getSize()).toString() }));
+              "label.removed_columns",
+              new String[] { Integer.valueOf(trimRegion.getSize())
+                      .toString() }));
 
       addHistoryItem(trimRegion);
 
@@ -2511,8 +2605,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(removeGapCols);
 
     statusBar.setText(MessageManager.formatMessage(
-            "label.removed_empty_columns", new String[]
-            { Integer.valueOf(removeGapCols.getSize()).toString() }));
+            "label.removed_empty_columns",
+            new Object[] { Integer.valueOf(removeGapCols.getSize())
+                    .toString() }));
 
     // This is to maintain viewport position on first residue
     // of first sequence
@@ -2582,16 +2677,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSequences());
   }
 
-  // else
-  {
-    // if (justifySeqs>0)
-    {
-      // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
-    }
-  }
-
-  // }
-
   /**
    * DOCUMENT ME!
    * 
@@ -2604,74 +2689,85 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     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.
+   * Create a new view of the current alignment.
    */
-  public AlignmentPanel newView(String viewTitle)
+  @Override
+  public void newView_actionPerformed(ActionEvent e)
   {
-    return newView(viewTitle, true);
+    newView(null, true);
   }
 
   /**
+   * Creates and shows a new view of the current alignment.
    * 
    * @param viewTitle
-   *          title of newly created view
+   *          title of newly created view; if null, one will be generated
    * @param copyAnnotation
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
    */
   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
   {
+    /*
+     * Create a new AlignmentPanel (with its own, new Viewport)
+     */
     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
             true);
     if (!copyAnnotation)
     {
-      // just remove all the current annotation except for the automatic stuff
+      /*
+       * remove all groups and 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.getAlignment().deleteAllAnnotations(false);
     }
 
-    newap.av.gatherViewsHere = false;
+    newap.av.setGatherViewsHere(false);
 
     if (viewport.viewName == null)
     {
-      viewport.viewName = "Original";
+      viewport.viewName = MessageManager
+              .getString("label.view_name_original");
     }
 
-    newap.av.historyList = viewport.historyList;
-    newap.av.redoList = viewport.redoList;
+    /*
+     * Views share the same edits undo and redo stacks
+     */
+    newap.av.setHistoryList(viewport.getHistoryList());
+    newap.av.setRedoList(viewport.getRedoList());
+
+    /*
+     * Views share the same mappings; need to deregister any new mappings
+     * created by copyAlignPanel, and register the new reference to the shared
+     * mappings
+     */
+    newap.av.replaceMappings(viewport.getAlignment());
+
+    newap.av.viewName = getNewViewName(viewTitle);
+
+    addAlignmentPanel(newap, true);
+    newap.alignmentChanged();
+
+    if (alignPanels.size() == 2)
+    {
+      viewport.setGatherViewsHere(true);
+    }
+    tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+    return newap;
+  }
 
+  /**
+   * Make a new name for the view, ensuring it is unique within the current
+   * sequenceSetId. (This used to be essential for Jalview Project archives, but
+   * these now use viewId. Unique view names are still desirable for usability.)
+   * 
+   * @param viewTitle
+   * @return
+   */
+  protected String getNewViewName(String viewTitle)
+  {
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
-    // 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)
     {
@@ -2683,45 +2779,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       index = 1;// we count from 1 if given a specific name
     }
     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
-    Vector comps = (Vector) PaintRefresher.components.get(viewport
+
+    List<Component> comps = PaintRefresher.components.get(viewport
             .getSequenceSetId());
-    Vector existingNames = new Vector();
-    for (int i = 0; i < comps.size(); i++)
+
+    List<String> existingNames = getExistingViewNames(comps);
+
+    while (existingNames.contains(newViewName))
+    {
+      newViewName = viewTitle + " " + (++index);
+    }
+    return newViewName;
+  }
+
+  /**
+   * Returns a list of distinct view names found in the given list of
+   * components. View names are held on the viewport of an AlignmentPanel.
+   * 
+   * @param comps
+   * @return
+   */
+  protected List<String> getExistingViewNames(List<Component> comps)
+  {
+    List<String> existingNames = new ArrayList<String>();
+    for (Component comp : comps)
     {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
+      if (comp instanceof AlignmentPanel)
       {
-        AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
+        AlignmentPanel ap = (AlignmentPanel) comp;
         if (!existingNames.contains(ap.av.viewName))
         {
-          existingNames.addElement(ap.av.viewName);
+          existingNames.add(ap.av.viewName);
         }
       }
     }
+    return existingNames;
+  }
 
-    while (existingNames.contains(newViewName))
-    {
-      newViewName = viewTitle + " " + (++index);
-    }
-
-    newap.av.viewName = newViewName;
-
-    addAlignmentPanel(newap, true);
-    newap.alignmentChanged();
-
-    if (alignPanels.size() == 2)
-    {
-      viewport.gatherViewsHere = true;
-    }
-    tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
-    return newap;
-  }
-
+  /**
+   * Explode tabbed views into separate windows.
+   */
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.explodeViews(this);
+    Desktop.explodeViews(this);
   }
 
+  /**
+   * Gather views in separate windows back into a tabbed presentation.
+   */
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
@@ -2751,8 +2857,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
-            .calculateIdWidth());
+    alignPanel.getIdPanel().getIdCanvas()
+            .setPreferredSize(alignPanel.calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
 
@@ -2766,7 +2872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
-    viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+    viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -2778,10 +2884,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void followHighlight_actionPerformed()
   {
-    if (viewport.followHighlight = this.followHighlightMenuItem.getState())
+    /*
+     * Set the 'follow' flag on the Viewport (and scroll to position if now
+     * true).
+     */
+    final boolean state = this.followHighlightMenuItem.getState();
+    viewport.setFollowHighlight(state);
+    if (state)
     {
-      alignPanel.scrollToPosition(
-              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
+      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
     }
   }
 
@@ -2811,7 +2922,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(wrapMenuItem.isSelected());
     scaleRight.setVisible(wrapMenuItem.isSelected());
     viewport.setWrapAlignment(wrapMenuItem.isSelected());
-    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+    alignPanel.updateLayout();
   }
 
   @Override
@@ -2825,13 +2936,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     repaint();
+    viewport.sendSelection();
   }
 
   @Override
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    alignPanel.paintAlignment(true);
+    // alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2850,9 +2962,7 @@ 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.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -2880,8 +2990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         hideSelSequences_actionPerformed(null);
         hide = true;
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         showAllSeqs_actionPerformed(null);
       }
@@ -2889,7 +2998,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         hideSelColumns_actionPerformed(null);
         if (!toggleSeqs)
@@ -2915,6 +3024,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
+    viewport.sendSelection();
   }
 
   /*
@@ -2932,6 +3042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   /*
@@ -2947,6 +3058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -2954,6 +3066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -3044,6 +3157,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public FeatureSettings featureSettings;
 
   @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return featureSettings;
+  }
+
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -3078,30 +3197,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Set or clear 'Show Sequence Features'
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
-  {
-    viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
-            .isSelected());
-    if (viewport.isShowSequenceFeaturesHeight())
-    {
-      // ensure we're actually displaying features
-      viewport.setShowSequenceFeatures(true);
-      showSeqFeatures.setSelected(true);
-    }
-    alignPanel.paintAlignment(true);
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-  }
-
-  /**
    * Action on toggle of the 'Show annotations' menu item. This shows or hides
    * the annotations panel as a whole.
    * 
@@ -3115,11 +3210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    alignPanel.setAnnotationVisible(setVisible);
     this.showAllSeqAnnotations.setEnabled(setVisible);
     this.hideAllSeqAnnotations.setEnabled(setVisible);
     this.showAllAlAnnotations.setEnabled(setVisible);
     this.hideAllAlAnnotations.setEnabled(setVisible);
+    alignPanel.updateLayout();
   }
 
   @Override
@@ -3130,14 +3225,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
             .formatAsHtml();
     editPane.setText(MessageManager.formatMessage("label.html_content",
-            new String[]
-            { contents.toString() }));
+            new Object[] { contents.toString() }));
     JInternalFrame frame = new JInternalFrame();
     frame.getContentPane().add(new JScrollPane(editPane));
 
-    Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage(
-            "label.alignment_properties", new String[]
-            { getTitle() }), 500, 400);
+    Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+            "label.alignment_properties", new Object[] { getTitle() }),
+            500, 400);
   }
 
   /**
@@ -3158,8 +3252,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager.formatMessage(
-            "label.overview_params", new String[]
-            { this.getTitle() }), frame.getWidth(), frame.getHeight());
+            "label.overview_params", new Object[] { this.getTitle() }),
+            frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -3176,146 +3270,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void textColour_actionPerformed(ActionEvent e)
+  public void textColour_actionPerformed()
   {
     new TextColourChooser().chooseColour(alignPanel, null);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-    changeColour(null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void clustalColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ClustalxColourScheme(viewport.getAlignment(),
-            viewport.getHiddenRepSequences()));
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void zappoColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new ZappoColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void taylorColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TaylorColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HydrophobicColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void helixColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new HelixColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void strandColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new StrandColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void turnColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new TurnColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void buriedColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new BuriedColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @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) {
+   * public void covariationColour_actionPerformed() {
    * changeColour(new
    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
    * ()[0])); }
    */
   @Override
-  public void annotationColour_actionPerformed(ActionEvent e)
+  public void annotationColour_actionPerformed()
   {
     new AnnotationColourChooser(viewport, alignPanel);
   }
@@ -3326,314 +3293,130 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new AnnotationColumnChooser(viewport, alignPanel);
   }
 
+  /**
+   * Action on the user checking or unchecking the option to apply the selected
+   * colour scheme to all groups. If unchecked, groups may have their own
+   * independent colour schemes.
+   * 
+   * @param selected
+   */
   @Override
-  public void rnahelicesColour_actionPerformed(ActionEvent e)
+  public void applyToAllGroups_actionPerformed(boolean selected)
   {
-    new RNAHelicesColourChooser(viewport, alignPanel);
+    viewport.setColourAppliesToAllGroups(selected);
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on user selecting a colour from the colour menu
    * 
-   * @param e
-   *          DOCUMENT ME!
+   * @param name
+   *          the name (not the menu item label!) of the colour scheme
    */
   @Override
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  public void changeColour_actionPerformed(String name)
   {
-    viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+    /*
+     * 'User Defined' opens a panel to configure or load a
+     * user-defined colour scheme
+     */
+    if (ResidueColourScheme.USER_DEFINED.equals(name))
+    {
+      new UserDefinedColours(alignPanel, null);
+      return;
+    }
+
+    /*
+     * otherwise set the chosen colour scheme (or null for 'None')
+     */
+    ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport.getAlignment(), viewport.getHiddenRepSequences());
+    changeColour(cs);
   }
 
   /**
-   * DOCUMENT ME!
+   * Actions on setting or changing the alignment colour scheme
    * 
    * @param cs
-   *          DOCUMENT ME!
    */
+  @Override
   public void changeColour(ColourSchemeI cs)
   {
-    // TODO: compare with applet and pull up to model method
-    int threshold = 0;
-
+    // TODO: pull up to controller method
     if (cs != null)
     {
-      if (viewport.getAbovePIDThreshold())
-      {
-        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
-                "Background");
-        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-      }
-      else
-      {
-        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-      }
-
-      if (viewport.getConservationSelected())
-      {
-
-        Alignment al = (Alignment) viewport.getAlignment();
-        Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0,
-                al.getWidth() - 1);
-
-        c.calculate();
-        c.verdict(false, viewport.getConsPercGaps());
-
-        cs.setConservation(c);
-
-        cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
-                cs, "Background"));
-      }
-      else
-      {
-        cs.setConservation(null);
-      }
-
-      cs.setConsensus(viewport.getSequenceConsensusHash());
+      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
     }
 
     viewport.setGlobalColourScheme(cs);
 
-    if (viewport.getColourAppliesToAllGroups())
-    {
-
-      for (SequenceGroup sg : viewport.getAlignment().getGroups())
-      {
-        if (cs == null)
-        {
-          sg.cs = null;
-          continue;
-        }
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg,
-                  viewport.getHiddenRepSequences());
-        }
-        else if (cs instanceof UserColourScheme)
-        {
-          sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-          }
-        }
-
-        if (viewport.getAbovePIDThreshold()
-                || cs instanceof PIDColourScheme
-                || cs instanceof Blosum62ColourScheme)
-        {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
-
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(viewport.getHiddenRepSequences()),
-                  sg.getStartRes(), sg.getEndRes() + 1));
-        }
-        else
-        {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
-        }
-
-        if (viewport.getConservationSelected())
-        {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(viewport
-                          .getHiddenRepSequences()), sg.getStartRes(),
-                  sg.getEndRes() + 1);
-          c.calculate();
-          c.verdict(false, viewport.getConsPercGaps());
-          sg.cs.setConservation(c);
-        }
-        else
-        {
-          sg.cs.setConservation(null);
-        }
-      }
-    }
-
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-
     alignPanel.paintAlignment(true);
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  protected void modifyPID_actionPerformed(ActionEvent e)
-  {
-    if (viewport.getAbovePIDThreshold()
-            && viewport.getGlobalColourScheme() != null)
-    {
-      SliderPanel.setPIDSliderSource(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
-      SliderPanel.showPIDSlider();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the PID threshold slider panel
    */
   @Override
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed()
   {
-    if (viewport.getConservationSelected()
-            && viewport.getGlobalColourScheme() != null)
-    {
-      SliderPanel.setConservationSlider(alignPanel,
-              viewport.getGlobalColourScheme(), "Background");
-      SliderPanel.showConservationSlider();
-    }
+    SliderPanel.setPIDSliderSource(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showPIDSlider();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Show the Conservation slider panel
    */
   @Override
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void modifyConservation_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.isSelected());
-
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setSelected(false);
-
-    changeColour(viewport.getGlobalColourScheme());
-
-    modifyConservation_actionPerformed(null);
+    SliderPanel.setConservationSlider(alignPanel,
+            viewport.getViewportColourScheme(), alignPanel.getViewName());
+    SliderPanel.showConservationSlider();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on selecting or deselecting (Colour) By Conservation
    */
   @Override
-  public void abovePIDThreshold_actionPerformed(ActionEvent e)
+  public void conservationMenuItem_actionPerformed(boolean selected)
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
-
-    conservationMenuItem.setSelected(false);
-    viewport.setConservationSelected(false);
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
+    viewport.getViewportColourScheme().setConservationApplied(selected);
 
     changeColour(viewport.getGlobalColourScheme());
-
-    modifyPID_actionPerformed(null);
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    if (e.getActionCommand().equals(
-            MessageManager.getString("action.user_defined")))
+    if (selected)
     {
-      new UserDefinedColours(alignPanel, null);
+      modifyConservation_actionPerformed();
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours
-              .getUserColourSchemes().get(e.getActionCommand());
-
-      changeColour(udc);
+      SliderPanel.hideConservationSlider();
     }
   }
 
-  public void updateUserColourMenu()
+  /**
+   * Action on selecting or deselecting (Colour) Above PID Threshold
+   */
+  @Override
+  public void abovePIDThreshold_actionPerformed(boolean selected)
   {
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
+    if (!selected)
+    {
+      viewport.getViewportColourScheme().setThreshold(0,
+              viewport.isIgnoreGapsConsensus());
+    }
 
-    Component[] menuItems = colourMenu.getMenuComponents();
-    int i, iSize = menuItems.length;
-    for (i = 0; i < iSize; i++)
+    changeColour(viewport.getGlobalColourScheme());
+    if (selected)
     {
-      if (menuItems[i].getName() != null
-              && menuItems[i].getName().equals("USER_DEFINED"))
-      {
-        colourMenu.remove(menuItems[i]);
-        iSize--;
-      }
+      modifyPID_actionPerformed();
     }
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    else
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
-      {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-                userColours.nextElement().toString());
-        radioItem.setName("USER_DEFINED");
-        radioItem.addMouseListener(new MouseAdapter()
-        {
-          @Override
-          public void mousePressed(MouseEvent evt)
-          {
-            if (evt.isControlDown()
-                    || SwingUtilities.isRightMouseButton(evt))
-            {
-              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-              int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
-                      MessageManager
-                              .getString("label.remove_from_default_list"),
-                      MessageManager
-                              .getString("label.remove_user_defined_colour"),
-                      JOptionPane.YES_NO_OPTION);
-              if (option == JOptionPane.YES_OPTION)
-              {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
-                colourMenu.remove(radioItem);
-              }
-              else
-              {
-                radioItem.addActionListener(new ActionListener()
-                {
-                  @Override
-                  public void actionPerformed(ActionEvent evt)
-                  {
-                    userDefinedColour_actionPerformed(evt);
-                  }
-                });
-              }
-            }
-          }
-        });
-        radioItem.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent evt)
-          {
-            userDefinedColour_actionPerformed(evt);
-          }
-        });
-
-        colourMenu.insert(radioItem, 15);
-        colours.add(radioItem);
-      }
+      SliderPanel.hidePIDSlider();
     }
   }
 
@@ -3644,30 +3427,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          DOCUMENT ME!
    */
   @Override
-  public void PIDColour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new PIDColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-    changeColour(new Blosum62ColourScheme());
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
@@ -3751,10 +3510,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if ((viewport.getSelectionGroup() == null)
             || (viewport.getSelectionGroup().getSize() < 2))
     {
-      JOptionPane.showInternalMessageDialog(this, MessageManager
+      JvOptionPane.showInternalMessageDialog(this, MessageManager
               .getString("label.you_must_select_least_two_sequences"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
@@ -3780,14 +3539,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSelectionGroup().getSize() > 0))
             || (viewport.getAlignment().getHeight() < 4))
     {
-      JOptionPane
+      JvOptionPane
               .showInternalMessageDialog(
                       this,
                       MessageManager
                               .getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
                       MessageManager
                               .getString("label.sequence_selection_insufficient"),
-                      JOptionPane.WARNING_MESSAGE);
+                      JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
@@ -3827,7 +3586,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("AV", "PID", "Average distance tree using PID");
+    newTreePanel("AV", "PID", "Average distance tree using PID");
   }
 
   /**
@@ -3839,7 +3598,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
+    newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
   }
 
   /**
@@ -3851,7 +3610,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
+    newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
   }
 
   /**
@@ -3863,7 +3622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
+    newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
   /**
@@ -3876,7 +3635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param title
    *          DOCUMENT ME!
    */
-  void NewTreePanel(String type, String pwType, String title)
+  void newTreePanel(String type, String pwType, String title)
   {
     TreePanel tp;
 
@@ -3885,14 +3644,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (viewport.getSelectionGroup().getSize() < 3)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.you_need_more_two_sequences_selected_build_tree"),
                         MessageManager
                                 .getString("label.not_enough_sequences"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         return;
       }
 
@@ -3903,14 +3662,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         if (_s.getLength() < sg.getEndRes())
         {
-          JOptionPane
+          JvOptionPane
                   .showMessageDialog(
                           Desktop.desktop,
                           MessageManager
                                   .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
                           MessageManager
                                   .getString("label.sequences_selection_not_aligned"),
-                          JOptionPane.WARNING_MESSAGE);
+                          JvOptionPane.WARNING_MESSAGE);
 
           return;
         }
@@ -3924,14 +3683,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // are the visible sequences aligned?
       if (!viewport.getAlignment().isAligned(false))
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("label.sequences_must_be_aligned_before_creating_tree"),
                         MessageManager
                                 .getString("label.sequences_not_aligned"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
 
         return;
       }
@@ -3967,7 +3726,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
-    final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title}));
+    final JMenuItem item = new JMenuItem(MessageManager.formatMessage(
+            "action.by_title_param", new Object[] { title }));
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
@@ -4086,16 +3846,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     calculateTree.removeAll();
     // build the calculate menu
 
-    for (final String type : new String[]
-    { "NJ", "AV" })
+    for (final String type : new String[] { "NJ", "AV" })
     {
       String treecalcnm = MessageManager.getString("label.tree_calc_"
               + type.toLowerCase());
-      for (final Object pwtype : ResidueProperties.scoreMatrices.keySet())
+      for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+                || sm.isProtein() == !viewport.getAlignment()
+                        .isNucleotide())
         {
           String smn = MessageManager.getStringOrReturn(
                   "label.score_model_", sm.getName());
@@ -4107,7 +3868,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              NewTreePanel(type, (String) pwtype, title);
+              newTreePanel(type, pwtype, title);
             }
           });
           calculateTree.add(tm);
@@ -4117,21 +3878,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     sortByTreeMenu.removeAll();
 
-    Vector comps = (Vector) PaintRefresher.components.get(viewport
+    List<Component> comps = PaintRefresher.components.get(viewport
             .getSequenceSetId());
-    Vector treePanels = new Vector();
-    int i, iSize = comps.size();
-    for (i = 0; i < iSize; i++)
+    List<TreePanel> treePanels = new ArrayList<TreePanel>();
+    for (Component comp : comps)
     {
-      if (comps.elementAt(i) instanceof TreePanel)
+      if (comp instanceof TreePanel)
       {
-        treePanels.add(comps.elementAt(i));
+        treePanels.add((TreePanel) comp);
       }
     }
 
-    iSize = treePanels.size();
-
-    if (iSize < 1)
+    if (treePanels.size() < 1)
     {
       sortByTreeMenu.setVisible(false);
       return;
@@ -4139,17 +3897,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
-    for (i = 0; i < treePanels.size(); i++)
+    for (final TreePanel tp : treePanels)
     {
-      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)
         {
-          tp.sortByTree_actionPerformed(null);
+          tp.sortByTree_actionPerformed();
           addHistoryItem(tp.sortAlignmentIn(alignPanel));
 
         }
@@ -4199,11 +3955,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() == 1)
     {
-      int option = JOptionPane.showConfirmDialog(this,
+      int option = JvOptionPane.showConfirmDialog(this,
               MessageManager.getString("warn.oneseq_msainput_selection"),
               MessageManager.getString("label.invalid_selection"),
-              JOptionPane.OK_CANCEL_OPTION);
-      if (option == JOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION);
+      if (option == JvOptionPane.OK_OPTION)
       {
         msa = viewport.getAlignmentView(false);
       }
@@ -4241,8 +3997,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
     if (!viewport.getAlignment().isAligned(false))
     {
-      seqs.setSequences(new SeqCigar[]
-      { seqs.getSequences()[0] });
+      seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
       // TODO: if seqs.getSequences().length>1 then should really have warned
       // user!
 
@@ -4257,7 +4012,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          DOCUMENT ME!
    */
   @Override
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -4276,35 +4031,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       jalview.io.NewickFile fin = null;
       try
       {
-        fin = new jalview.io.NewickFile(choice, "File");
+        fin = new NewickFile(choice, DataSourceType.FILE);
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
-        JOptionPane
+        JvOptionPane
                 .showMessageDialog(
                         Desktop.desktop,
                         ex.getMessage(),
                         MessageManager
                                 .getString("label.problem_reading_tree_file"),
-                        JOptionPane.WARNING_MESSAGE);
+                        JvOptionPane.WARNING_MESSAGE);
         ex.printStackTrace();
       }
       if (fin != null && fin.hasWarningMessage())
       {
-        JOptionPane.showMessageDialog(Desktop.desktop, fin
+        JvOptionPane.showMessageDialog(Desktop.desktop, fin
                 .getWarningMessage(), MessageManager
                 .getString("label.possible_problem_with_tree_file"),
-                JOptionPane.WARNING_MESSAGE);
+                JvOptionPane.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);
@@ -4389,7 +4138,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception e)
       {
       }
-      ;
     }
     final AlignFrame me = this;
     buildingMenu = true;
@@ -4401,8 +4149,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
         try
         {
-          System.err.println("Building ws menu again "
-                  + Thread.currentThread());
+          // System.err.println("Building ws menu again "
+          // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
           // alignment and current selection
@@ -4415,22 +4163,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // object broker mechanism.
           final Vector<JMenu> wsmenu = new Vector<JMenu>();
           final IProgressIndicator af = me;
+
+          /*
+           * do not i18n these strings - they are hard-coded in class
+           * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
+           * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
+           */
           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");
-          // final JMenu msawsmenu = new
-          // JMenu(MessageManager.getString("label.alignment"));
-          // final JMenu secstrmenu = new
-          // JMenu(MessageManager.getString("label.secondary_structure_prediction"));
-          // final JMenu seqsrchmenu = new
-          // JMenu(MessageManager.getString("label.sequence_database_search"));
-          // final JMenu analymenu = new
-          // JMenu(MessageManager.getString("label.analysis"));
-          // final JMenu dismenu = new
-          // JMenu(MessageManager.getString("label.protein_disorder"));
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
@@ -4544,14 +4288,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .debug("Exception during web service menu building process.",
                                 e);
               }
-              ;
             }
           });
         } catch (Exception e)
         {
         }
-        ;
-
         buildingMenu = false;
       }
     }).start();
@@ -4582,91 +4323,56 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // 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);
-    }
-  }
-
-  /*
-   * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
-   * chooser = new JalviewFileChooser(jalview.bin.Cache.
-   * getProperty("LAST_DIRECTORY"));
-   * 
-   * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
-   * to Vamsas file"); chooser.setToolTipText("Export");
-   * 
-   * int value = chooser.showSaveDialog(this);
-   * 
-   * if (value == JalviewFileChooser.APPROVE_OPTION) {
-   * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
-   * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
-   * chooser.getSelectedFile().getAbsolutePath(), this); } }
-   */
-  /**
-   * prototype of an automatically enabled/disabled analysis function
-   * 
-   */
-  protected void setShowProductsEnabled()
-  {
-    SequenceI[] selection = viewport.getSequenceSelection();
-    if (canShowProducts(selection, viewport.getSelectionGroup() != null,
-            viewport.getAlignment().getDataset()))
-    {
-      showProducts.setEnabled(true);
-
-    }
-    else
+
+    for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
+            .getRestClients())
     {
-      showProducts.setEnabled(false);
+      client.attachWSMenuEntry(
+              JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
+              this);
     }
   }
 
   /**
-   * search selection for sequence xRef products and build the show products
-   * menu.
+   * Searches the alignment sequences for xRefs and builds the Show
+   * Cross-References menu (formerly called Show Products), with database
+   * sources for which cross-references are found (protein sources for a
+   * nucleotide alignment and vice versa)
    * 
-   * @param selection
-   * @param dataset
-   * @return true if showProducts menu should be enabled.
+   * @return true if Show Cross-references menu should be enabled
    */
-  public boolean canShowProducts(SequenceI[] selection,
-          boolean isRegionSelection, Alignment dataset)
+  public boolean canShowProducts()
   {
+    SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+    AlignmentI dataset = viewport.getAlignment().getDataset();
+
+    showProducts.removeAll();
+    final boolean dna = viewport.getAlignment().isNucleotide();
+
+    if (seqs == null || seqs.length == 0)
+    {
+      // nothing to see here.
+      return false;
+    }
+
     boolean showp = false;
     try
     {
-      showProducts.removeAll();
-      final boolean dna = viewport.getAlignment().isNucleotide();
-      final Alignment ds = dataset;
-      String[] ptypes = (selection == null || selection.length == 0) ? null
-              : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
-      // Object[] prods =
-      // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
-      // selection, dataset, true);
-      final SequenceI[] sel = selection;
-      for (int t = 0; ptypes != null && t < ptypes.length; t++)
+      List<String> ptypes = new CrossRef(seqs, dataset)
+              .findXrefSourcesForSequences(dna);
+
+      for (final String source : ptypes)
       {
         showp = true;
-        final boolean isRegSel = isRegionSelection;
         final AlignFrame af = this;
-        final String source = ptypes[t];
-        JMenuItem xtype = new JMenuItem(ptypes[t]);
+        JMenuItem xtype = new JMenuItem(source);
         xtype.addActionListener(new ActionListener()
         {
-
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            // TODO: new thread for this call with vis-delay
-            af.showProductsFor(af.viewport.getSequenceSelection(), ds,
-                    isRegSel, dna, source);
+            showProductsFor(af.viewport.getSequenceSelection(), dna, source);
           }
-
         });
         showProducts.add(xtype);
       }
@@ -4674,240 +4380,126 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
-              .warn("canTranslate threw an exception - please report to help@jalview.org",
+      Cache.log
+              .warn("canShowProducts threw an exception - please report to help@jalview.org",
                       e);
       return false;
     }
     return showp;
   }
 
-  protected void showProductsFor(SequenceI[] sel, Alignment ds,
-          boolean isRegSel, boolean dna, String source)
-  {
-    final boolean fisRegSel = isRegSel;
-    final boolean fdna = dna;
-    final String fsrc = source;
-    final AlignFrame ths = this;
-    final SequenceI[] fsel = sel;
-    Runnable foo = new Runnable()
-    {
-
-      @Override
-      public void run()
-      {
-        final long sttime = System.currentTimeMillis();
-        ths.setProgressBar(MessageManager.formatMessage("status.searching_for_sequences_from", new String[]{fsrc}), sttime);
-        try
-        {
-          Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
-          // our local
-          // dataset
-          // reference
-          Alignment prods = CrossRef
-                  .findXrefSequences(fsel, fdna, fsrc, ds);
-          if (prods != null)
-          {
-            SequenceI[] sprods = new SequenceI[prods.getHeight()];
-            for (int s = 0; s < sprods.length; s++)
-            {
-              sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
-              if (ds.getSequences() == null
-                      || !ds.getSequences().contains(
-                              sprods[s].getDatasetSequence()))
-              {
-                ds.addSequence(sprods[s].getDatasetSequence());
-              }
-              sprods[s].updatePDBIds();
-            }
-            Alignment al = new Alignment(sprods);
-            AlignedCodonFrame[] cf = prods.getCodonFrames();
-            al.setDataset(ds);
-            for (int s = 0; cf != null && s < cf.length; s++)
-            {
-              al.addCodonFrame(cf[s]);
-              cf[s] = null;
-            }
-            AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
-                    DEFAULT_HEIGHT);
-            String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
-                    + " for " + ((fisRegSel) ? "selected region of " : "")
-                    + getTitle();
-            Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
-                    DEFAULT_HEIGHT);
-          }
-          else
-          {
-            System.err.println("No Sequences generated for xRef type "
-                    + fsrc);
-          }
-        } catch (Exception e)
-        {
-          jalview.bin.Cache.log.error(
-                  "Exception when finding crossreferences", e);
-        } catch (OutOfMemoryError e)
-        {
-          new OOMWarning("whilst fetching crossreferences", e);
-        } catch (Error e)
-        {
-          jalview.bin.Cache.log.error("Error when finding crossreferences",
-                  e);
-        }
-        ths.setProgressBar(MessageManager.formatMessage("status.finished_searching_for_sequences_from", new String[]{fsrc}),
-                sttime);
-      }
-
-    };
-    Thread frunner = new Thread(foo);
-    frunner.start();
-  }
-
-  public boolean canShowTranslationProducts(SequenceI[] selection,
-          AlignmentI alignment)
-  {
-    // old way
-    try
-    {
-      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",
-                      e);
-      return false;
-    }
-  }
-
-  @Override
-  public void showProducts_actionPerformed(ActionEvent e)
+  /**
+   * Finds and displays cross-references for the selected sequences (protein
+   * products for nucleotide sequences, dna coding sequences for peptides).
+   * 
+   * @param sel
+   *          the sequences to show cross-references for
+   * @param dna
+   *          true if from a nucleotide alignment (so showing proteins)
+   * @param source
+   *          the database to show cross-references for
+   */
+  protected void showProductsFor(final SequenceI[] sel,
+          final boolean _odna, final String source)
   {
-    // /////////////////////////////
-    // Collect Data to be translated/transferred
-
-    SequenceI[] selection = viewport.getSequenceSelection();
-    AlignmentI al = null;
-    try
-    {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
-              .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
-              viewport.getAlignment().getDataset());
-    } catch (Exception ex)
-    {
-      al = null;
-      jalview.bin.Cache.log.debug("Exception during translation.", ex);
-    }
-    if (al == null)
-    {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
-                      MessageManager.getString("label.translation_failed"),
-                      JOptionPane.WARNING_MESSAGE);
-    }
-    else
-    {
-      AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, MessageManager.formatMessage(
-              "label.translation_of_params", new String[]
-              { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
-    }
+    new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+            .start();
   }
 
+  /**
+   * Construct and display a new frame containing the translation of this
+   * frame's DNA sequences to their aligned protein (amino acid) equivalents.
+   */
   @Override
   public void showTranslation_actionPerformed(ActionEvent e)
   {
-    // /////////////////////////////
-    // Collect Data to be translated/transferred
-
-    SequenceI[] selection = viewport.getSequenceSelection();
-    String[] seqstring = viewport.getViewAsString(true);
     AlignmentI al = null;
     try
     {
-      al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
-              viewport.getViewAsVisibleContigs(true), viewport
-                      .getGapCharacter(), viewport.getAlignment()
-                      .getAlignmentAnnotation(), viewport.getAlignment()
-                      .getWidth(), viewport.getAlignment().getDataset());
+      Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+      al = dna.translateCdna();
     } catch (Exception ex)
     {
-      al = null;
       jalview.bin.Cache.log.error(
               "Exception during translation. Please report this !", ex);
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.error_when_translating_sequences_submit_bug_report"),
-                      MessageManager
-                              .getString("label.implementation_error")
-                              + MessageManager
-                                      .getString("translation_failed"),
-                      JOptionPane.ERROR_MESSAGE);
+      final String msg = MessageManager
+              .getString("label.error_when_translating_sequences_submit_bug_report");
+      final String errorTitle = MessageManager
+              .getString("label.implementation_error")
+              + MessageManager.getString("label.translation_failed");
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.ERROR_MESSAGE);
       return;
     }
-    if (al == null)
+    if (al == null || al.getHeight() == 0)
     {
-      JOptionPane
-              .showMessageDialog(
-                      Desktop.desktop,
-                      MessageManager
-                              .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"),
-                      MessageManager.getString("label.translation_failed"),
-                      JOptionPane.WARNING_MESSAGE);
+      final String msg = MessageManager
+              .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
+      final String errorTitle = MessageManager
+              .getString("label.translation_failed");
+      JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+              JvOptionPane.WARNING_MESSAGE);
     }
     else
     {
       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
-      Desktop.addInternalFrame(af, MessageManager.formatMessage(
-              "label.translation_of_params", new String[]
-              { this.getTitle() }), DEFAULT_WIDTH, DEFAULT_HEIGHT);
+      af.setFileFormat(this.currentFileFormat);
+      final String newTitle = MessageManager.formatMessage(
+              "label.translation_of_params",
+              new Object[] { this.getTitle() });
+      af.setTitle(newTitle);
+      if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+      {
+        final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+        viewport.openSplitFrame(af, new Alignment(seqs));
+      }
+      else
+      {
+        Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
+                DEFAULT_HEIGHT);
+      }
     }
   }
 
   /**
+   * Set the file format
+   * 
+   * @param format
+   */
+  public void setFileFormat(FileFormatI format)
+  {
+    this.currentFileFormat = format;
+  }
+
+  /**
    * Try to load a features file onto the alignment.
    * 
    * @param file
    *          contents or path to retrieve file
-   * @param type
+   * @param sourceType
    *          access mode of file (see jalview.io.AlignFile)
-   * @return true if features file was parsed corectly.
+   * @return true if features file was parsed correctly.
    */
-  public boolean parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType)
   {
-    boolean featuresFile = false;
-    try
-    {
-      featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().getFeatureColours(), false,
-              jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
+    return avc.parseFeaturesFile(file, sourceType,
+            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+
+  }
 
-    if (featuresFile)
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    // note - currently this is only still here rather than in the controller
+    // because of the featureSettings hard reference that is yet to be
+    // abstracted
+    if (enableIfNecessary)
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      if (alignPanel.getSeqPanel().seqCanvas.fr != null)
-      {
-        // update the min/max ranges where necessary
-        alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
-      }
-      if (featureSettings != null)
-      {
-        featureSettings.setTableData();
-      }
-      alignPanel.paintAlignment(true);
     }
 
-    return featuresFile;
   }
 
   @Override
@@ -4933,50 +4525,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void drop(DropTargetDropEvent evt)
   {
+    // JAL-1552 - acceptDrop required before getTransferable call for
+    // Java's Transferable for native dnd
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    java.util.List files = null;
+    List<String> files = new ArrayList<String>();
+    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 
     try
     {
-      DataFlavor uriListFlavor = new DataFlavor(
-              "text/uri-list;class=java.lang.String");
-      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-      {
-        // Works on Windows and MacOSX
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t
-                .getTransferData(DataFlavor.javaFileListFlavor);
-      }
-      else if (t.isDataFlavorSupported(uriListFlavor))
-      {
-        // This is used by Unix drag system
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        String data = (String) t.getTransferData(uriListFlavor);
-        files = new java.util.ArrayList(1);
-        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
-                data, "\r\n"); st.hasMoreTokens();)
-        {
-          String s = st.nextToken();
-          if (s.startsWith("#"))
-          {
-            // the line is a comment (as per the RFC 2483)
-            continue;
-          }
-
-          java.net.URI uri = new java.net.URI(s);
-          // check to see if we can handle this kind of URI
-          if (uri.getScheme().toLowerCase().startsWith("http"))
-          {
-            files.add(uri.toString());
-          }
-          else
-          {
-            // otherwise preserve old behaviour: catch all for file objects
-            java.io.File file = new java.io.File(uri);
-            files.add(file.toString());
-          }
-        }
-      }
+      Desktop.transferFromDropTarget(files, protocols, evt, t);
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -4998,13 +4556,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           String file = files.get(i).toString();
           String pdbfn = "";
-          String protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == jalview.io.FormatAdapter.FILE)
+          DataSourceType protocol = FormatAdapter.checkProtocol(file);
+          if (protocol == DataSourceType.FILE)
           {
             File fl = new File(file);
             pdbfn = fl.getName();
           }
-          else if (protocol == jalview.io.FormatAdapter.URL)
+          else if (protocol == DataSourceType.URL)
           {
             URL url = new URL(file);
             pdbfn = url.getFile();
@@ -5028,22 +4586,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             }
             if (mtch != null)
             {
-              String type = null;
+              FileFormatI type = null;
               try
               {
-                type = new IdentifyFile().Identify(file, protocol);
+                type = new IdentifyFile().identify(file, protocol);
               } catch (Exception ex)
               {
                 type = null;
               }
-              if (type != null)
+              if (type != null && type.isStructureFile())
               {
-                if (type.equalsIgnoreCase("PDB"))
-                {
-                  filesmatched.add(new Object[]
-                  { file, protocol, mtch });
-                  continue;
-                }
+                filesmatched.add(new Object[] { file, protocol, mtch });
+                continue;
               }
             }
             // File wasn't named like one of the sequences or wasn't a PDB file.
@@ -5054,20 +4608,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (filesmatched.size() > 0)
         {
           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                  || JOptionPane
+                  || JvOptionPane
                           .showConfirmDialog(
                                   this,
                                   MessageManager
                                           .formatMessage(
-                                                  "label.automatically_associate_pdb_files_with_sequences_same_name",
-                                                  new String[]
-                                                  { Integer.valueOf(
-                                                          filesmatched
-                                                                  .size())
+                                                  "label.automatically_associate_structure_files_with_sequences_same_name",
+                                                  new Object[] { Integer
+                                                          .valueOf(
+                                                                  filesmatched
+                                                                          .size())
                                                           .toString() }),
                                   MessageManager
-                                          .getString("label.automatically_associate_pdb_files_by_name"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+                                          .getString("label.automatically_associate_structure_files_by_name"),
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
 
           {
             for (Object[] fm : filesmatched)
@@ -5079,7 +4633,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false,
+                                (DataSourceType) fm[1], toassoc, false,
                                 Desktop.instance);
                 if (pe != null)
                 {
@@ -5097,20 +4651,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           if (assocfiles > 0
                   && (Cache.getDefault(
-                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+                          "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
                           .showConfirmDialog(
                                   this,
-                                  "<html>"+MessageManager
-                                          .formatMessage(
-                                                  "label.ignore_unmatched_dropped_files_info",
-                                                  new String[]
-                                                  { Integer.valueOf(
-                                                          filesnotmatched
-                                                                  .size())
-                                                          .toString() })+"</html>",
+                                  "<html>"
+                                          + MessageManager
+                                                  .formatMessage(
+                                                          "label.ignore_unmatched_dropped_files_info",
+                                                          new Object[] { Integer
+                                                                  .valueOf(
+                                                                          filesnotmatched
+                                                                                  .size())
+                                                                  .toString() })
+                                          + "</html>",
                                   MessageManager
                                           .getString("label.ignore_unmatched_dropped_files"),
-                                  JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+                                  JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
           {
             return;
           }
@@ -5129,29 +4685,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * Attempt to load a "dropped" file or URL string: First by testing whether
-   * it's and Annotation file, then a JNet file, and finally a features file. If
+   * it's an Annotation file, then a JNet file, and finally a features file. If
    * all are false then the user may have dropped an alignment file onto this
    * AlignFrame.
    * 
    * @param file
    *          either a filename or a URL string.
    */
-  public void loadJalviewDataFile(String file, String protocol,
-          String format, SequenceI assocSeq)
+  public void loadJalviewDataFile(String file, DataSourceType sourceType,
+          FileFormatI format, SequenceI assocSeq)
   {
     try
     {
-      if (protocol == null)
+      if (sourceType == null)
       {
-        protocol = jalview.io.FormatAdapter.checkProtocol(file);
+        sourceType = FormatAdapter.checkProtocol(file);
       }
       // 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()
-              .annotateAlignmentView(viewport, file, protocol)
-              : false;
+      boolean isAnnotation = (format == null || FileFormat.Pfam
+              .equals(format)) ? new AnnotationFile()
+              .annotateAlignmentView(viewport, file, sourceType) : false;
 
       if (!isAnnotation)
       {
@@ -5159,13 +4714,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         TCoffeeScoreFile tcf = null;
         try
         {
-          tcf = new TCoffeeScoreFile(file, protocol);
+          tcf = new TCoffeeScoreFile(file, sourceType);
           if (tcf.isValid())
           {
             if (tcf.annotateAlignment(viewport.getAlignment(), true))
             {
-              tcoffeeColour.setEnabled(true);
-              tcoffeeColour.setSelected(true);
+              buildColourMenu();
               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
               isAnnotation = true;
               statusBar
@@ -5176,7 +4730,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
               // some problem - if no warning its probable that the ID matching
               // process didn't work
-              JOptionPane
+              JvOptionPane
                       .showMessageDialog(
                               Desktop.desktop,
                               tcf.getWarningMessage() == null ? MessageManager
@@ -5184,7 +4738,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                       : tcf.getWarningMessage(),
                               MessageManager
                                       .getString("label.problem_reading_tcoffee_score_file"),
-                              JOptionPane.WARNING_MESSAGE);
+                              JvOptionPane.WARNING_MESSAGE);
             }
           }
           else
@@ -5205,52 +4759,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // try to parse it as a features file
           if (format == null)
           {
-            format = new IdentifyFile().Identify(file, protocol);
+            format = new IdentifyFile().identify(file, sourceType);
           }
-          if (format.equalsIgnoreCase("JnetFile"))
+          if (FileFormat.Jnet.equals(format))
           {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                    file, protocol);
-            new JnetAnnotationMaker().add_annotation(predictions,
+            JPredFile predictions = new JPredFile(file, sourceType);
+            new JnetAnnotationMaker();
+            JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
+            SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
+            viewport.getAlignment().setSeqrep(repseq);
+            ColumnSelection cs = new ColumnSelection();
+            cs.hideInsertionsFor(repseq);
+            viewport.setColumnSelection(cs);
             isAnnotation = true;
           }
-          else
+          // else if (IdentifyFile.FeaturesFile.equals(format))
+          else if (FileFormat.Features.equals(format))
           {
-            /*
-             * 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
+            if (parseFeaturesFile(file, sourceType))
             {
               alignPanel.paintAlignment(true);
             }
           }
+          else
+          {
+            new FileLoader().LoadFile(viewport, file, sourceType, format);
+          }
         }
       }
       if (isAnnotation)
@@ -5272,42 +4807,87 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception x)
       {
       }
-      ;
       new OOMWarning(
               "loading data "
-                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
-                              : "using " + protocol + " from " + file)
+                      + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
+                              : "using " + sourceType + " from " + file)
                               : ".")
                       + (format != null ? "(parsing as '" + format
                               + "' file)" : ""), oom, Desktop.desktop);
     }
   }
 
+  /**
+   * Method invoked by the ChangeListener on the tabbed pane, in other words
+   * when a different tabbed pane is selected by the user or programmatically.
+   */
   @Override
   public void tabSelectionChanged(int index)
   {
     if (index > -1)
     {
-      alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
+      alignPanel = alignPanels.get(index);
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
     }
+
+    /*
+     * 'focus' any colour slider that is open to the selected viewport
+     */
+    if (viewport.getConservationSelected())
+    {
+      SliderPanel.setConservationSlider(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
+    if (viewport.getAbovePIDThreshold())
+    {
+      SliderPanel.setPIDSliderSource(alignPanel,
+              viewport.getViewportColourScheme(), alignPanel.getViewName());
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
+
+    /*
+     * If there is a frame linked to this one in a SplitPane, switch it to the
+     * same view tab index. No infinite recursion of calls should happen, since
+     * tabSelectionChanged() should not get invoked on setting the selected
+     * index to an unchanged value. Guard against setting an invalid index
+     * before the new view peer tab has been created.
+     */
+    final AlignViewportI peer = viewport.getCodingComplement();
+    if (peer != null)
+    {
+      AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame;
+      if (linkedAlignFrame.tabbedPane.getTabCount() > index)
+      {
+        linkedAlignFrame.tabbedPane.setSelectedIndex(index);
+      }
+    }
   }
 
+  /**
+   * On right mouse click on view tab, prompt for and set new view name.
+   */
   @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
-    if (SwingUtilities.isRightMouseButton(e))
+    if (e.isPopupTrigger())
     {
-      String reply = JOptionPane.showInternalInputDialog(this,
-              MessageManager.getString("label.enter_view_name"),
-              MessageManager.getString("label.enter_view_name"),
-              JOptionPane.QUESTION_MESSAGE);
+      String msg = MessageManager.getString("label.enter_view_name");
+      String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+              JvOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
       {
         viewport.viewName = reply;
+        // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
     }
@@ -5347,7 +4927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
-    viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+    viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
   }
 
   /*
@@ -5359,7 +4939,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
-    viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+    viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
   }
 
   /**
@@ -5368,7 +4948,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param av
    */
-  public boolean closeView(AlignViewport av)
+  public boolean closeView(AlignViewportI av)
   {
     if (viewport == av)
     {
@@ -5431,13 +5011,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
-
           @Override
           public void run()
           {
-            new jalview.ws.DBRefFetcher(alignPanel.av
-                    .getSequenceSelection(), alignPanel.alignFrame)
-                    .fetchDBRefs(false);
+            boolean isNucleotide = alignPanel.alignFrame.getViewport()
+                    .getAlignment().isNucleotide();
+            DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
+                    .getSequenceSelection(), alignPanel.alignFrame, null,
+                    alignPanel.alignFrame.featureSettings, isNucleotide);
+            dbRefFetcher.addListener(new FetchFinishedListenerI()
+            {
+              @Override
+              public void finished()
+              {
+                AlignFrame.this.setMenusForViewport();
+              }
+            });
+            dbRefFetcher.fetchDBRefs(false);
           }
         }).start();
 
@@ -5451,7 +5041,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       @Override
       public void run()
       {
-        final jalview.ws.SequenceFetcher sf = SequenceFetcher
+        final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
                 .getSequenceFetcherSingleton(me);
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
@@ -5505,16 +5095,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        new jalview.ws.DBRefFetcher(alignPanel.av
-                                .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
-                                .fetchDBRefs(false);
+                        boolean isNucleotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
+                        DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                alignPanel.av.getSequenceSelection(),
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNucleotide);
+                        dbRefFetcher
+                                .addListener(new FetchFinishedListenerI()
+                                {
+                                  @Override
+                                  public void finished()
+                                  {
+                                    AlignFrame.this.setMenusForViewport();
+                                  }
+                                });
+                        dbRefFetcher.fetchDBRefs(false);
                       }
                     }).start();
                   }
 
                 });
-                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()})));
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                        MessageManager.formatMessage(
+                                "label.fetch_retrieve_from",
+                                new Object[] { src.getDbName() })));
                 dfetch.add(fetchr);
                 comp++;
               }
@@ -5525,8 +5132,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 // fetch all entry
                 DbSourceProxy src = otherdb.get(0);
                 fetchr = new JMenuItem(MessageManager.formatMessage(
-                        "label.fetch_all_param", new String[]
-                        { src.getDbSource() }));
+                        "label.fetch_all_param",
+                        new Object[] { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
                   @Override
@@ -5538,20 +5145,42 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        new jalview.ws.DBRefFetcher(alignPanel.av
-                                .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
-                                .fetchDBRefs(false);
+                        boolean isNucleotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
+                        DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                alignPanel.av.getSequenceSelection(),
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNucleotide);
+                        dbRefFetcher
+                                .addListener(new FetchFinishedListenerI()
+                                {
+                                  @Override
+                                  public void finished()
+                                  {
+                                    AlignFrame.this.setMenusForViewport();
+                                  }
+                                });
+                        dbRefFetcher.fetchDBRefs(false);
                       }
                     }).start();
                   }
                 });
 
-                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{Integer.valueOf(otherdb.size()).toString(), src.getDbSource(), src.getDbName()})));
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
+                        MessageManager.formatMessage(
+                                "label.fetch_retrieve_from_all_sources",
+                                new Object[] {
+                                    Integer.valueOf(otherdb.size())
+                                            .toString(), src.getDbSource(),
+                                    src.getDbName() })));
                 dfetch.add(fetchr);
                 comp++;
                 // and then build the rest of the individual menus
-                ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()}));
+                ifetch = new JMenu(MessageManager.formatMessage(
+                        "label.source_from_db_source",
+                        new Object[] { src.getDbSource() }));
                 icomp = 0;
                 String imname = null;
                 int i = 0;
@@ -5564,11 +5193,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           0, 10) + "..." : dbname;
                   if (imname == null)
                   {
-                    imname = MessageManager.formatMessage("label.from_msname", new String[]{sname});
+                    imname = MessageManager.formatMessage(
+                            "label.from_msname", new Object[] { sname });
                   }
                   fetchr = new JMenuItem(msname);
-                  final DbSourceProxy[] dassrc =
-                  { sproxy };
+                  final DbSourceProxy[] dassrc = { sproxy };
                   fetchr.addActionListener(new ActionListener()
                   {
 
@@ -5581,17 +5210,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         @Override
                         public void run()
                         {
-                          new jalview.ws.DBRefFetcher(alignPanel.av
-                                  .getSequenceSelection(),
-                                  alignPanel.alignFrame, dassrc)
-                                  .fetchDBRefs(false);
+                          boolean isNucleotide = alignPanel.alignFrame
+                                  .getViewport().getAlignment()
+                                  .isNucleotide();
+                          DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                  alignPanel.av.getSequenceSelection(),
+                                  alignPanel.alignFrame, dassrc,
+                                  alignPanel.alignFrame.featureSettings,
+                                  isNucleotide);
+                          dbRefFetcher
+                                  .addListener(new FetchFinishedListenerI()
+                                  {
+                                    @Override
+                                    public void finished()
+                                    {
+                                      AlignFrame.this.setMenusForViewport();
+                                    }
+                                  });
+                          dbRefFetcher.fetchDBRefs(false);
                         }
                       }).start();
                     }
 
                   });
                   fetchr.setToolTipText("<html>"
-                          + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname}));
+                          + MessageManager.formatMessage(
+                                  "label.fetch_retrieve_from", new Object[]
+                                  { dbname }));
                   ifetch.add(fetchr);
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
@@ -5646,10 +5291,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.firePropertyChange("alignment", null, al);
   }
 
+  @Override
   public void setShowSeqFeatures(boolean b)
   {
-    showSeqFeatures.setSelected(true);
-    viewport.setShowSequenceFeatures(true);
+    showSeqFeatures.setSelected(b);
+    viewport.setShowSequenceFeatures(b);
   }
 
   /*
@@ -5755,10 +5401,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.paintAlignment(true);
     }
   }
+
   public void clearAlignmentSeqRep()
   {
     // TODO refactor alignmentseqrep to controller
-    if (viewport.getAlignment().hasSeqrep()) {
+    if (viewport.getAlignment().hasSeqrep())
+    {
       viewport.getAlignment().setSeqrep(null);
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
@@ -5794,10 +5442,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!viewport.getSequenceSetId().equals(
             alignmentPanel.av.getSequenceSetId()))
     {
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_show_view_alignment_frame"));
     }
     if (tabbedPane != null
-            & alignPanels.indexOf(alignmentPanel) != tabbedPane
+            && tabbedPane.getTabCount() > 0
+            && alignPanels.indexOf(alignmentPanel) != tabbedPane
                     .getSelectedIndex())
     {
       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
@@ -5817,9 +5468,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignPanel.getAlignment()
+            .getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return;
+    }
+    for (AlignmentAnnotation aa : anns)
     {
+      /*
+       * don't display non-positional annotations on an alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
       boolean apply = (aa.sequenceRef == null && forAlignment)
               || (aa.sequenceRef != null && forSequences);
       if (apply)
@@ -5827,7 +5490,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         aa.visible = visible;
       }
     }
-    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.validateAnnotationDimensions(true);
     alignPanel.alignmentChanged();
   }
 
@@ -5845,12 +5508,197 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /**
    * 
-   * @return alignment panels in this alignemnt frame
+   * @return alignment panels in this alignment frame
    */
-  public List<AlignmentViewPanel> getAlignPanels()
+  public List<? extends AlignmentViewPanel> getAlignPanels()
   {
     return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
   }
+
+  /**
+   * Open a new alignment window, with the cDNA associated with this (protein)
+   * alignment, aligned as is the protein.
+   */
+  protected void viewAsCdna_actionPerformed()
+  {
+    // TODO no longer a menu action - refactor as required
+    final AlignmentI alignment = getViewport().getAlignment();
+    List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+    if (mappings == null)
+    {
+      return;
+    }
+    List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+    for (SequenceI aaSeq : alignment.getSequences())
+    {
+      for (AlignedCodonFrame acf : mappings)
+      {
+        SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
+        if (dnaSeq != null)
+        {
+          /*
+           * There is a cDNA mapping for this protein sequence - add to new
+           * alignment. It will share the same dataset sequence as other mapped
+           * cDNA (no new mappings need to be created).
+           */
+          final Sequence newSeq = new Sequence(dnaSeq);
+          newSeq.setDatasetSequence(dnaSeq);
+          cdnaSeqs.add(newSeq);
+        }
+      }
+    }
+    if (cdnaSeqs.size() == 0)
+    {
+      // show a warning dialog no mapped cDNA
+      return;
+    }
+    AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
+            .size()]));
+    GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+    cdna.alignAs(alignment);
+    String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+            + this.title;
+    Desktop.addInternalFrame(alignFrame, newtitle,
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+  }
+
+  /**
+   * Set visibility of dna/protein complement view (available when shown in a
+   * split frame).
+   * 
+   * @param show
+   */
+  @Override
+  protected void showComplement_actionPerformed(boolean show)
+  {
+    SplitContainerI sf = getSplitViewContainer();
+    if (sf != null)
+    {
+      sf.setComplementVisible(this, show);
+    }
+  }
+
+  /**
+   * Generate the reverse (optionally complemented) of the selected sequences,
+   * and add them to the alignment
+   */
+  @Override
+  protected void showReverse_actionPerformed(boolean complement)
+  {
+    AlignmentI al = null;
+    try
+    {
+      Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+      al = dna.reverseCdna(complement);
+      viewport.addAlignment(al, "");
+      addHistoryItem(new EditCommand(
+              MessageManager.getString("label.add_sequences"),
+              Action.PASTE, al.getSequencesArray(), 0, al.getWidth(),
+              viewport.getAlignment()));
+    } catch (Exception ex)
+    {
+      System.err.println(ex.getMessage());
+      return;
+    }
+  }
+
+  /**
+   * Try to run a script in the Groovy console, having first ensured that this
+   * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
+   * be targeted at this alignment.
+   */
+  @Override
+  protected void runGroovy_actionPerformed()
+  {
+    Jalview.setCurrentAlignFrame(this);
+    groovy.ui.Console console = Desktop.getGroovyConsole();
+    if (console != null)
+    {
+      try
+      {
+        console.runScript();
+      } catch (Exception ex)
+      {
+        System.err.println((ex.toString()));
+        JvOptionPane
+                .showInternalMessageDialog(Desktop.desktop, MessageManager
+                        .getString("label.couldnt_run_groovy_script"),
+                        MessageManager
+                                .getString("label.groovy_support_failed"),
+                        JvOptionPane.ERROR_MESSAGE);
+      }
+    }
+    else
+    {
+      System.err.println("Can't run Groovy script as console not found");
+    }
+  }
+
+  /**
+   * Hides columns containing (or not containing) a specified feature, provided
+   * that would not leave all columns hidden
+   * 
+   * @param featureType
+   * @param columnsContaining
+   * @return
+   */
+  public boolean hideFeatureColumns(String featureType,
+          boolean columnsContaining)
+  {
+    boolean notForHiding = avc.markColumnsContainingFeatures(
+            columnsContaining, false, false, featureType);
+    if (notForHiding)
+    {
+      if (avc.markColumnsContainingFeatures(!columnsContaining, false,
+              false, featureType))
+      {
+        getViewport().hideSelectedColumns();
+        return true;
+      }
+    }
+    return false;
+  }
+
+  @Override
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // include key modifier check in case user selects from menu
+    avc.markHighlightedColumns(
+            (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0,
+            true,
+            (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
+  }
+
+  /**
+   * Rebuilds the Colour menu, including any user-defined colours which have
+   * been loaded either on startup or during the session
+   */
+  public void buildColourMenu()
+  {
+    colourMenu.removeAll();
+
+    colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
+    colourMenu.addSeparator();
+
+    ColourMenuHelper.addMenuItems(colourMenu, this,
+            viewport.getAlignment(), false);
+
+    colourMenu.addSeparator();
+    colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
+
+    ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
+    String schemeName = colourScheme == null ? null : colourScheme
+            .getSchemeName();
+
+    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+  }
 }
 
 class PrintThread extends Thread