X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=6ce68c3986146ce38cca17b57c819baa4a70149d;hb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;hp=4634142538f449d7efbad6d89c4609a2c03e24b7;hpb=838aac5c22366a99df93de174971ff1ca016f417;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
old mode 100755
new mode 100644
index 4634142..6ce68c3
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,23 +17,81 @@
  */
 package jalview.appletgui;
 
-import java.net.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
+import jalview.io.TCoffeeScoreFile;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
-        ItemListener, KeyListener
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemListener, KeyListener
 {
   public AlignmentPanel alignPanel;
 
@@ -44,11 +102,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   int DEFAULT_HEIGHT = 500;
 
   String jalviewServletURL;
+  
 
-  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
-          String title, boolean embedded)
+  public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)
   {
-
     if (applet != null)
     {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -69,12 +126,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConsensus(alignPanel);
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
-    displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+    displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.getFollowHighlight());
-    showGroupConsensus.setState(viewport.showGroupConsensus);
-    showGroupConservation.setState(viewport.showGroupConservation);
-    showConsensusHistogram.setState(viewport.showConsensusHistogram);
-    showSequenceLogo.setState(viewport.showSequenceLogo);
+    showGroupConsensus.setState(viewport.isShowGroupConsensus());
+    showGroupConservation.setState(viewport.isShowGroupConservation());
+    showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
+    showSequenceLogo.setState(viewport.isShowSequenceLogo());
 
     seqLimits.setState(viewport.showJVSuffix);
 
@@ -131,7 +188,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
 
     }
-
+    if (viewport.getAlignment().isNucleotide())
+    {
+      viewport.updateStrucConsensus(alignPanel);
+      if (viewport.getAlignment().hasRNAStructure())
+      {
+        RNAHelixColour.setEnabled(true);
+      }
+      else {
+        RNAHelixColour.setEnabled(false);
+      }
+    } else {
+      RNAHelixColour.setEnabled(false);
+      purinePyrimidineColour.setEnabled(false);
+    }
     // Some JVMS send keyevents to Top frame or lowest panel,
     // Havent worked out why yet. So add to both this frame and seqCanvas for
     // now
@@ -144,7 +214,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
     alignPanel.alabels.addKeyListener(this);
     createAlignFrameWindow(embedded, title);
-    alignPanel.validate();
+
+    validate();
+    alignPanel.adjustAnnotationHeight();
     alignPanel.paintAlignment(true);
   }
 
@@ -159,20 +231,35 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Load a features file onto the alignment
    * 
-   * @param String
-   *          DOCUMENT ME!
+   * @param file file URL, content, or other resolvable path
+   * @param type is protocol for accessing data referred to by file
    */
 
-  public void parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, String type)
   {
+    return parseFeaturesFile(file, type, true);
+  }
+  
+  /**
+   * Load a features file onto the alignment
+   * 
+   * @param file file URL, content, or other resolvable path
+   * @param type is protocol for accessing data referred to by file
+   * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded
+   * @return true if data parsed as a features file
+   */
+  public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)
+  {    
+    // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.
+    
     Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
     {
       featuresFile = new jalview.io.FeaturesFile(file, type)
-              .parse(viewport.alignment,
+              .parse(viewport.getAlignment(),
                       alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
                       featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));
     } catch (Exception ex)
@@ -186,15 +273,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
       }
-      viewport.showSequenceFeatures = true;
-      sequenceFeatures.setState(true);
+      if (autoenabledisplay)
+      {
+        viewport.showSequenceFeatures = true;
+        sequenceFeatures.setState(true);
+      }
       if (viewport.featureSettings != null)
       {
         viewport.featureSettings.refreshTable();
       }
       alignPanel.paintAlignment(true);
+      statusBar.setText("Successfully added features to alignment.");
     }
-
+    return featuresFile;
   }
 
   public void keyPressed(KeyEvent evt)
@@ -471,7 +562,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel
+      if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()
               .getSelected().size() > 0)
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
@@ -495,12 +586,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleSeqs)
     {
-      if (sg != null && sg.getSize() != viewport.alignment.getHeight())
+      if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
       {
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))
+      else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -508,12 +599,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleCols)
     {
-      if (viewport.colSel.getSelected().size() > 0)
+      if (viewport.getColumnSelection().getSelected().size() > 0)
       {
         viewport.hideSelectedColumns();
         if (!toggleSeqs)
         {
-          viewport.selectionGroup = sg;
+          viewport.setSelectionGroup(sg);
         }
       }
       else if (!hide)
@@ -597,7 +688,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (evt.getSource() == autoCalculate)
     {
-      viewport.autocalculateConsensus = autoCalculate.getState();
+      viewport.autoCalculateConsensus = autoCalculate.getState();
+    }
+    else if (evt.getSource() == sortByTree)
+    {
+      viewport.sortByTree = sortByTree.getState();
     }
     else if (evt.getSource() == this.centreColumnLabelFlag)
     {
@@ -843,7 +938,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == alProperties)
     {
       StringBuffer contents = new jalview.io.AlignmentProperties(
-              viewport.alignment).formatAsString();
+              viewport.getAlignment()).formatAsString();
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       cap.setText(contents.toString());
       Frame frame = new Frame();
@@ -862,9 +957,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else if (source == clustalColour)
     {
       abovePIDThreshold.setState(false);
-      changeColour(new ClustalxColourScheme(
-              viewport.alignment.getSequences(),
-              viewport.alignment.getWidth()));
+      changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));
     }
     else if (source == zappoColour)
     {
@@ -898,6 +991,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new NucleotideColourScheme());
     }
+    else if (source == purinePyrimidineColour)
+    {
+      changeColour(new PurinePyrimidineColourScheme());
+    }
+    else if (source == RNAHelixColour)
+    {
+      new RNAHelicesColourChooser(viewport, alignPanel);
+    }
     else if (source == modifyPID)
     {
       modifyPID_actionPerformed();
@@ -918,6 +1019,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new Blosum62ColourScheme());
     }
+    else if (source == tcoffeeColour) {
+        changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+    }
     else if (source == annotationColour)
     {
       new AnnotationColourChooser(viewport, alignPanel);
@@ -1000,21 +1104,21 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void loadAnnotations()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
-    cap.setText("Paste your features / annotations file here.");
+    cap.setText("Paste your features / annotations / T-coffee score file here.");
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
 
   }
-
+  
   public String outputAnnotations(boolean displayTextbox)
   {
     String annotation = new AnnotationFile().printAnnotations(
-            viewport.showAnnotation ? viewport.alignment
-                    .getAlignmentAnnotation() : null, viewport.alignment
+            viewport.showAnnotation ? viewport.getAlignment()
+                    .getAlignmentAnnotation() : null, viewport.getAlignment()
                     .getGroups(),
-            ((Alignment) viewport.alignment).alignmentProperties);
+            ((Alignment) viewport.getAlignment()).alignmentProperties);
 
     if (displayTextbox)
     {
@@ -1030,7 +1134,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   private Hashtable getDisplayedFeatureCols()
   {
-    if (alignPanel.getFeatureRenderer() != null)
+    if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)
     {
       FeatureRenderer fr = alignPanel.getFeatureRenderer();
       Hashtable fcols = new Hashtable();
@@ -1051,24 +1155,37 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (format.equalsIgnoreCase("Jalview"))
     {
       features = new FeaturesFile().printJalviewFormat(
-              viewport.alignment.getSequencesArray(),
+              viewport.getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
     else
     {
       features = new FeaturesFile().printGFFFormat(
-              viewport.alignment.getSequencesArray(),
+              viewport.getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
 
     if (displayTextbox)
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      boolean frimport=false;
+      if (features==null || features.equals("No Features Visible"))
+      {
+        features = "# No features visible - paste some and import them here.";
+        frimport=true;
+      }
+      
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
+      if (frimport)
+      {
+        cap.setAnnotationImport();
+      }
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
-
       cap.setText(features);
+    } else {
+      if (features==null)
+        features = "";
     }
 
     return features;
@@ -1168,19 +1285,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void closeMenuItem_actionPerformed()
   {
     PaintRefresher.RemoveComponent(alignPanel);
-    PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
-    PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+    if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)
+    {
+      PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
+    }
+    if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {
+      PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
+    }
 
     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
     {
       System.exit(0);
+    } else {
     }
-
+    viewport = null;
+    alignPanel = null;
     this.dispose();
   }
 
   /**
-   * DOCUMENT ME!
+   * TODO: JAL-1104
    */
   void updateEditMenuBar()
   {
@@ -1211,6 +1335,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
   }
 
+  /**
+   * TODO: JAL-1104
+   */
   public void addHistoryItem(CommandI command)
   {
     if (command.getSize() > 0)
@@ -1218,11 +1345,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       viewport.historyList.push(command);
       viewport.redoList.removeAllElements();
       updateEditMenuBar();
-      viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+      viewport.updateHiddenColumns();
     }
   }
 
   /**
+   * TODO: JAL-1104
    * DOCUMENT ME!
    * 
    * @param e
@@ -1240,14 +1368,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     command.undoCommand(null);
 
     AlignViewport originalSource = getOriginatingSource(command);
-
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    // JBPNote Test
+    if (originalSource!=viewport) {
+      System.err.println("Warning: Viewport object mismatch whilst undoing");
+    }
+    originalSource.updateHiddenColumns(); //    originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;
     updateEditMenuBar();
     originalSource.firePropertyChange("alignment", null,
-            originalSource.alignment.getSequences());
+            originalSource.getAlignment().getSequences());
   }
 
   /**
+   * TODO: JAL-1104
    * DOCUMENT ME!
    * 
    * @param e
@@ -1265,11 +1397,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     command.doCommand(null);
 
     AlignViewport originalSource = getOriginatingSource(command);
-    originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
+    // JBPNote Test
+    if (originalSource!=viewport) {
+      System.err.println("Warning: Viewport object mismatch whilst re-doing");
+    }
+    originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;
 
     updateEditMenuBar();
     originalSource.firePropertyChange("alignment", null,
-            originalSource.alignment.getSequences());
+            originalSource.getAlignment().getSequences());
   }
 
   AlignViewport getOriginatingSource(CommandI command)
@@ -1289,7 +1425,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         if (comps.elementAt(i) instanceof AlignmentPanel)
         {
-          if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)
+          if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
           {
             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
             break;
@@ -1304,7 +1440,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // the current view against the closed view first
       if (al != null)
       {
-        PaintRefresher.validateSequences(al, viewport.alignment);
+        PaintRefresher.validateSequences(al, viewport.getAlignment());
       }
 
       originalSource = viewport;
@@ -1323,42 +1459,42 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (up)
     {
-      for (int i = 1; i < viewport.alignment.getHeight(); i++)
+      for (int i = 1; i < viewport.getAlignment().getHeight(); i++)
       {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
+        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
         if (!sg.getSequences(null).contains(seq))
         {
           continue;
         }
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
+        SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);
         if (sg.getSequences(null).contains(temp))
         {
           continue;
         }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i - 1);
+        viewport.getAlignment().getSequences().setElementAt(temp, i);
+        viewport.getAlignment().getSequences().setElementAt(seq, i - 1);
       }
     }
     else
     {
-      for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)
+      for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)
       {
-        SequenceI seq = viewport.alignment.getSequenceAt(i);
-        if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))
+        SequenceI seq = viewport.getAlignment().getSequenceAt(i);
+        if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))
         {
           continue;
         }
 
-        SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
-        if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))
+        SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);
+        if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))
         {
           continue;
         }
 
-        viewport.alignment.getSequences().setElementAt(temp, i);
-        viewport.alignment.getSequences().setElementAt(seq, i + 1);
+        viewport.getAlignment().getSequences().setElementAt(temp, i);
+        viewport.getAlignment().getSequences().setElementAt(seq, i + 1);
       }
     }
 
@@ -1367,18 +1503,18 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   synchronized void slideSequences(boolean right, int size)
   {
-    Vector sg = new Vector();
+    List<SequenceI>sg = new Vector<SequenceI>();
     if (viewport.cursorMode)
     {
-      sg.addElement(viewport.alignment
+      sg.add(viewport.getAlignment()
               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
     }
     else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport.alignment
+            && viewport.getSelectionGroup().getSize() != viewport.getAlignment()
                     .getHeight())
     {
       sg = viewport.getSelectionGroup().getSequences(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
     }
 
     if (sg.size() < 1)
@@ -1386,19 +1522,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       return;
     }
 
-    Vector invertGroup = new Vector();
+    Vector<SequenceI> invertGroup = new Vector();
 
-    for (int i = 0; i < viewport.alignment.getHeight(); i++)
+    for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
-      if (!sg.contains(viewport.alignment.getSequenceAt(i)))
-        invertGroup.addElement(viewport.alignment.getSequenceAt(i));
+      if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+        invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
     }
 
-    SequenceI[] seqs1 = new SequenceI[sg.size()];
-    for (int i = 0; i < sg.size(); i++)
-      seqs1[i] = (SequenceI) sg.elementAt(i);
+    SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
 
-    SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
+    SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);
     for (int i = 0; i < invertGroup.size(); i++)
       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
 
@@ -1466,14 +1600,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     for (int i = 0; i < sg.getSize(); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
+      int index = viewport.getAlignment().findIndex(seq);
       orderedSeqs.put(index + "", seq);
     }
 
     int index = 0, startRes, endRes;
     char ch;
 
-    if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)
+    if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
@@ -1620,17 +1754,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     for (int i = 0; i < seqs.length; i++)
     {
-      viewport.alignment.addSequence(seqs[i]);
+      viewport.getAlignment().addSequence(seqs[i]);
     }
 
     // !newAlignment
     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
-            seqs, 0, viewport.alignment.getWidth(), viewport.alignment));
+            seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));
 
-    viewport.setEndSeq(viewport.alignment.getHeight());
-    viewport.alignment.getWidth();
+    viewport.setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null,
-            viewport.alignment.getSequences());
+            viewport.getAlignment().getSequences());
 
   }
 
@@ -1658,7 +1792,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     // If the cut affects all sequences, remove highlighted columns
-    if (sg.getSize() == viewport.alignment.getHeight())
+    if (sg.getSize() == viewport.getAlignment().getHeight())
     {
       viewport.getColumnSelection().removeElements(sg.getStartRes(),
               sg.getEndRes() + 1);
@@ -1675,10 +1809,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
      */
     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
-            viewport.alignment));
+            viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
-    viewport.alignment.deleteGroup(sg);
+    viewport.getAlignment().deleteGroup(sg);
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -1748,8 +1882,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport.getSequenceSelection(),
               viewport.getAlignmentView(true).getSequenceStrings(
                       viewport.getGapCharacter()),
-              viewport.alignment.getGroups());
-      viewport.alignment.deleteAllGroups();
+              viewport.getAlignment().getGroups());
+      viewport.getAlignment().deleteAllGroups();
       viewport.sequenceColours = null;
       viewport.setSelectionGroup(null);
       // set view properties for each group
@@ -1757,13 +1891,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
-        viewport.alignment.addGroup(gps[g]);
+        viewport.getAlignment().addGroup(gps[g]);
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
-        for (Enumeration sq = gps[g].getSequences(null).elements(); sq
-                .hasMoreElements(); viewport.setSequenceColour(
-                (SequenceI) sq.nextElement(), col))
+        for (SequenceI sq : gps[g].getSequences(null))
+          viewport.setSequenceColour(
+                sq, col)
           ;
       }
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
@@ -1774,7 +1908,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void deleteGroups_actionPerformed()
   {
-    viewport.alignment.deleteAllGroups();
+    viewport.getAlignment().deleteAllGroups();
     viewport.sequenceColours = null;
     viewport.setSelectionGroup(null);
 
@@ -1788,7 +1922,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
     }
-    sg.setEndRes(viewport.alignment.getWidth() - 1);
+    sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
     alignPanel.paintAlignment(true);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
@@ -1852,11 +1986,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       if (viewport.getSelectionGroup() != null)
       {
         seqs = viewport.getSelectionGroup().getSequencesAsArray(
-                viewport.hiddenRepSequences);
+                viewport.getHiddenRepSequences());
       }
       else
       {
-        seqs = viewport.alignment.getSequencesArray();
+        seqs = viewport.getAlignment().getSequencesArray();
       }
 
       TrimRegionCommand trimRegion;
@@ -1864,32 +1998,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left",
                 TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.alignment, viewport.colSel,
-                viewport.selectionGroup);
+                viewport.getAlignment(), viewport.getColumnSelection(),
+                viewport.getSelectionGroup());
         viewport.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right",
                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.alignment, viewport.colSel,
-                viewport.selectionGroup);
+                viewport.getAlignment(), viewport.getColumnSelection(),
+                viewport.getSelectionGroup());
       }
 
       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
 
       addHistoryItem(trimRegion);
 
-      Vector groups = viewport.alignment.getGroups();
 
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
+      for (SequenceGroup sg:viewport.getAlignment().getGroups())
+      {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
-          viewport.alignment.deleteGroup(sg);
+          viewport.getAlignment().deleteGroup(sg);
         }
       }
 
@@ -1900,23 +2032,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
       seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
     {
-      seqs = viewport.alignment.getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
 
     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
-            "Remove Gapped Columns", seqs, start, end, viewport.alignment);
+            "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());
 
     addHistoryItem(removeGapCols);
 
@@ -1925,7 +2057,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
@@ -1940,28 +2072,28 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.alignment.getWidth() - 1;
+    int start = 0, end = viewport.getAlignment().getWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
     {
       seqs = viewport.getSelectionGroup().getSequencesAsArray(
-              viewport.hiddenRepSequences);
+              viewport.getHiddenRepSequences());
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes();
     }
     else
     {
-      seqs = viewport.alignment.getSequencesArray();
+      seqs = viewport.getAlignment().getSequencesArray();
     }
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.alignment.getSequenceAt(0);
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
     int startRes = seq.findPosition(viewport.startRes);
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.alignment));
+            viewport.getAlignment()));
 
     viewport.setStartRes(seq.findIndex(startRes) - 1);
 
@@ -1984,30 +2116,30 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame newView(String viewtitle)
   {
     AlignmentI newal;
-    if (viewport.hasHiddenRows)
+    if (viewport.hasHiddenRows())
     {
       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
               .getFullAlignment().getSequencesArray());
     }
     else
     {
-      newal = new Alignment(viewport.alignment.getSequencesArray());
+      newal = new Alignment(viewport.getAlignment().getSequencesArray());
     }
 
-    if (viewport.alignment.getAlignmentAnnotation() != null)
+    if (viewport.getAlignment().getAlignmentAnnotation() != null)
     {
-      for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)
+      for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
       {
-        if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+        if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
         {
-          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+          newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);
         }
       }
     }
 
     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
 
-    newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();
+    newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
     PaintRefresher.Register(newaf.alignPanel,
             newaf.alignPanel.av.getSequenceSetId());
@@ -2152,11 +2284,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             overview.getPreferredSize().height + 50);
 
     frame.pack();
+    final AlignmentPanel ap=alignPanel;
     frame.addWindowListener(new WindowAdapter()
     {
       public void windowClosing(WindowEvent e)
       {
-        alignPanel.setOverviewPanel(null);
+        if (ap!=null) {
+          ap.setOverviewPanel(null);
+        }
       };
     });
 
@@ -2187,13 +2322,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       if (viewport.getConservationSelected())
       {
 
-        Alignment al = (Alignment) viewport.alignment;
+        Alignment al = (Alignment) viewport.getAlignment();
         Conservation c = new Conservation("All",
                 ResidueProperties.propHash, 3, al.getSequences(), 0,
                 al.getWidth() - 1);
 
         c.calculate();
-        c.verdict(false, viewport.ConsPercGaps);
+        c.verdict(false, viewport.getConsPercGaps());
 
         cs.setConservation(c);
 
@@ -2206,14 +2341,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         cs.setConservation(null);
       }
 
-      cs.setConsensus(viewport.hconsensus);
+      cs.setConsensus(viewport.getSequenceConsensusHash());
 
-    }
+    }             
     viewport.setGlobalColourScheme(cs);
 
     if (viewport.getColourAppliesToAllGroups())
     {
-      Vector groups = viewport.alignment.getGroups();
+      Vector groups = viewport.getAlignment().getGroups();
       for (int i = 0; i < groups.size(); i++)
       {
         SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
@@ -2226,14 +2361,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         if (cs instanceof ClustalxColourScheme)
         {
           sg.cs = new ClustalxColourScheme(
-                  sg.getSequences(viewport.hiddenRepSequences),
+                  sg.getSequences(viewport.getHiddenRepSequences()),
                   sg.getWidth());
         }
         else
         {
           try
           {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+            sg.cs = cs.getClass().newInstance();
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -2247,7 +2382,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
           sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(viewport.hiddenRepSequences), 0,
+                  sg.getSequences(viewport.getHiddenRepSequences()), 0,
                   sg.getWidth()));
         }
         else
@@ -2259,10 +2394,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         {
           Conservation c = new Conservation("Group",
                   ResidueProperties.propHash, 3,
-                  sg.getSequences(viewport.hiddenRepSequences), 0,
-                  viewport.alignment.getWidth() - 1);
+                  sg.getSequences(viewport.getHiddenRepSequences()), 0,
+                  viewport.getAlignment().getWidth() - 1);
           c.calculate();
-          c.verdict(false, viewport.ConsPercGaps);
+          c.verdict(false, viewport.getConsPercGaps());
           sg.cs.setConservation(c);
         }
         else
@@ -2280,7 +2415,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager().sequenceColoursChanged(
+            .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(
                     alignPanel);
 
     alignPanel.paintAlignment(true);
@@ -2289,7 +2424,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   protected void modifyPID_actionPerformed()
   {
     if (viewport.getAbovePIDThreshold()
-            && viewport.globalColourScheme != null)
+            && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setPIDSliderSource(alignPanel,
               viewport.getGlobalColourScheme(), "Background");
@@ -2300,10 +2435,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   protected void modifyConservation_actionPerformed()
   {
     if (viewport.getConservationSelected()
-            && viewport.globalColourScheme != null)
+            && viewport.getGlobalColourScheme() != null)
     {
       SliderPanel.setConservationSlider(alignPanel,
-              viewport.globalColourScheme, "Background");
+              viewport.getGlobalColourScheme(), "Background");
       SliderPanel.showConservationSlider();
     }
   }
@@ -2339,7 +2474,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getAlignment().getSequenceAt(0), null);
 
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2347,7 +2482,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByID(viewport.getAlignment());
-    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));
+    addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2356,7 +2491,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByLength(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2365,7 +2500,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByGroup(viewport.getAlignment());
     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
 
   }
@@ -2390,7 +2525,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void PCAMenuItem_actionPerformed()
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned(false))
+    if (!viewport.getAlignment().isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2447,7 +2582,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   void NewTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned(false))
+    if (!viewport.getAlignment().isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2467,7 +2602,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if ((viewport.getSelectionGroup() != null && viewport
             .getSelectionGroup().getSize() > 1)
-            || (viewport.getSelectionGroup() == null && viewport.alignment
+            || (viewport.getSelectionGroup() == null && viewport.getAlignment()
                     .getHeight() > 1))
     {
       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
@@ -2511,7 +2646,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
     // HistoryItem.SORT));
     addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
-            viewport.alignment));
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
   }
 
@@ -2534,7 +2669,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         sortByTree(treePanel, title); // treePanel.getTitle());
       }
     });
-
+    
     treePanel.addWindowListener(new WindowAdapter()
     {
       public void windowOpened(WindowEvent e)
@@ -2563,14 +2698,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
     if (undoname!=null)
     {
-      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));
+      addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));
     }
     alignPanel.paintAlignment(true);
     return true;
   }
+
   protected void documentation_actionPerformed()
   {
-    showURL("http://www.jalview.org/help.html", "HELP");
+    alignPanel.av.applet.openJalviewHelpUrl();
   }
 
   protected void about_actionPerformed()
@@ -2641,45 +2777,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      try
-      {
-        if (url.indexOf(":") == -1)
-        {
-          // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
-          // form valid URL
-          // Should really use docbase, not codebase.
-          if (url.indexOf("/") == 0)
-          {
-            String codebase = viewport.applet.getCodeBase().toString();
-            url = codebase.substring(0, codebase.length()
-                    - viewport.applet.getCodeBase().getFile().length())
-                    + url;
-          }
-          else
-          {
-            url = viewport.applet.getCodeBase() + url;
-          }
-          System.out.println("Show url (prepended codebase): " + url);
-        }
-        else
-        {
-          System.out.println("Show url: " + url);
-        }
-        if (url.indexOf("javascript:") == 0)
-        {
-          // no target for the javascript context
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url));
-        }
-        else
-        {
-          viewport.applet.getAppletContext().showDocument(
-                  new java.net.URL(url), target);
-        }
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
+      viewport.applet.showURL(url, target);
     }
   }
 
@@ -2695,7 +2793,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   MenuItem loadTree = new MenuItem("Load Associated Tree ...");
 
   MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
-
+  
   MenuItem outputFeatures = new MenuItem("Export Features ...");
 
   MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
@@ -2768,11 +2866,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem buriedColour = new MenuItem();
 
+  MenuItem purinePyrimidineColour = new MenuItem();
+  MenuItem RNAHelixColour = new MenuItem();
+  
   MenuItem userDefinedColour = new MenuItem();
 
   MenuItem PIDColour = new MenuItem();
 
   MenuItem BLOSUM62Colour = new MenuItem();
+  
+  MenuItem tcoffeeColour = new MenuItem();
 
   MenuItem njTreeBlosumMenuItem = new MenuItem();
 
@@ -2839,6 +2942,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
           "Autocalculate Consensus", true);
 
+  CheckboxMenuItem sortByTree = new CheckboxMenuItem(
+          "Sort Alignment With New Tree", true);
+
   Menu sortByTreeMenu = new Menu();
 
   Menu sort = new Menu();
@@ -2953,14 +3059,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     turnColour.addActionListener(this);
     buriedColour.setLabel("Buried Index");
     buriedColour.addActionListener(this);
+    purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+    purinePyrimidineColour.addActionListener(this);
+    RNAHelixColour.setLabel("by RNA Helices");
+    RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel("User Defined...");
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel("Percentage Identity");
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62 Score");
     BLOSUM62Colour.addActionListener(this);
-    avDistanceTreeBlosumMenuItem
-            .setLabel("Average Distance Using BLOSUM62");
+    tcoffeeColour.setLabel("T-Coffee Scores");
+    tcoffeeColour.setEnabled(false);	// it will enabled only if a score file is provided
+    tcoffeeColour.addActionListener(this);
+    avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");
     avDistanceTreeBlosumMenuItem.addActionListener(this);
     njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(this);
@@ -3034,6 +3146,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sort.setLabel("Sort");
     calculate.setLabel("Calculate Tree");
     autoCalculate.addItemListener(this);
+    sortByTree.addItemListener(this);
     inputText.setLabel("Input from textbox");
     inputText.addActionListener(this);
     centreColumnLabelFlag.setLabel("Centre column labels");
@@ -3104,7 +3217,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     fileMenu.add(inputText);
     fileMenu.add(loadTree);
     fileMenu.add(loadAnnotations);
-
+    
     fileMenu.addSeparator();
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(outputFeatures);
@@ -3165,6 +3278,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
+    colourMenu.add(purinePyrimidineColour);
+    colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -3172,12 +3287,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
+    colourMenu.add(RNAHelixColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
     this.add(statusBar, BorderLayout.SOUTH);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
@@ -3511,7 +3628,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (applet.useXtrnalSviewer)
     {
       // register the association(s) and quit, don't create any windows.
-      if (StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
+      if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {
         System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");
       }
       return;
@@ -3572,4 +3689,70 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     alignPanel.seqPanel.selection(sel, csel, null);
   }
+
+  public void scrollTo(int row, int column)
+  {
+    alignPanel.seqPanel.scrollTo(row, column);    
+  }
+  public void scrollToRow(int row)
+  {
+    alignPanel.seqPanel.scrollToRow(row);    
+  }
+  public void scrollToColumn(int column)
+  {
+    alignPanel.seqPanel.scrollToColumn(column);    
+  }
+  /**
+   * @return the alignments unique ID.
+   */
+  public String getSequenceSetId() {
+    return viewport.getSequenceSetId();
+  }
+  
+  
+  /**
+   * Load the (T-Coffee) score file from the specified url 
+   * 
+   * @param source File/URL/T-COFFEE score file contents
+   * @throws IOException 
+   * @return true if alignment was annotated with data from source
+   */
+  public boolean loadScoreFile( String source ) throws IOException {
+
+    TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));
+	  if( !file.isValid()) {
+	    // TODO: raise dialog for gui
+	    System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());
+	    System.err.println("Origin was:\n"+source);
+	    return false;
+	  }
+	  
+	  /*
+	   * check that the score matrix matches the alignment dimensions
+	   */
+	  AlignmentI aln; 
+	  if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
+	    // TODO: raise a dialog box here rather than bomb out.
+	    System.err.println("The scores matrix does not match the alignment dimensions");
+		  
+	  }
+	  
+	   // TODO add parameter to indicate if matching should be done
+	  if (file.annotateAlignment(alignPanel.getAlignment(), false))
+	  {
+	    alignPanel.fontChanged();
+	    tcoffeeColour.setEnabled(true);
+	          // switch to this color
+	          changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+	          return true;
+          } else {
+            System.err.println("Problems resolving T-Coffee scores:");
+            if (file.getWarningMessage()!=null) {
+              System.err.println(file.getWarningMessage());
+            }
+          }
+	  return false;
+  }
+  
+  
 }