X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cd9c5337c23744694350cacc5292b7ca24791f4e;hb=2a9991ef1eb02d97e9c8ed1644f292117ae6f600;hp=41685169e7ce5a0e028ea3dc0cf4720e74d15324;hpb=51cf18a50c67ce904cde4a869e434d06b209394a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4168516..cd9c533 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.
  * 
@@ -20,20 +20,72 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.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.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.Set;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
 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.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.commands.CommandI;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.commands.OrderCommand;
 import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
@@ -46,17 +98,19 @@ 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.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
-import jalview.io.FeaturesFile;
+import jalview.io.BioJsHTMLOutput;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
-import jalview.io.HTMLOutput;
+import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -82,58 +136,14 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 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;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.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;
-
 /**
  * DOCUMENT ME!
  * 
@@ -144,19 +154,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI
 {
 
-  /** 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
@@ -229,6 +240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this(al, hiddenColumns, width, height, null);
   }
 
+
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
@@ -278,8 +290,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     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);
+      viewport.setHasHiddenRows(true);
+    }
+    alignPanel = new AlignmentPanel(this, viewport);
+    addAlignmentPanel(alignPanel, true);
+    init();
+  }
+
+
   /**
-   * Make a new AlignFrame from exisiting alignmentPanels
+   * Make a new AlignFrame from existing alignmentPanels
    * 
    * @param ap
    *          AlignmentPanel
@@ -300,6 +335,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -334,9 +371,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
     buildTreeMenu();
-    buildShowHideAnnotationMenus();
     
-    if (viewport.wrapAlignment)
+    if (viewport.getWrapAlignment())
     {
       wrapMenuItem_actionPerformed(null);
     }
@@ -348,6 +384,76 @@ 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();
+
+                }
+              }
+            });
+    formatMenu.add(vsel);
+
   }
 
   /**
@@ -362,10 +468,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void setFileName(String file, String 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()
@@ -378,7 +488,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
                 && Character.isDigit(evt.getKeyChar()))
-          alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+        {
+          alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
+        }
 
         switch (evt.getKeyCode())
         {
@@ -390,38 +502,54 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
         case KeyEvent.VK_DOWN:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(false);
+          }
           if (viewport.cursorMode)
-            alignPanel.seqPanel.moveCursor(0, 1);
+          {
+            alignPanel.getSeqPanel().moveCursor(0, 1);
+          }
           break;
 
         case KeyEvent.VK_UP:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             moveSelectedSequences(true);
+          }
           if (viewport.cursorMode)
-            alignPanel.seqPanel.moveCursor(0, -1);
+          {
+            alignPanel.getSeqPanel().moveCursor(0, -1);
+          }
 
           break;
 
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
-            slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+          {
+            slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1());
+          }
           else
-            alignPanel.seqPanel.moveCursor(-1, 0);
+          {
+            alignPanel.getSeqPanel().moveCursor(-1, 0);
+          }
 
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
-            slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+          {
+            slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
+          }
           else
-            alignPanel.seqPanel.moveCursor(1, 0);
+          {
+            alignPanel.getSeqPanel().moveCursor(1, 0);
+          }
           break;
 
         case KeyEvent.VK_SPACE:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
           break;
@@ -445,7 +573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
+            alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
                     || evt.isShiftDown() || evt.isAltDown());
           }
 
@@ -454,19 +582,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_S:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRow();
+            alignPanel.getSeqPanel().setCursorRow();
           }
           break;
         case KeyEvent.VK_C:
           if (viewport.cursorMode && !evt.isControlDown())
           {
-            alignPanel.seqPanel.setCursorColumn();
+            alignPanel.getSeqPanel().setCursorColumn();
           }
           break;
         case KeyEvent.VK_P:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorPosition();
+            alignPanel.getSeqPanel().setCursorPosition();
           }
           break;
 
@@ -474,20 +602,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_COMMA:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setCursorRowAndColumn();
+            alignPanel.getSeqPanel().setCursorRowAndColumn();
           }
           break;
 
         case KeyEvent.VK_Q:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(true);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
           }
           break;
         case KeyEvent.VK_M:
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.setSelectionAreaAtCursor(false);
+            alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
           }
           break;
 
@@ -498,23 +626,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-            alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
+            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
           }
-          alignPanel.seqPanel.seqCanvas.repaint();
+          alignPanel.getSeqPanel().seqCanvas.repaint();
           break;
 
         case KeyEvent.VK_F1:
           try
           {
-            ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
-            java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
-                    "help/help");
-            javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
-
-            javax.help.HelpBroker hb = hs.createHelpBroker();
-            hb.setCurrentID("home");
-            hb.setDisplayed(true);
+            Help.showHelpWindow();
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -528,7 +649,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           break;
         }
         case KeyEvent.VK_PAGE_UP:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(true);
           }
@@ -539,7 +660,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
-          if (viewport.wrapAlignment)
+          if (viewport.getWrapAlignment())
           {
             alignPanel.scrollUp(false);
           }
@@ -559,14 +680,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
+          {
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
+          }
           break;
         }
       }
@@ -579,7 +704,7 @@ 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());
 
@@ -622,7 +747,7 @@ 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);
   }
@@ -683,6 +808,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }).start();
   }
 
+  /**
+   * Configure menu items that vary according to whether the alignment is
+   * nucleotide or protein
+   * 
+   * @param nucleotide
+   */
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible(nucleotide);
@@ -691,16 +822,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     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(MessageManager
+            .getString(nucleotide ? "label.protein" : "label.nucleotide"));
+    setColourSelected(jalview.bin.Cache.getDefault(
+            nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+                    : Preferences.DEFAULT_COLOUR_PROT, "None"));
   }
 
   /**
-   * 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.
    */
@@ -719,20 +849,27 @@ 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());
     conservationMenuItem.setSelected(av.getConservationSelected());
     seqLimits.setSelected(av.getShowJVSuffix());
-    idRightAlign.setSelected(av.rightAlignIds);
-    centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
-    renderGapsMenuItem.setSelected(av.renderGaps);
-    wrapMenuItem.setSelected(av.wrapAlignment);
-    scaleAbove.setVisible(av.wrapAlignment);
-    scaleLeft.setVisible(av.wrapAlignment);
-    scaleRight.setVisible(av.wrapAlignment);
-    annotationPanelMenuItem.setState(av.showAnnotation);
-    viewBoxesMenuItem.setSelected(av.showBoxes);
-    viewTextMenuItem.setSelected(av.showText);
+    idRightAlign.setSelected(av.isRightAlignIds());
+    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
+     */
+    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    viewBoxesMenuItem.setSelected(av.getShowBoxes());
+    viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
     showGroupConsensus.setSelected(av.isShowGroupConsensus());
     showGroupConservation.setSelected(av.isShowGroupConservation());
@@ -743,11 +880,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
-    showSeqFeatures.setSelected(av.showSequenceFeatures);
-    hiddenMarkers.setState(av.showHiddenMarkers);
+    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
+    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);
@@ -758,9 +895,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     updateEditMenuBar();
   }
 
-  // methods for implementing IProgressIndicator
-  // need to refactor to a reusable stub class
-  Hashtable progressBars, progressBarHandlers;
+  private IProgressIndicator progressBar;
 
   /*
    * (non-Javadoc)
@@ -770,82 +905,14 @@ 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(
-              "call setProgressBar before registering the progress bar's 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(
-                  "Cancelled "
-                          + ((JLabel) progressPanel.getComponent(0))
-                                  .getText(), id);
-        }
-      });
-      progressPanel.add(cancel, BorderLayout.EAST);
-    }
+    progressBar.registerHandler(id, handler);
   }
 
   /**
@@ -855,18 +922,14 @@ 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
@@ -878,7 +941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public FeatureRenderer getFeatureRenderer()
   {
-    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+    return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
   }
 
   @Override
@@ -1004,7 +1067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file");
+    chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -1012,7 +1075,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       currentFileFormat = chooser.getSelectedFormat();
-      if (currentFileFormat == null)
+      while (currentFileFormat == null)
       {
         JOptionPane
                 .showInternalMessageDialog(
@@ -1022,8 +1085,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         MessageManager
                                 .getString("label.file_format_not_specified"),
                         JOptionPane.WARNING_MESSAGE);
+        currentFileFormat = chooser.getSelectedFormat();
         value = chooser.showSaveDialog(this);
-        return;
+        if (value != JalviewFileChooser.APPROVE_OPTION)
+        {
+          return;
+        }
       }
 
       fileName = chooser.getSelectedFile().getPath();
@@ -1055,10 +1122,10 @@ 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[]
+              "label.successfully_saved_to_file_in_format", new Object[]
               { fileName, format }));
 
     }
@@ -1073,30 +1140,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         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();
+      ExportData exportData = getAlignmentForExport();
+      FormatAdapter f = new FormatAdapter(viewport);
       String output = f.formatSequences(format,
-              viewport.getAlignment(), // class cast exceptions will
+              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)
@@ -1115,7 +1165,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
                   "label.successfully_saved_to_file_in_format",
-                  new String[]
+                  new Object[]
                   { fileName, format }));
         } catch (Exception ex)
         {
@@ -1128,7 +1178,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!success)
     {
       JOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new String[]
+              .formatMessage("label.couldnt_save_file", new Object[]
               { fileName }), MessageManager
               .getString("label.error_saving_file"),
               JOptionPane.WARNING_MESSAGE);
@@ -1137,6 +1187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return success;
   }
 
+
   private void warningMessage(String warning, String title)
   {
     if (new jalview.util.Platform().isHeadless())
@@ -1161,9 +1212,45 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void outputText_actionPerformed(ActionEvent e)
   {
+
+    ExportData exportData = getAlignmentForExport();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+
+    try
+    {
+      cap.setText(new FormatAdapter(viewport).formatSequences(
+              e.getActionCommand(),
+ exportData.getAlignment(),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
+              viewport.getColumnSelection()));
+      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+              "label.alignment_output_command", new Object[]
+              { e.getActionCommand() }), 600, 500);
+    } catch (OutOfMemoryError oom)
+    {
+      new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
+      cap.dispose();
+    }
+
+  }
+
+  public ExportData getAlignmentForExport()
+  {
+    AlignmentI alignmentToExport = null;
     String[] omitHidden = null;
+    int[] alignmentStartEnd = new int[2];
+    FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
+    viewport.setFeatureRenderer(fr);
+    HiddenSequences hiddenSeqs = viewport.getAlignment()
+            .getHiddenSequences();
 
-    if (viewport.hasHiddenColumns())
+
+    alignmentToExport = viewport.getAlignment();
+    alignmentStartEnd = new int[]
+    { 0, alignmentToExport.getWidth() - 1 };
+
+    if (viewport.hasHiddenColumns() || hiddenSeqs.getSize() > 0)
     {
       int reply = JOptionPane
               .showInternalConfirmDialog(
@@ -1177,27 +1264,83 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (reply == JOptionPane.YES_OPTION)
       {
+        // export only visible region
         omitHidden = viewport.getViewAsString(false);
+        alignmentToExport = viewport.getAlignment();
+        alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+                .getColumnSelection().getHiddenColumns());
+        viewport.setIncludeHiddenRegion(false);
+      }
+      else
+      {
+        // export all region including visible
+        alignmentToExport = hiddenSeqs.getFullAlignment();
+        viewport.setIncludeHiddenRegion(true);
       }
     }
 
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    cap.setForInput(null);
+    return new ExportData(alignmentToExport, omitHidden, alignmentStartEnd);
+  }
 
-    try
+  private static int[] getStartEnd(int[] aligmentStartEnd,
+          List<int[]> hiddenCols)
+  {
+    int startPos = aligmentStartEnd[0];
+    int endPos = aligmentStartEnd[1];
+
+    int[] lowestRange = new int[2];
+    int[] higestRange = new int[2];
+
+    for (int[] hiddenCol : hiddenCols)
     {
-      cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-              viewport.getAlignment(), omitHidden,
-              viewport.getColumnSelection()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.alignment_output_command", new String[]
-              { e.getActionCommand() }), 600, 500);
-    } catch (OutOfMemoryError oom)
+      // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
+
+      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+    }
+    // System.out.println("min : " + lowestRange[0] + "-" + lowestRange[1]);
+    // System.out.println("max : " + higestRange[0] + "-" + higestRange[1]);
+
+    if (lowestRange[0] == 0 && lowestRange[1] == 0)
     {
-      new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
-      cap.dispose();
+      startPos = aligmentStartEnd[0];
+    }
+    else
+    {
+      startPos = lowestRange[1] + 1;
+    }
+
+    if (higestRange[0] == 0 && higestRange[1] == 0)
+    {
+      endPos = aligmentStartEnd[1];
+    }
+    else
+    {
+      endPos = higestRange[0];
     }
 
+    // System.out.println("Export range : " + minPos + " - " + maxPos);
+    return new int[]
+    { startPos, endPos };
+  }
+
+  public static void main(String[] args)
+  {
+    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
+    hiddenCols.add(new int[]
+    { 0, 4 });
+    hiddenCols.add(new int[]
+    { 6, 9 });
+    hiddenCols.add(new int[]
+    { 11, 12 });
+    hiddenCols.add(new int[]
+    { 33, 33 });
+    hiddenCols.add(new int[]
+    { 45, 50 });
+
+    int[] x = getStartEnd(new int[]
+    { 0, 50 }, hiddenCols);
+    // System.out.println("Export range : " + x[0] + " - " + x[1]);
   }
 
   /**
@@ -1209,11 +1352,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    new HTMLOutput(alignPanel,
-            alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+    // new HTMLOutput(alignPanel,
+    // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+    // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    new HtmlSvgOutput(null, alignPanel);
   }
 
+  @Override
+  public void bioJSMenuItem_actionPerformed(ActionEvent e)
+  {
+    BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel,
+            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+    bjs.exportJalviewAlignmentAsBioJsHtmlFile();
+  }
   public void createImageMap(File file, String image)
   {
     alignPanel.makePNGImageMap(file, image);
@@ -1243,6 +1394,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.makeEPS(f);
   }
 
+  public void createSVG(File f)
+  {
+    alignPanel.makeSVG(f);
+  }
   @Override
   public void pageSetup_actionPerformed(ActionEvent e)
   {
@@ -1273,11 +1428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
-    new AnnotationExporter().exportAnnotations(alignPanel,
-            viewport.showAnnotation ? viewport.getAlignment()
-                    .getAlignmentAnnotation() : null, viewport
-                    .getAlignment().getGroups(), ((Alignment) viewport
-                    .getAlignment()).alignmentProperties);
+    new AnnotationExporter().exportAnnotations(alignPanel);
   }
 
   @Override
@@ -1329,7 +1480,7 @@ 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();
             }
           }
@@ -1351,22 +1502,17 @@ 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();
@@ -1386,12 +1532,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   void updateEditMenuBar()
   {
 
-    if (viewport.historyList.size() > 0)
+    if (viewport.getHistoryList().size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) viewport.historyList.peek();
+      CommandI command = viewport.getHistoryList().peek();
       undoMenuItem.setText(MessageManager.formatMessage(
-              "label.undo_command", new String[]
+              "label.undo_command", new Object[]
               { command.getDescription() }));
     }
     else
@@ -1400,13 +1546,13 @@ 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 = (CommandI) viewport.redoList.peek();
+      CommandI command = viewport.getRedoList().peek();
       redoMenuItem.setText(MessageManager.formatMessage(
-              "label.redo_command", new String[]
+              "label.redo_command", new Object[]
               { command.getDescription() }));
     }
     else
@@ -1420,8 +1566,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (command.getSize() > 0)
     {
-      viewport.historyList.push(command);
-      viewport.redoList.clear();
+      viewport.addToHistoryList(command);
+      viewport.clearRedoList();
       updateEditMenuBar();
       viewport.updateHiddenColumns();
       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
@@ -1439,11 +1585,11 @@ 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;
     }
@@ -1464,13 +1610,15 @@ 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 = (CommandI) 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)
@@ -1500,16 +1648,16 @@ 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 = (CommandI) 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)
@@ -1531,9 +1679,9 @@ 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
@@ -1542,16 +1690,16 @@ 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;
           }
         }
@@ -1594,11 +1742,11 @@ 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(
-              alignPanel.seqPanel.seqCanvas.cursorY));
+              alignPanel.getSeqPanel().seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() != viewport
@@ -1613,42 +1761,58 @@ 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)))
-        invertGroup.add(viewport.getAlignment().getSequenceAt(i));
+      if (!sg.contains(seq))
+      {
+        invertGroup.add(seq);
+      }
     }
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
 
     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;
     if (right)
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
               size, viewport.getGapCharacter());
+    }
     else
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
               size, viewport.getGapCharacter());
+    }
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
     {
       if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor(size, 0);
+      {
+        alignPanel.getSeqPanel().moveCursor(size, 0);
+      }
       else
+      {
         groupAdjustment = size;
+      }
     }
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
-        alignPanel.seqPanel.moveCursor(-size, 0);
+      {
+        alignPanel.getSeqPanel().moveCursor(-size, 0);
+      }
       else
+      {
         groupAdjustment = -size;
+      }
     }
 
     if (groupAdjustment != 0)
@@ -1660,16 +1824,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     boolean appendHistoryItem = false;
-    if (viewport.historyList != null && viewport.historyList.size() > 0
-            && viewport.historyList.peek() instanceof SlideSequencesCommand)
+    Deque<CommandI> historyList = viewport.getHistoryList();
+    if (historyList != null
+            && historyList.size() > 0
+            && historyList.peek() instanceof SlideSequencesCommand)
     {
       appendHistoryItem = ssc
-              .appendSlideCommand((SlideSequencesCommand) viewport.historyList
+              .appendSlideCommand((SlideSequencesCommand) historyList
                       .peek());
     }
 
     if (!appendHistoryItem)
+    {
       addHistoryItem(ssc);
+    }
 
     repaint();
   }
@@ -1699,7 +1867,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     String output = new FormatAdapter().formatSequences("Fasta", seqs,
-            omitHidden);
+            omitHidden, null);
 
     StringSelection ss = new StringSelection(output);
 
@@ -1719,20 +1887,17 @@ 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[]
+          hiddenColumns.add(new int[]
           { region[0] - hiddenOffset, region[1] - hiddenOffset });
         }
       }
@@ -1741,7 +1906,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.jalviewClipboard = new Object[]
     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
     statusBar.setText(MessageManager.formatMessage(
-            "label.copied_sequences_to_clipboard", new String[]
+            "label.copied_sequences_to_clipboard", new Object[]
             { Integer.valueOf(seqs.length).toString() }));
   }
 
@@ -1949,7 +2114,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // /////
         // ADD HISTORY ITEM
         //
-        addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.add_sequences"),
+                Action.PASTE,
                 sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
@@ -2004,7 +2171,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
             if (sann == null)
+            {
               continue;
+            }
             for (int avnum = 0; avnum < alview.length; avnum++)
             {
               if (alview[avnum] != alignment)
@@ -2035,7 +2204,7 @@ 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);
           }
@@ -2055,19 +2224,18 @@ 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]);
           }
         }
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
-        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+        af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
                 .transferSettings(
-                        alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                        alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
         // TODO: maintain provenance of an alignment, rather than just make the
         // title a concatenation of operations.
@@ -2115,19 +2283,18 @@ 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]);
         }
       }
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
               .transferSettings(
-                      alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+                      alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 
       // TODO: maintain provenance of an alignment, rather than just make the
       // title a concatenation of operations.
@@ -2184,32 +2351,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Vector seqs = new Vector();
-    SequenceI seq;
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      seq = sg.getSequenceAt(i);
-      seqs.addElement(seq);
-    }
-
-    // If the cut affects all sequences, 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)
+      {
+        return;
+      }
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
     }
 
-    SequenceI[] cut = new SequenceI[seqs.size()];
-    for (int i = 0; i < seqs.size(); i++)
-    {
-      cut[i] = (SequenceI) seqs.elementAt(i);
-    }
+    SequenceI[] cut = sg.getSequences()
+            .toArray(new SequenceI[sg.getSize()]);
 
-    /*
-     * //ADD HISTORY ITEM
-     */
-    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
-            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.cut_sequences"), Action.CUT,
+            cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
             viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
@@ -2280,14 +2446,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (viewport.cursorMode)
     {
-      alignPanel.seqPanel.keyboardNo1 = null;
-      alignPanel.seqPanel.keyboardNo2 = null;
+      alignPanel.getSeqPanel().keyboardNo1 = null;
+      alignPanel.getSeqPanel().keyboardNo2 = null;
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
-    alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.idPanel.idCanvas.searchResults = null;
+    alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null);
+    alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
@@ -2448,7 +2614,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     addHistoryItem(removeGapCols);
 
     statusBar.setText(MessageManager.formatMessage(
-            "label.removed_empty_columns", new String[]
+            "label.removed_empty_columns", new Object[]
             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
     // This is to maintain viewport position on first residue
@@ -2519,16 +2685,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .getSequences());
   }
 
-  // else
-  {
-    // if (justifySeqs>0)
-    {
-      // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
-    }
-  }
-
-  // }
-
   /**
    * DOCUMENT ME!
    * 
@@ -2541,78 +2697,84 @@ 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.
+   * Create a new view of the current alignment.
    */
-  public AlignmentPanel newView(boolean copyAnnotation)
-  {
-    return newView(null, copyAnnotation);
-  }
-
-  /**
-   * 
-   * @param viewTitle
-   *          title of newly created view
-   * @return new alignment panel, already displayed.
-   */
-  public AlignmentPanel newView(String viewTitle)
+  @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, mappings.
+     */
+    newap.av.setHistoryList(viewport.getHistoryList());
+    newap.av.setRedoList(viewport.getRedoList());
+    newap.av.getAlignment().setCodonFrames(
+            viewport.getAlignment().getCodonFrames());
+
+    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)
     {
-      viewTitle = "View";
+      viewTitle = MessageManager.getString("action.view");
       addFirstIndex = true;
     }
     else
@@ -2620,45 +2782,55 @@ 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++)
-    {
-      if (comps.elementAt(i) instanceof AlignmentPanel)
-      {
-        AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
-        if (!existingNames.contains(ap.av.viewName))
-        {
-          existingNames.addElement(ap.av.viewName);
-        }
-      }
-    }
+
+    List<String> existingNames = getExistingViewNames(comps);
 
     while (existingNames.contains(newViewName))
     {
       newViewName = viewTitle + " " + (++index);
     }
+    return newViewName;
+  }
 
-    newap.av.viewName = newViewName;
-
-    addAlignmentPanel(newap, true);
-    newap.alignmentChanged();
-
-    if (alignPanels.size() == 2)
+  /**
+   * 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)
     {
-      viewport.gatherViewsHere = true;
+      if (comp instanceof AlignmentPanel)
+      {
+        AlignmentPanel ap = (AlignmentPanel) comp;
+        if (!existingNames.contains(ap.av.viewName))
+        {
+          existingNames.add(ap.av.viewName);
+        }
+      }
     }
-    tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
-    return newap;
+    return existingNames;
   }
 
+  /**
+   * Explode tabbed views into separate windows.
+   */
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
     Desktop.instance.explodeViews(this);
   }
 
+  /**
+   * Gather views in separate windows back into a tabbed presentation.
+   */
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
@@ -2688,7 +2860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowJVSuffix(seqLimits.isSelected());
 
-    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
+    alignPanel.getIdPanel().getIdCanvas().setPreferredSize(alignPanel
             .calculateIdWidth());
     alignPanel.paintAlignment(true);
   }
@@ -2696,14 +2868,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void idRightAlign_actionPerformed(ActionEvent e)
   {
-    viewport.rightAlignIds = idRightAlign.isSelected();
+    viewport.setRightAlignIds(idRightAlign.isSelected());
     alignPanel.paintAlignment(true);
   }
 
   @Override
   public void centreColumnLabels_actionPerformed(ActionEvent e)
   {
-    viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
+    viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
     alignPanel.paintAlignment(true);
   }
 
@@ -2715,10 +2887,16 @@ 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.seqPanel.seqCanvas.searchResults, false);
+              alignPanel.getSeqPanel().seqCanvas.searchResults, false);
     }
   }
 
@@ -2748,7 +2926,7 @@ 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
@@ -2768,7 +2946,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelSequences_actionPerformed(ActionEvent e)
   {
     viewport.hideAllSelectedSeqs();
-    alignPanel.paintAlignment(true);
+//    alignPanel.paintAlignment(true);
   }
 
   /**
@@ -2981,6 +3159,12 @@ 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)
@@ -3025,7 +3209,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
             .isSelected());
-    if (viewport.getShowSequenceFeaturesHeight())
+    if (viewport.isShowSequenceFeaturesHeight())
     {
       // ensure we're actually displaying features
       viewport.setShowSequenceFeatures(true);
@@ -3039,16 +3223,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on toggle of the 'Show annotations' menu item. This shows or hides
+   * the annotations panel as a whole.
+   * 
+   * The options to show/hide all annotations should be enabled when the panel
+   * is shown, and disabled when the panel is hidden.
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
-    alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
+    final boolean setVisible = annotationPanelMenuItem.isSelected();
+    viewport.setShowAnnotation(setVisible);
+    this.showAllSeqAnnotations.setEnabled(setVisible);
+    this.hideAllSeqAnnotations.setEnabled(setVisible);
+    this.showAllAlAnnotations.setEnabled(setVisible);
+    this.hideAllAlAnnotations.setEnabled(setVisible);
+    alignPanel.updateLayout();
   }
 
   @Override
@@ -3059,13 +3251,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
             .formatAsHtml();
     editPane.setText(MessageManager.formatMessage("label.html_content",
-            new String[]
+            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[]
+    Desktop.addInternalFrame(frame, MessageManager.formatMessage(
+            "label.alignment_properties", new Object[]
             { getTitle() }), 500, 400);
   }
 
@@ -3087,7 +3279,7 @@ 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[]
+            "label.overview_params", new Object[]
             { this.getTitle() }), frame.getWidth(), frame.getHeight());
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -3250,6 +3442,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void annotationColumn_actionPerformed(ActionEvent e)
+  {
+    new AnnotationColumnChooser(viewport, alignPanel);
+  }
+
+  @Override
   public void rnahelicesColour_actionPerformed(ActionEvent e)
   {
     new RNAHelicesColourChooser(viewport, alignPanel);
@@ -3284,11 +3482,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-        cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
       }
       else
       {
-        cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+        cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
       }
 
       if (viewport.getConservationSelected())
@@ -3351,7 +3549,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 || cs instanceof PIDColourScheme
                 || cs instanceof Blosum62ColourScheme)
         {
-          sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
 
           sg.cs.setConsensus(AAFrequency.calculate(
                   sg.getSequences(viewport.getHiddenRepSequences()),
@@ -3359,7 +3557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
         else
         {
-          sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
+          sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
         }
 
         if (viewport.getConservationSelected())
@@ -3488,8 +3686,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
 
     Component[] menuItems = colourMenu.getMenuComponents();
-    int i, iSize = menuItems.length;
-    for (i = 0; i < iSize; i++)
+    int iSize = menuItems.length;
+    for (int i = 0; i < iSize; i++)
     {
       if (menuItems[i].getName() != null
               && menuItems[i].getName().equals("USER_DEFINED"))
@@ -3750,7 +3948,7 @@ 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");
   }
 
   /**
@@ -3762,7 +3960,7 @@ 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");
   }
 
   /**
@@ -3774,7 +3972,7 @@ 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");
   }
 
   /**
@@ -3786,7 +3984,7 @@ 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");
   }
 
   /**
@@ -3799,7 +3997,7 @@ 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;
 
@@ -3890,7 +4088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
-    final JMenuItem item = new JMenuItem("by " + 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()
     {
@@ -4014,7 +4212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       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);
@@ -4030,7 +4228,7 @@ 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);
@@ -4040,21 +4238,18 @@ 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;
@@ -4062,17 +4257,15 @@ 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));
 
         }
@@ -4119,16 +4312,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.oneseq_msainput_selection"),
+              MessageManager.getString("label.invalid_selection"),
+              JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+    }
     else
     {
-      /*
-       * Vector seqs = viewport.getAlignment().getSequences();
-       * 
-       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
-       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
-       * seqs.elementAt(i); } }
-       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -4176,7 +4373,7 @@ 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(
@@ -4308,7 +4505,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       } catch (Exception e)
       {
       }
-      ;
     }
     final AlignFrame me = this;
     buildingMenu = true;
@@ -4340,6 +4536,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           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)
@@ -4453,14 +4659,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         .debug("Exception during web service menu building process.",
                                 e);
               }
-              ;
             }
           });
         } catch (Exception e)
         {
         }
-        ;
-
         buildingMenu = false;
       }
     }).start();
@@ -4572,7 +4775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           public void actionPerformed(ActionEvent e)
           {
             // TODO: new thread for this call with vis-delay
-            af.showProductsFor(af.viewport.getSequenceSelection(), ds,
+            af.showProductsFor(af.viewport.getSequenceSelection(),
                     isRegSel, dna, source);
           }
 
@@ -4591,14 +4794,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return showp;
   }
 
-  protected void showProductsFor(SequenceI[] sel, Alignment ds,
-          boolean isRegSel, boolean dna, String source)
+  protected void showProductsFor(final SequenceI[] sel,
+          final boolean isRegSel, final boolean dna, final 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()
     {
 
@@ -4606,15 +4804,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void run()
       {
         final long sttime = System.currentTimeMillis();
-        ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
+        AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+                "status.searching_for_sequences_from", new Object[]
+                { source }), sttime);
         try
         {
-          Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
-          // our local
-          // dataset
-          // reference
+          // update our local dataset reference
+          Alignment ds = AlignFrame.this.getViewport().getAlignment()
+                  .getDataset();
           Alignment prods = CrossRef
-                  .findXrefSequences(fsel, fdna, fsrc, ds);
+                  .findXrefSequences(sel, dna, source, ds);
           if (prods != null)
           {
             SequenceI[] sprods = new SequenceI[prods.getHeight()];
@@ -4624,29 +4823,81 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               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++)
+
+            /*
+             * Copy dna-to-protein mappings to new alignment
+             */
+            // TODO 1: no mappings are set up for EMBL product
+            // TODO 2: if they were, should add them to protein alignment, not
+            // dna
+            Set<AlignedCodonFrame> cf = prods.getCodonFrames();
+            for (AlignedCodonFrame acf : cf)
             {
-              al.addCodonFrame(cf[s]);
-              cf[s] = null;
+              al.addCodonFrame(acf);
             }
             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
                     DEFAULT_HEIGHT);
-            String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
-                    + " for " + ((fisRegSel) ? "selected region of " : "")
+            String newtitle = "" + ((dna) ? "Proteins" : "Nucleotides")
+                    + " for " + ((isRegSel) ? "selected region of " : "")
                     + getTitle();
-            Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
-                    DEFAULT_HEIGHT);
+            naf.setTitle(newtitle);
+
+            // temporary flag until SplitFrame is released
+            boolean asSplitFrame = Cache.getDefault(
+                    Preferences.ENABLE_SPLIT_FRAME, false);
+            if (asSplitFrame)
+            {
+              /*
+               * Make a copy of this alignment (sharing the same dataset
+               * sequences). If we are DNA, drop introns and update mappings
+               */
+              AlignmentI copyAlignment = null;
+              final SequenceI[] sequenceSelection = AlignFrame.this.viewport
+                      .getSequenceSelection();
+              if (dna)
+              {
+                copyAlignment = AlignmentUtils.makeExonAlignment(
+                        sequenceSelection, cf);
+                al.getCodonFrames().clear();
+                al.getCodonFrames().addAll(cf);
+                final StructureSelectionManager ssm = StructureSelectionManager
+                        .getStructureSelectionManager(Desktop.instance);
+                ssm.addMappings(cf);
+              }
+              else
+              {
+                copyAlignment = new Alignment(new Alignment(
+                        sequenceSelection));
+              }
+              AlignFrame copyThis = new AlignFrame(copyAlignment,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+              copyThis.setTitle(AlignFrame.this.getTitle());
+              // SplitFrame with dna above, protein below
+              SplitFrame sf = new SplitFrame(dna ? copyThis : naf,
+                      dna ? naf : copyThis);
+              naf.setVisible(true);
+              copyThis.setVisible(true);
+              String linkedTitle = MessageManager
+                      .getString("label.linked_view_title");
+              Desktop.addInternalFrame(sf, linkedTitle, -1, -1);
+            }
+            else
+            {
+              Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+                      DEFAULT_HEIGHT);
+            }
           }
           else
           {
             System.err.println("No Sequences generated for xRef type "
-                    + fsrc);
+                    + source);
           }
         } catch (Exception e)
         {
@@ -4660,7 +4911,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           jalview.bin.Cache.log.error("Error when finding crossreferences",
                   e);
         }
-        ths.setProgressBar("Finished searching for sequences from " + fsrc,
+        AlignFrame.this.setProgressBar(MessageManager.formatMessage(
+                "status.finished_searching_for_sequences_from",
+                new Object[]
+                { source }),
                 sttime);
       }
 
@@ -4686,137 +4940,103 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  @Override
-  public void showProducts_actionPerformed(ActionEvent e)
-  {
-    // /////////////////////////////
-    // 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);
-    }
-  }
-
+  /**
+   * 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 title = MessageManager
+              .getString("label.implementation_error")
+              + MessageManager.getString("translation_failed");
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+              JOptionPane.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 title = MessageManager
+              .getString("label.translation_failed");
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+              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);
+      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, false))
+      {
+        final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
+        viewport.openSplitFrame(af, new Alignment(seqs),
+                al.getCodonFrames());
+      }
+      else
+      {
+        Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
+                DEFAULT_HEIGHT);
+      }
     }
   }
 
   /**
+   * Set the file format
+   * 
+   * @param fileFormat
+   */
+  public void setFileFormat(String fileFormat)
+  {
+    this.currentFileFormat = fileFormat;
+  }
+
+  /**
    * Try to load a features file onto the alignment.
    * 
    * @param file
    *          contents or path to retrieve file
    * @param type
    *          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)
   {
-    boolean featuresFile = false;
-    try
-    {
-      featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
-              .getFeatureRenderer().featureColours, false,
-              jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
+    return avc.parseFeaturesFile(file, type,
+            jalview.bin.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.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      if (alignPanel.seqPanel.seqCanvas.fr != null)
-      {
-        // update the min/max ranges where necessary
-        alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
-      }
-      if (featureSettings != null)
-      {
-        featureSettings.setTableData();
-      }
-      alignPanel.paintAlignment(true);
     }
 
-    return featuresFile;
-  }
 
+  }
   @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
@@ -4967,7 +5187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   MessageManager
                                           .formatMessage(
                                                   "label.automatically_associate_pdb_files_with_sequences_same_name",
-                                                  new String[]
+                                                  new Object[]
                                                   { Integer.valueOf(
                                                           filesmatched
                                                                   .size())
@@ -4986,7 +5206,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 PDBEntry pe = new AssociatePdbFileWithSeq()
                         .associatePdbWithSeq((String) fm[0],
-                                (String) fm[1], toassoc, false);
+                                (String) fm[1], toassoc, false,
+                                Desktop.instance);
                 if (pe != null)
                 {
                   System.err.println("Associated file : "
@@ -5006,14 +5227,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
                           .showConfirmDialog(
                                   this,
-                                  MessageManager
+                                  "<html>"+MessageManager
                                           .formatMessage(
                                                   "label.ignore_unmatched_dropped_files_info",
-                                                  new String[]
+                                                  new Object[]
                                                   { Integer.valueOf(
                                                           filesnotmatched
                                                                   .size())
-                                                          .toString() }),
+                                                          .toString() })+"</html>",
                                   MessageManager
                                           .getString("label.ignore_unmatched_dropped_files"),
                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
@@ -5056,7 +5277,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // try to parse as annotation.
       boolean isAnnotation = (format == null || format
               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
-              .readAnnotationFile(viewport.getAlignment(), file, protocol)
+              .annotateAlignmentView(viewport, file, protocol)
               : false;
 
       if (!isAnnotation)
@@ -5117,8 +5338,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                     file, protocol);
-            new JnetAnnotationMaker().add_annotation(predictions,
+            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
@@ -5189,31 +5416,55 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  /**
+   * 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);
     }
+
+    /*
+     * 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))
     {
-      String reply = JOptionPane.showInternalInputDialog(this,
-              MessageManager.getString("label.enter_view_name"),
-              MessageManager.getString("label.enter_view_name"),
+      String msg = MessageManager.getString("label.enter_view_name");
+      String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
               JOptionPane.QUESTION_MESSAGE);
 
       if (reply != null)
       {
         viewport.viewName = reply;
+        // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
     }
@@ -5253,7 +5504,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
-    viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
+    viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
   }
 
   /*
@@ -5265,7 +5516,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
-    viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
+    viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
   }
 
   /**
@@ -5274,7 +5525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param av
    */
-  public boolean closeView(AlignViewport av)
+  public boolean closeView(AlignViewportI av)
   {
     if (viewport == av)
     {
@@ -5420,9 +5671,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
 
                 });
-                fetchr.setToolTipText("<html>"
-                        + JvSwingUtils.wrapTooltip("Retrieve from "
-                                + src.getDbName()) + "<html>");
+                fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{src.getDbName()})));
                 dfetch.add(fetchr);
                 comp++;
               }
@@ -5433,7 +5682,7 @@ 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[]
+                        "label.fetch_all_param", new Object[]
                         { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
@@ -5455,15 +5704,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                 });
 
-                fetchr.setToolTipText("<html>"
-                        + JvSwingUtils.wrapTooltip("Retrieve from all "
-                                + otherdb.size() + " sources in "
-                                + src.getDbSource() + "<br>First is :"
-                                + src.getDbName()) + "<html>");
+                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("Sources from " + src.getDbSource());
+                ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new Object[]{src.getDbSource()}));
                 icomp = 0;
                 String imname = null;
                 int i = 0;
@@ -5476,7 +5721,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           0, 10) + "..." : dbname;
                   if (imname == null)
                   {
-                    imname = "from '" + sname + "'";
+                    imname = MessageManager.formatMessage("label.from_msname", new Object[]{sname});
                   }
                   fetchr = new JMenuItem(msname);
                   final DbSourceProxy[] dassrc =
@@ -5503,8 +5748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
                   });
                   fetchr.setToolTipText("<html>"
-                          + JvSwingUtils.wrapTooltip("Retrieve from "
-                                  + dbname) + "</html>");
+                          + MessageManager.formatMessage("label.fetch_retrieve_from", new Object[]{dbname}));
                   ifetch.add(fetchr);
                   ++i;
                   if (++icomp >= mcomp || i == (otherdb.size()))
@@ -5561,8 +5805,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public void setShowSeqFeatures(boolean b)
   {
-    showSeqFeatures.setSelected(true);
-    viewport.setShowSequenceFeatures(true);
+    showSeqFeatures.setSelected(b);
+    viewport.setShowSequenceFeatures(b);
   }
 
   /*
@@ -5668,6 +5912,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       alignPanel.paintAlignment(true);
     }
   }
+  public void clearAlignmentSeqRep()
+  {
+    // TODO refactor alignmentseqrep to controller
+    if (viewport.getAlignment().hasSeqrep()) {
+      viewport.getAlignment().setSeqrep(null);
+      PaintRefresher.Refresh(this, viewport.getSequenceSetId());
+      alignPanel.updateAnnotation();
+      alignPanel.paintAlignment(true);
+    }
+  }
 
   @Override
   protected void createGroup_actionPerformed(ActionEvent e)
@@ -5697,11 +5951,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!viewport.getSequenceSetId().equals(
             alignmentPanel.av.getSequenceSetId()))
     {
-      throw new Error(
-              "Implementation error: cannot show a view from another alignment in an AlignFrame.");
+      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));
@@ -5709,93 +5963,169 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * On menu option, open a panel to allow choice of annotation types to
-   * show/hide.
+   * Action on selection of menu options to Show or Hide annotations.
+   * 
+   * @param visible
+   * @param forSequences
+   *          update sequence-related annotations
+   * @param forAlignment
+   *          update non-sequence-related annotations
    */
   @Override
-  protected void chooseAnnotations_actionPerformed()
-  {
-    new AnnotationChooser(this.alignPanel);
-  }
-
-  /**
-   * Get a list of unique annotation types for the alignment, optionally
-   * restricted to sequence-specific annotations.
-   */
-  protected List<String> getAnnotationTypes(boolean sequenceSpecificOnly)
+  protected void setAnnotationsVisibility(boolean visible,
+          boolean forSequences, boolean forAlignment)
   {
-    // TODO move this to an AlignmentUtils class or similar
-    List<String> types = new ArrayList<String>();
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
-      if (sequenceSpecificOnly && aa.sequenceRef == null)
+      /*
+       * don't display non-positional annotations on an alignment
+       */
+      if (aa.annotations == null)
       {
         continue;
       }
-      String type = aa.label;
-      if (!types.contains(type))
+      boolean apply = (aa.sequenceRef == null && forAlignment)
+              || (aa.sequenceRef != null && forSequences);
+      if (apply)
       {
-        types.add(type);
+        aa.visible = visible;
       }
     }
-    return types;
+    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.alignmentChanged();
   }
 
   /**
-   * Action on selection of an annotation type to Show or Hide.
-   * 
-   * @param type
-   * @param doShow
+   * Store selected annotation sort order for the view and repaint.
    */
   @Override
-  protected void showHideAnnotation_actionPerformed(String type, boolean doShow)
+  protected void sortAnnotations_actionPerformed()
   {
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
+    this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+    this.alignPanel.av
+            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * 
+   * @return alignment panels in this alignment frame
+   */
+  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();
+    Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+    if (mappings == null)
     {
-      if (type.equals(aa.label))
-      {
-        aa.visible = doShow;
+      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);
+        }
       }
     }
-    this.alignPanel.paintAlignment(true);
+    if (cdnaSeqs.size() == 0)
+    {
+      // show a warning dialog no mapped cDNA
+      return;
+    }
+    AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
+            .size()]));
+    AlignFrame 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);
   }
 
   /**
-   * Dynamically build the list of annotation types to show or hide.
+   * Set visibility of dna/protein complement view (available when shown in a
+   * split frame).
+   * 
+   * @param show
    */
   @Override
-  protected void buildShowHideAnnotationMenus()
+  protected void showComplement_actionPerformed(boolean show)
+  {
+    SplitContainerI sf = getSplitViewContainer();
+    if (sf != null) {
+      sf.setComplementVisible(this, show);
+    }
+  }
+
+  public class ExportData
   {
-    showAnnotations.removeAll();
-    hideAnnotations.removeAll();
+    private AlignmentI alignment;
+
+    private String[] omitHidden;
 
-    List<String> types = getAnnotationTypes(false);
-    for (final String type : types)
+    private int[] startEnd;
+
+    public ExportData(AlignmentI align, String[] ommit, int[] startEnd)
     {
-      final JMenuItem showitem = new JMenuItem(type);
-      showitem.addActionListener(new java.awt.event.ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          showHideAnnotation_actionPerformed(type, true);
-        }
-      });
-      showAnnotations.add(showitem);
-      final JMenuItem hideitem = new JMenuItem(type);
-      hideitem.addActionListener(new java.awt.event.ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          showHideAnnotation_actionPerformed(type, false);
-        }
-      });
-      hideAnnotations.add(hideitem);
+      this.alignment = align;
+      this.omitHidden = ommit;
+      this.startEnd = startEnd;
+    }
+
+    public AlignmentI getAlignment()
+    {
+      return alignment;
+    }
+
+    public void setAlignment(AlignmentI alignment)
+    {
+      this.alignment = alignment;
+    }
+
+    public String[] getOmitHidden()
+    {
+      return omitHidden;
+    }
+
+    public void setOmitHidden(String[] omitHidden)
+    {
+      this.omitHidden = omitHidden;
+    }
+
+    public int[] getStartEndPostions()
+    {
+      return startEnd;
+    }
+
+    public void setStartEndPostions(int[] startEnd)
+    {
+      this.startEnd = startEnd;
     }
   }
+
 }
 
 class PrintThread extends Thread